dwit1-epi.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "5abf89fc",
   "metadata": {},
   "outputs": [],
   "source": [
    "import nest_asyncio\n",
    "nest_asyncio.apply()\n",
    "import pydra"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "ae14afef",
   "metadata": {},
   "outputs": [],
   "source": [
    "import toimportfunctions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "89ec63dd",
   "metadata": {},
   "outputs": [],
   "source": [
    "from os import getenv\n",
    "from pathlib import Path\n",
    "\n",
    "clinica_data_ci_dir = \"/Users/matthieu.joulot/Documents/DWI/ci-complete\"\n",
    "\n",
    "pipeline_dir = Path(clinica_data_ci_dir) / \"DWIPreprocessingUsingT1\"\n",
    "pipeline_in_dir = pipeline_dir / \"in\"\n",
    "pipeline_ref_dir = pipeline_dir / \"ref\"\n",
    "pipeline_out_dir = pipeline_dir / \"out\"\n",
    "working_dir = \"/Users/matthieu.joulot/Desktop/working_directory\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "2b7b79e9",
   "metadata": {},
   "outputs": [],
   "source": [
    "from nipype.interfaces.mrtrix3.preprocess import DWIBiasCorrect\n",
    "\n",
    "from pydra.mark import annotate, task"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "c31f131f",
   "metadata": {},
   "outputs": [],
   "source": [
    "from nipype.interfaces.io import BIDSDataGrabber\n",
    "\n",
    "bids_data_grabber = BIDSDataGrabber(\n",
    "    outfields=[\"t1w\", \"dwi\", \"dwi_json\", \"bvec\", \"bval\"],\n",
    "    output_query={\n",
    "        \"t1w\": {\n",
    "            \"datatype\": \"anat\",\n",
    "            \"suffix\": \"T1w\",\n",
    "            \"extension\": \".nii.gz\",\n",
    "        },\n",
    "        \"dwi\": { \"datatype\": \"dwi\", \"suffix\": \"dwi\", \"extension\": \".nii.gz\"},\n",
    "        \"dwi_json\": { \"datatype\": \"dwi\", \"suffix\": \"dwi\", \"extension\": \".json\"},\n",
    "        \"bvec\": { \"datatype\": \"dwi\", \"suffix\": \"dwi\", \"extension\": \".bvec\"},\n",
    "        \"bval\": { \"datatype\": \"dwi\", \"suffix\": \"dwi\", \"extension\": \".bval\"},\n",
    "    }\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "568305a4",
   "metadata": {},
   "outputs": [],
   "source": [
    "from nipype.interfaces.fsl.preprocess import BET\n",
    "\n",
    "bet_2 = BET(frac=0.3,robust=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "bb23253b",
   "metadata": {},
   "outputs": [],
   "source": [
    "@task\n",
    "@annotate({\"return\": {\"image_id\": str, \"t1w\": str, \"dwi\": str, \"bvec\": str, \"bval\": str, \"total_readout_time\": str,\"phase_encoding_direction\": str}})\n",
    "def init_input_node(t1w, dwi, bvec, bval, dwi_json):\n",
    "    \"\"\"Initialize the pipeline.\"\"\"\n",
    "    \n",
    "    # Extract image ID\n",
    "    image_id = toimportfunctions.get_subject_id(t1w)\n",
    "\n",
    "    # Check that the number of DWI, bvec & bval are the same\n",
    "    toimportfunctions.check_dwi_volume(dwi, bvec, bval)\n",
    "\n",
    "    # Read metadata from DWI JSON file:\n",
    "    [total_readout_time, phase_encoding_direction] = toimportfunctions.extract_metadata_from_json(\n",
    "        dwi_json, [\"TotalReadoutTime\", \"PhaseEncodingDirection\"]\n",
    "    )\n",
    "    phase_encoding_direction = toimportfunctions.bids_dir_to_fsl_dir(phase_encoding_direction)\n",
    "\n",
    "    # Print begin message\n",
    "    toimportfunctions.print_begin_image(\n",
    "        image_id,\n",
    "        [\"TotalReadoutTime\", \"PhaseEncodingDirection\"],\n",
    "        [str(total_readout_time), phase_encoding_direction],\n",
    "    )\n",
    "\n",
    "    return (\n",
    "        image_id,\n",
    "        t1w,\n",
    "        dwi,\n",
    "        bvec,\n",
    "        bval,\n",
    "        total_readout_time,\n",
    "        phase_encoding_direction,\n",
    "    )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "a3c0151d",
   "metadata": {},
   "outputs": [],
   "source": [
    "@task\n",
    "@annotate({\"return\": {\"out_reference_b0\": str, \"out_b0_dwi_merge\":str, \"out_updated_bval\":str, \"out_updated_bvec\":str}})\n",
    "def prepare_reference_b0_1(in_dwi, in_bval, in_bvec, low_bval=5, working_directory=working_dir):\n",
    "    \"\"\"Prepare reference b=0 image.\n",
    "\n",
    "    This function prepare the data for further corrections. It co-registers the B0 images\n",
    "    and then average it in order to obtain only one average B0 images.\n",
    "\n",
    "    Args:\n",
    "        in_dwi (str): Input DWI file.\n",
    "        in_bvec (str): Vector file of the diffusion directions of the DWI dataset.\n",
    "        in_bval (str): B-values file.\n",
    "        low_bval (optional, int): Set b<=low_bval such that images are considered b0. Defaults to 5.\n",
    "        working_directory (str): Temporary folder results where the results are stored. Defaults to None.\n",
    "\n",
    "    Returns:\n",
    "        out_reference_b0 (str): Average of the B0 images or the only B0 image.\n",
    "        out_b0_dwi_merge (str): Average of B0 images merged to the DWIs.\n",
    "        out_updated_bval (str): Updated gradient values table.\n",
    "        out_updated_bvec (str): Updated gradient vectors table.\n",
    "    \"\"\"\n",
    "    import hashlib\n",
    "    import os\n",
    "    import tempfile\n",
    "\n",
    "\n",
    "    # Count the number of b0s\n",
    "    nb_b0s = toimportfunctions.count_b0s(in_bval=in_bval, low_bval=low_bval)\n",
    "\n",
    "    # Split dataset into two datasets: the b0 and the b>low_bval datasets\n",
    "    [extracted_b0, out_split_dwi, out_split_bval, out_split_bvec] = toimportfunctions.b0_dwi_split(\n",
    "        in_dwi=in_dwi, in_bval=in_bval, in_bvec=in_bvec, low_bval=low_bval\n",
    "    )\n",
    "    \n",
    "    \n",
    "    if nb_b0s == 1:\n",
    "        # The reference b0 is the extracted b0\n",
    "        # cprint('Only one b0 for %s' % in_dwi)\n",
    "        out_reference_b0 = extracted_b0\n",
    "    elif nb_b0s > 1:\n",
    "        if working_directory is None:\n",
    "            working_directory = tempfile.mkdtemp()\n",
    "        tmp_dir = os.path.join(\n",
    "            working_directory, hashlib.md5(in_dwi.encode()).hexdigest()\n",
    "        )\n",
    "        b0_flirt_results = toimportfunctions.build_n_run_flirt(nb_b0s, extracted_b0, tmp_dir)\n",
    "        print(\"b0_flirt_results: \", b0_flirt_results)\n",
    "        out_reference_b0 = toimportfunctions.b0_average(in_file=b0_flirt_results[1].get_output_field('out_file'))\n",
    "        print(\"out_reference_b0: \", out_reference_b0)\n",
    "    else:\n",
    "        raise ValueError(\n",
    "            f\"The number of b0s should be strictly positive (b-val file: {in_bval}).\"\n",
    "        )\n",
    "    # Merge datasets such that bval(DWI) = (0 b1 ... bn)\n",
    "    [out_b0_dwi_merge, out_updated_bval, out_updated_bvec] = toimportfunctions.insert_b0_into_dwi(\n",
    "        in_b0=out_reference_b0,\n",
    "        in_dwi=out_split_dwi,\n",
    "        in_bval=out_split_bval,\n",
    "        in_bvec=out_split_bvec,\n",
    "    )\n",
    "    return out_reference_b0, out_b0_dwi_merge, out_updated_bval, out_updated_bvec"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "abc1e768",
   "metadata": {},
   "outputs": [],
   "source": [
    "@task\n",
    "@annotate({\"return\":{\"out_acq\": str}})\n",
    "def generate_acq_file(\n",
    "    in_dwi, fsl_phase_encoding_direction, total_readout_time, image_id=None\n",
    "):\n",
    "    \"\"\"Generate [`image_id`]_acq.txt file for FSL eddy command.\n",
    "\n",
    "    Args:\n",
    "        in_dwi (str): DWI file.\n",
    "        fsl_phase_encoding_direction (str): PhaseEncodingDirection from BIDS specifications in FSL format (i.e. x/y/z instead of i/j/k).\n",
    "        total_readout_time (str): TotalReadoutTime from BIDS specifications.\n",
    "        image_id (str, optional): Optional prefix. Defaults to None.\n",
    "\n",
    "    Returns:\n",
    "        out_acq: [`image_id`]_acq.txt or acq.txt file.\n",
    "    \"\"\"\n",
    "    import os\n",
    "\n",
    "    import nibabel as nb\n",
    "    import numpy as np\n",
    "\n",
    "    if image_id:\n",
    "        out_acq = os.path.abspath(f\"{image_id}_acq.txt\")\n",
    "    else:\n",
    "        out_acq = os.path.abspath(\"acq.txt\")\n",
    "    vols = nb.load(in_dwi).get_fdata().shape[-1]\n",
    "    arr = np.ones([vols, 4])\n",
    "    for i in range(vols):\n",
    "        if fsl_phase_encoding_direction == \"y-\":\n",
    "            arr[i, :] = np.array((0, -1, 0, total_readout_time))\n",
    "        elif fsl_phase_encoding_direction == \"y\":\n",
    "            arr[i, :] = np.array((0, 1, 0, total_readout_time))\n",
    "        elif fsl_phase_encoding_direction == \"x\":\n",
    "            arr[i, :] = np.array((1, 0, 0, total_readout_time))\n",
    "        elif fsl_phase_encoding_direction == \"x-\":\n",
    "            arr[i, :] = np.array((-1, 0, 0, total_readout_time))\n",
    "        elif fsl_phase_encoding_direction == \"z\":\n",
    "            arr[i, :] = np.array((0, 1, 0, total_readout_time))\n",
    "        elif fsl_phase_encoding_direction == \"z-\":\n",
    "            arr[i, :] = np.array((0, 0, -1, total_readout_time))\n",
    "        else:\n",
    "            raise RuntimeError(\n",
    "                f\"FSL PhaseEncodingDirection (found value: {fsl_phase_encoding_direction}) \"\n",
    "                f\"is unknown, it should be a value in (x, y, z, x-, y-, z-)\"\n",
    "            )\n",
    "\n",
    "    np.savetxt(out_acq, arr, fmt=\"%d \" * 3 + \"%f\")\n",
    "\n",
    "    return out_acq"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "e7c7114b",
   "metadata": {},
   "outputs": [],
   "source": [
    "@task\n",
    "@annotate({\"return\":{\"out_index\": str}})\n",
    "def generate_index_file(in_bval, low_bval=5.0, image_id=None):\n",
    "    \"\"\"Generate [`image_id`]_index.txt file for FSL eddy command.\n",
    "\n",
    "    Args:\n",
    "        in_bval (str): Bval file.\n",
    "        low_bval (float): Define the b0 volumes as all volume bval <= low_bval. Default to 5.0.\n",
    "        image_id (str, optional): Optional prefix. Defaults to None.\n",
    "\n",
    "    Returns:\n",
    "        out_index: [`image_id`]_index.txt or index.txt file.\n",
    "    \"\"\"\n",
    "    import os\n",
    "\n",
    "    import numpy as np\n",
    "\n",
    "    assert os.path.isfile(in_bval)\n",
    "    bvals = np.loadtxt(in_bval)\n",
    "    idx_low_bvals = np.where(bvals <= low_bval)\n",
    "    b0_index = idx_low_bvals[0].tolist()\n",
    "\n",
    "    if not b0_index:\n",
    "        raise ValueError(\n",
    "            f\"Could not find b-value <= {low_bval} in bval file ({in_bval}). Found values: {bvals}\"\n",
    "        )\n",
    "\n",
    "    if image_id:\n",
    "        out_index = os.path.abspath(f\"{image_id}_index.txt\")\n",
    "    else:\n",
    "        out_index = os.path.abspath(\"index.txt\")\n",
    "\n",
    "    vols = len(bvals)\n",
    "    index_list = []\n",
    "    for i in range(0, len(b0_index)):\n",
    "        if i == (len(b0_index) - 1):\n",
    "            index_list.extend([i + 1] * (vols - b0_index[i]))\n",
    "        else:\n",
    "            index_list.extend([i + 1] * (b0_index[i + 1] - b0_index[i]))\n",
    "    index_array = np.asarray(index_list)\n",
    "    try:\n",
    "        len(index_list) == vols\n",
    "    except ValueError:\n",
    "        raise ValueError(\n",
    "            \"It seems that you do not define the index file for FSL eddy correctly!\"\n",
    "        )\n",
    "    np.savetxt(out_index, index_array.T)\n",
    "\n",
    "    return out_index\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "d626a80b",
   "metadata": {},
   "outputs": [],
   "source": [
    "from nipype.interfaces.fsl.epi import Eddy\n",
    "\n",
    "use_cuda=False\n",
    "initrand=False\n",
    "eddy = Eddy(repol=True, use_cuda=use_cuda, initrand=initrand)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "2ec03ce6",
   "metadata": {},
   "outputs": [],
   "source": [
    "## Workflow definition\n",
    "from pydra import Workflow\n",
    "from pydra.tasks.nipype1.utils import Nipype1Task\n",
    "\n",
    "workflow = Workflow(\n",
    "    name = \"dwi_preprocessing_using_t1\",\n",
    "    input_spec = [\"input_dir\"],\n",
    "    input_dir = str(pipeline_in_dir / \"bids\"))\n",
    "\n",
    "\n",
    "\n",
    "#bids_data_grabber\n",
    "workflow.add(\n",
    "    Nipype1Task(\n",
    "        name=\"bids_data_grabber\", \n",
    "        interface=bids_data_grabber, \n",
    "        base_dir=workflow.lzin.input_dir\n",
    "    )\n",
    ")\n",
    "\n",
    "#init_input_node\n",
    "workflow.add(\n",
    "    init_input_node(\n",
    "        name=\"init_input_node\",\n",
    "        interface=init_input_node, \n",
    "        t1w=workflow.bids_data_grabber.lzout.t1w,\n",
    "        dwi=workflow.bids_data_grabber.lzout.dwi,\n",
    "        dwi_json=workflow.bids_data_grabber.lzout.dwi_json,\n",
    "        bvec=workflow.bids_data_grabber.lzout.bvec,\n",
    "        bval=workflow.bids_data_grabber.lzout.bval,\n",
    "    )\n",
    ")\n",
    "workflow.init_input_node.split([\"t1w\", \"dwi\", \"dwi_json\", \"bvec\", \"bval\"])\n",
    "\n",
    "workflow.add(\n",
    "    prepare_reference_b0_1(\n",
    "        name=\"prepare_reference_b0_1\",\n",
    "        interface=prepare_reference_b0_1,\n",
    "        in_dwi=workflow.init_input_node.lzout.dwi,\n",
    "        in_bval=workflow.init_input_node.lzout.bval,\n",
    "        in_bvec=workflow.init_input_node.lzout.bvec,\n",
    "        low_bval=5,\n",
    "        working_directory=working_dir,\n",
    "    )\n",
    ")\n",
    "workflow.add(\n",
    "    Nipype1Task(\n",
    "        name=\"bet_2\",\n",
    "        interface=bet_2,\n",
    "        in_file=workflow.prepare_reference_b0_1.lzout.out_reference_b0,\n",
    "        mask=True,\n",
    "    )\n",
    ")\n",
    "\n",
    "## Eddy pipeline parts: generate_acq, generate_index, eddy\n",
    "workflow.add(\n",
    "    generate_acq_file(\n",
    "        name=\"generate_acq_file\",\n",
    "        interface=generate_acq_file,\n",
    "        in_dwi=workflow.prepare_reference_b0_1.lzout.out_b0_dwi_merge, \n",
    "        fsl_phase_encoding_direction=workflow.init_input_node.lzout.phase_encoding_direction,\n",
    "        total_readout_time=workflow.init_input_node.lzout.total_readout_time,\n",
    "        image_id=None\n",
    "    )\n",
    ")\n",
    "workflow.add(\n",
    "    generate_index_file(\n",
    "        name=\"generate_index_file\",\n",
    "        interface=generate_index_file,\n",
    "        in_bval=workflow.prepare_reference_b0_1.lzout.out_updated_bval,\n",
    "        low_bval=5.0,\n",
    "        image_id=None\n",
    "    )\n",
    ")\n",
    "workflow.add(\n",
    "    Nipype1Task(\n",
    "        name=\"eddy\",\n",
    "        interface=eddy,\n",
    "        in_file=workflow.prepare_reference_b0_1.lzout.out_b0_dwi_merge,\n",
    "        in_mask=workflow.bet_2.lzout.mask_file,\n",
    "        in_bval=workflow.prepare_reference_b0_1.lzout.out_updated_bval,\n",
    "        in_bvec=workflow.prepare_reference_b0_1.lzout.out_updated_bvec,\n",
    "        in_acqp=workflow.generate_acq_file.lzout.out_acq,\n",
    "        in_index=workflow.generate_index_file.lzout.out_index,\n",
    "    )\n",
    ")\n",
    "## eddy pipeline end\n",
    "\n",
    "##epi pipeline\n",
    "\n",
    "##epi pipeline end\n",
    "workflow.set_output([\n",
    "    #(\"out_ref_b0_bet\", workflow.bet.lzout.mask_file)\n",
    "    #(\"out_reference_b0\", workflow.prepare_reference_b0_1.lzout.out_reference_b0), \n",
    "    #(\"out_b0_dwi_merge\", workflow.prepare_reference_b0_1.lzout.out_b0_dwi_merge), \n",
    "    #(\"out_updated_bval\", workflow.prepare_reference_b0_1.lzout.out_updated_bval), \n",
    "    #(\"out_updated_bvec\", workflow.prepare_reference_b0_1.lzout.out_updated_bvec),\n",
    "    (\"out_parameter\", workflow.eddy.lzout.out_parameter),\n",
    "    (\"out_corrected\", workflow.eddy.lzout.out_corrected),\n",
    "    (\"out_rotated_bvecs\", workflow.eddy.lzout.out_rotated_bvecs),\n",
    "])\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "1f9e7769",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "220610-10:08:43,416 nipype.workflow INFO:\n",
      "\t [Node] Setting-up \"bids_data_grabber\" in \"/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmpboapvdzy/Nipype1Task_1dcbacabd20302547437efbbb2ae13a0f479571d8b6629d402171fb38984e797/bids_data_grabber\".\n",
      "220610-10:08:43,422 nipype.workflow INFO:\n",
      "\t [Node] Executing \"bids_data_grabber\" <nipype.interfaces.io.BIDSDataGrabber>\n",
      "220610-10:08:43,844 nipype.workflow INFO:\n",
      "\t [Node] Finished \"bids_data_grabber\", elapsed time 0.267325s.\n",
      "Running pipeline for sub-PREVDEMALS0010025PG | ses-M00 (TotalReadoutTime = 0.0342002, PhaseEncodingDirection = y-)\n",
      "bvals:  [   0.    0. 1000. 1000. 1000. 1000. 1000. 1000. 1000. 1000. 1000. 1000.\n",
      " 1000. 1000. 1000. 1000. 1000. 1000.    0. 1000. 1000. 1000. 1000. 1000.\n",
      " 1000. 1000. 1000. 1000. 1000. 1000. 1000. 1000. 1000. 1000.    0. 1000.\n",
      " 1000. 1000. 1000. 1000. 1000. 1000. 1000. 1000. 1000. 1000. 1000. 1000.\n",
      " 1000. 1000.    0. 1000. 1000. 1000. 1000. 1000. 1000. 1000. 1000. 1000.\n",
      " 1000. 1000. 1000. 1000. 1000. 1000. 1000. 1000. 1000.    0.    0. 1000.\n",
      " 1000. 1000. 1000. 1000. 1000. 1000. 1000. 1000. 1000. 1000. 1000. 1000.\n",
      " 1000. 1000. 1000.    0. 1000. 1000. 1000. 1000. 1000. 1000. 1000. 1000.\n",
      " 1000. 1000. 1000. 1000. 1000. 1000. 1000.    0. 1000. 1000. 1000. 1000.\n",
      " 1000. 1000. 1000. 1000. 1000. 1000. 1000. 1000. 1000. 1000. 1000.    0.\n",
      " 1000. 1000. 1000. 1000. 1000. 1000. 1000. 1000. 1000. 1000. 1000. 1000.\n",
      " 1000. 1000. 1000. 1000. 1000. 1000.    0.]\n",
      "220610-10:08:50,918 nipype.workflow INFO:\n",
      "\t [Node] Setting-up \"fslroi_ref\" in \"/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmpwq_btkfi/Nipype1Task_ab8e8253bfc4959e6cc84b52ab9a3657610a49ba734f9c653db27d3f7cf19379/fslroi_ref\".\n",
      "220610-10:08:50,921 nipype.workflow INFO:\n",
      "\t [Node] Executing \"fslroi_ref\" <nipype.interfaces.fsl.utils.ExtractROI>\n",
      "220610-10:08:51,253 nipype.workflow INFO:\n",
      "\t [Node] Finished \"fslroi_ref\", elapsed time 0.304152s.\n",
      "220610-10:08:51,524 nipype.workflow INFO:\n",
      "\t [Node] Setting-up \"bet_ref\" in \"/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmpwq_btkfi/Nipype1Task_c4de2fa6568abe26d81cec4e2afb75fabdd727ef193241350421d8cf7e156079/bet_ref\".\n",
      "220610-10:08:51,529 nipype.workflow INFO:\n",
      "\t [Node] Executing \"bet_ref\" <nipype.interfaces.fsl.preprocess.BET>\n",
      "220610-10:08:53,925 nipype.workflow INFO:\n",
      "\t [Node] Finished \"bet_ref\", elapsed time 2.3948s.\n",
      "220610-10:08:54,159 nipype.workflow INFO:\n",
      "\t [Node] Setting-up \"dilate\" in \"/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmpwq_btkfi/Nipype1Task_f6d3ebbd2c958e5e5fe5ba667f9cf310ba108df4cd958220d8c9525c0236f0de/dilate\".\n",
      "220610-10:08:54,167 nipype.workflow INFO:\n",
      "\t [Node] Executing \"dilate\" <nipype.interfaces.fsl.maths.MathsCommand>\n",
      "220610-10:08:54,909 nipype.workflow INFO:\n",
      "\t [Node] Finished \"dilate\", elapsed time 0.74064s.\n",
      "220610-10:08:56,771 nipype.workflow INFO:\n",
      "\t [Node] Setting-up \"fslroi_moving\" in \"/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmpbwh10bzq/Nipype1Task_ab8e8253bfc4959e6cc84b52ab9a3657610a49ba734f9c653db27d3f7cf19379/fslroi_moving\".\n",
      "220610-10:08:56,775 nipype.workflow INFO:\n",
      "\t [Node] Executing \"fslroi_moving\" <nipype.interfaces.fsl.utils.ExtractROI>\n",
      "220610-10:08:57,975 nipype.workflow INFO:\n",
      "\t [Node] Finished \"fslroi_moving\", elapsed time 1.170792s.\n",
      "220610-10:08:58,121 nipype.workflow INFO:\n",
      "\t [Node] Setting-up \"split_moving\" in \"/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmpbwh10bzq/Nipype1Task_f7f846fca9f9401d135054edb2c101f74262c41dfa9767afb5a349c02c4f7620/split_moving\".\n",
      "220610-10:08:58,124 nipype.workflow INFO:\n",
      "\t [Node] Executing \"split_moving\" <nipype.interfaces.fsl.utils.Split>\n",
      "220610-10:08:59,277 nipype.workflow INFO:\n",
      "\t [Node] Finished \"split_moving\", elapsed time 1.152086s.\n",
      "220610-10:09:03,82 nipype.workflow INFO:\n",
      "\t [Node] Setting-up \"flirt\" in \"/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmp4_x59b1o/Nipype1Task_b34194d246af6de1e50efdb6c7ea175d77afd66d3d503243f1e7af88458c3d24/flirt\".\n",
      "220610-10:09:03,92 nipype.workflow INFO:\n",
      "\t [Node] Executing \"flirt\" <nipype.interfaces.fsl.preprocess.FLIRT>\n",
      "220610-10:09:03,124 nipype.workflow INFO:\n",
      "\t [Node] Setting-up \"flirt\" in \"/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmp4_x59b1o/Nipype1Task_284f9ff493a9d5a16ae8d8c65b84f6ff64fbff558e3960323533005cf9b37bbc/flirt\".\n",
      "220610-10:09:03,132 nipype.workflow INFO:\n",
      "\t [Node] Executing \"flirt\" <nipype.interfaces.fsl.preprocess.FLIRT>\n",
      "220610-10:09:03,143 nipype.workflow INFO:\n",
      "\t [Node] Setting-up \"flirt\" in \"/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmp4_x59b1o/Nipype1Task_be6bfaa39f2b2ef9ed54b752ad65754b5b14754dcf881ec638af62a306c7d78f/flirt\".\n",
      "220610-10:09:03,151 nipype.workflow INFO:\n",
      "\t [Node] Executing \"flirt\" <nipype.interfaces.fsl.preprocess.FLIRT>\n",
      "220610-10:09:03,158 nipype.workflow INFO:\n",
      "\t [Node] Setting-up \"flirt\" in \"/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmp4_x59b1o/Nipype1Task_2a8ec4d50a1b12f9d6aafc9e0106a1902fb63fcca82512e728fa04db1afca1fe/flirt\".\n",
      "220610-10:09:03,168 nipype.workflow INFO:\n",
      "\t [Node] Setting-up \"flirt\" in \"/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmp4_x59b1o/Nipype1Task_e4e54eff274a5d647d8c3ec660bd7a74ccd8d879fc8cce196bf104ba3399ace0/flirt\".\n",
      "220610-10:09:03,175 nipype.workflow INFO:\n",
      "\t [Node] Executing \"flirt\" <nipype.interfaces.fsl.preprocess.FLIRT>\n",
      "220610-10:09:03,177 nipype.workflow INFO:\n",
      "\t [Node] Executing \"flirt\" <nipype.interfaces.fsl.preprocess.FLIRT>\n",
      "220610-10:09:03,210 nipype.workflow INFO:\n",
      "\t [Node] Setting-up \"flirt\" in \"/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmp4_x59b1o/Nipype1Task_10e85f08573b942dca1751daac60295ff849e48f6ab288f61aab5d3fd3fe6fd3/flirt\".\n",
      "220610-10:09:03,212 nipype.workflow INFO:\n",
      "\t [Node] Setting-up \"flirt\" in \"/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmp4_x59b1o/Nipype1Task_46afea225804a004175ff32c6335e35cff1e1a7a344b41e58471a01818dfb223/flirt\".\n",
      "220610-10:09:03,222 nipype.workflow INFO:\n",
      "\t [Node] Executing \"flirt\" <nipype.interfaces.fsl.preprocess.FLIRT>\n",
      "220610-10:09:03,237 nipype.workflow INFO:\n",
      "\t [Node] Executing \"flirt\" <nipype.interfaces.fsl.preprocess.FLIRT>\n",
      "220610-10:09:03,240 nipype.workflow INFO:\n",
      "\t [Node] Setting-up \"flirt\" in \"/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmp4_x59b1o/Nipype1Task_ca87ea248895af0971ccc40f89819ea6d049a2882b48bc16140cb965cfb7ec56/flirt\".\n",
      "220610-10:09:03,256 nipype.workflow INFO:\n",
      "\t [Node] Executing \"flirt\" <nipype.interfaces.fsl.preprocess.FLIRT>\n",
      "220610-10:09:03,324 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.324703:The output image will use the sform from the reference image\n",
      "220610-10:09:03,326 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.324703:The output image will use the transformed sform from the input image\n",
      "220610-10:09:03,326 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.324703:Init Matrix = \n",
      "220610-10:09:03,333 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.324703:1.000000 0.000000 0.000000 0.000000 \n",
      "220610-10:09:03,333 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.324703:0.000000 1.000000 0.000000 0.000000 \n",
      "220610-10:09:03,333 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.324703:0.000000 0.000000 1.000000 0.000000 \n",
      "220610-10:09:03,342 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.324703:0.000000 0.000000 0.000000 1.000000 \n",
      "220610-10:09:03,345 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.324703:\n",
      "220610-10:09:03,349 nipype.interface INFO:\n",
      "\t stderr 2022-06-10T10:09:03.345519:WARNING: Both reference and input images have an sform matrix set\n",
      "220610-10:09:03,368 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.368608:The output image will use the sform from the reference image\n",
      "220610-10:09:03,369 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.368608:The output image will use the transformed sform from the input image\n",
      "220610-10:09:03,369 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.368608:Init Matrix = \n",
      "220610-10:09:03,369 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.368608:1.000000 0.000000 0.000000 0.000000 \n",
      "220610-10:09:03,369 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.368608:0.000000 1.000000 0.000000 0.000000 \n",
      "220610-10:09:03,371 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.368608:0.000000 0.000000 1.000000 0.000000 \n",
      "220610-10:09:03,371 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.368608:0.000000 0.000000 0.000000 1.000000 \n",
      "220610-10:09:03,372 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.368608:\n",
      "220610-10:09:03,373 nipype.interface INFO:\n",
      "\t stderr 2022-06-10T10:09:03.373024:WARNING: Both reference and input images have an sform matrix set\n",
      "220610-10:09:03,422 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.421883:The output image will use the sform from the reference image\n",
      "220610-10:09:03,422 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.421883:The output image will use the transformed sform from the input image\n",
      "220610-10:09:03,425 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.421883:Init Matrix = \n",
      "220610-10:09:03,425 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.421883:1.000000 0.000000 0.000000 0.000000 \n",
      "220610-10:09:03,425 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.421883:0.000000 1.000000 0.000000 0.000000 \n",
      "220610-10:09:03,426 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.421883:0.000000 0.000000 1.000000 0.000000 \n",
      "220610-10:09:03,426 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.421883:0.000000 0.000000 0.000000 1.000000 \n",
      "220610-10:09:03,427 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.421883:\n",
      "220610-10:09:03,427 nipype.interface INFO:\n",
      "\t stderr 2022-06-10T10:09:03.427549:WARNING: Both reference and input images have an sform matrix set\n",
      "220610-10:09:03,434 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.434418:The output image will use the sform from the reference image\n",
      "220610-10:09:03,434 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.434418:The output image will use the transformed sform from the input image\n",
      "220610-10:09:03,435 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.434418:Init Matrix = \n",
      "220610-10:09:03,435 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.434418:1.000000 0.000000 0.000000 0.000000 \n",
      "220610-10:09:03,435 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.434418:0.000000 1.000000 0.000000 0.000000 \n",
      "220610-10:09:03,436 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.434418:0.000000 0.000000 1.000000 0.000000 \n",
      "220610-10:09:03,436 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.434418:0.000000 0.000000 0.000000 1.000000 \n",
      "220610-10:09:03,436 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.434418:\n",
      "220610-10:09:03,436 nipype.interface INFO:\n",
      "\t stderr 2022-06-10T10:09:03.436956:WARNING: Both reference and input images have an sform matrix set\n",
      "220610-10:09:03,439 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.439545:The output image will use the sform from the reference image\n",
      "220610-10:09:03,440 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.439545:The output image will use the transformed sform from the input image\n",
      "220610-10:09:03,440 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.439545:Init Matrix = \n",
      "220610-10:09:03,440 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.439545:1.000000 0.000000 0.000000 0.000000 \n",
      "220610-10:09:03,441 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.439545:0.000000 1.000000 0.000000 0.000000 \n",
      "220610-10:09:03,442 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.439545:0.000000 0.000000 1.000000 0.000000 \n",
      "220610-10:09:03,442 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.439545:0.000000 0.000000 0.000000 1.000000 \n",
      "220610-10:09:03,442 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.439545:\n",
      "220610-10:09:03,442 nipype.interface INFO:\n",
      "\t stderr 2022-06-10T10:09:03.442950:WARNING: Both reference and input images have an sform matrix set\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "220610-10:09:03,575 nipype.interface INFO:\n",
      "\t stderr 2022-06-10T10:09:03.574957:WARNING: Both reference and input images have an sform matrix set\n",
      "220610-10:09:03,575 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.575639:The output image will use the sform from the reference image\n",
      "220610-10:09:03,575 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.575639:The output image will use the transformed sform from the input image\n",
      "220610-10:09:03,576 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.575639:Init Matrix = \n",
      "220610-10:09:03,576 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.575639:1.000000 0.000000 0.000000 0.000000 \n",
      "220610-10:09:03,577 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.575639:0.000000 1.000000 0.000000 0.000000 \n",
      "220610-10:09:03,577 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.575639:0.000000 0.000000 1.000000 0.000000 \n",
      "220610-10:09:03,577 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.575639:0.000000 0.000000 0.000000 1.000000 \n",
      "220610-10:09:03,578 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.575639:\n",
      "220610-10:09:03,583 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.582870:The output image will use the sform from the reference image\n",
      "220610-10:09:03,583 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.582870:The output image will use the transformed sform from the input image\n",
      "220610-10:09:03,583 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.582870:Init Matrix = \n",
      "220610-10:09:03,583 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.582870:1.000000 0.000000 0.000000 0.000000 \n",
      "220610-10:09:03,584 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.582870:0.000000 1.000000 0.000000 0.000000 \n",
      "220610-10:09:03,584 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.582870:0.000000 0.000000 1.000000 0.000000 \n",
      "220610-10:09:03,584 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.582870:0.000000 0.000000 0.000000 1.000000 \n",
      "220610-10:09:03,584 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.582870:\n",
      "220610-10:09:03,585 nipype.interface INFO:\n",
      "\t stderr 2022-06-10T10:09:03.585299:WARNING: Both reference and input images have an sform matrix set\n",
      "220610-10:09:03,649 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.648909:The output image will use the sform from the reference image\n",
      "220610-10:09:03,649 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.648909:The output image will use the transformed sform from the input image\n",
      "220610-10:09:03,649 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.648909:Init Matrix = \n",
      "220610-10:09:03,649 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.648909:1.000000 0.000000 0.000000 0.000000 \n",
      "220610-10:09:03,649 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.648909:0.000000 1.000000 0.000000 0.000000 \n",
      "220610-10:09:03,649 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.648909:0.000000 0.000000 1.000000 0.000000 \n",
      "220610-10:09:03,649 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.648909:0.000000 0.000000 0.000000 1.000000 \n",
      "220610-10:09:03,649 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:03.648909:\n",
      "220610-10:09:03,649 nipype.interface INFO:\n",
      "\t stderr 2022-06-10T10:09:03.649897:WARNING: Both reference and input images have an sform matrix set\n",
      "220610-10:09:04,332 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.332579: >> # 8mm scale\n",
      "220610-10:09:04,332 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.332579: >> setscale 8\n",
      "220610-10:09:04,343 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.343385: >> # 8mm scale\n",
      "220610-10:09:04,344 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.344601: >> setscale 8\n",
      "220610-10:09:04,357 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.357338: >> # 8mm scale\n",
      "220610-10:09:04,357 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.357338: >> setscale 8\n",
      "220610-10:09:04,379 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.379126: >> # 8mm scale\n",
      "220610-10:09:04,379 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.379126: >> setscale 8\n",
      "220610-10:09:04,379 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.379669: >> # 8mm scale\n",
      "220610-10:09:04,380 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.380427: >> setscale 8\n",
      "220610-10:09:04,476 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.476031: >> # 8mm scale\n",
      "220610-10:09:04,477 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.477280: >> setscale 8\n",
      "220610-10:09:04,483 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.483478: >> # 8mm scale\n",
      "220610-10:09:04,483 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.483683: >> setscale 8\n",
      "220610-10:09:04,507 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.507233: >> # 8mm scale\n",
      "220610-10:09:04,507 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.507233: >> setscale 8\n",
      "220610-10:09:04,811 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.811452: >> setoption smoothing 8\n",
      "220610-10:09:04,812 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.812027: >> clear S\n",
      "220610-10:09:04,812 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.812027: >> clear P\n",
      "220610-10:09:04,812 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.812027: >> search\n",
      "220610-10:09:04,821 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.821579: >> setoption smoothing 8\n",
      "220610-10:09:04,821 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.821579: >> clear S\n",
      "220610-10:09:04,821 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.821579: >> clear P\n",
      "220610-10:09:04,821 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.821579: >> search\n",
      "220610-10:09:04,835 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.835840: >> setoption smoothing 8\n",
      "220610-10:09:04,836 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.835840: >> clear S\n",
      "220610-10:09:04,836 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.835840: >> clear P\n",
      "220610-10:09:04,836 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.835840: >> search\n",
      "220610-10:09:04,851 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.851926: >> setoption smoothing 8\n",
      "220610-10:09:04,852 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.851926: >> clear S\n",
      "220610-10:09:04,852 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.851926: >> clear P\n",
      "220610-10:09:04,852 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.851926: >> search\n",
      "220610-10:09:04,858 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.858597: >> setoption smoothing 8\n",
      "220610-10:09:04,858 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.858791: >> clear S\n",
      "220610-10:09:04,858 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.858791: >> clear P\n",
      "220610-10:09:04,858 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.858791: >> search\n",
      "220610-10:09:04,942 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.942051: >> setoption smoothing 8\n",
      "220610-10:09:04,942 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.942051: >> clear S\n",
      "220610-10:09:04,942 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.942051: >> clear P\n",
      "220610-10:09:04,942 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.942051: >> search\n",
      "220610-10:09:04,957 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.957707: >> setoption smoothing 8\n",
      "220610-10:09:04,957 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.957707: >> clear S\n",
      "220610-10:09:04,957 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.957707: >> clear P\n",
      "220610-10:09:04,957 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.957707: >> search\n",
      "220610-10:09:04,971 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.971706: >> setoption smoothing 8\n",
      "220610-10:09:04,971 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.971706: >> clear S\n",
      "220610-10:09:04,971 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.971706: >> clear P\n",
      "220610-10:09:04,972 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:04.971706: >> search\n",
      "220610-10:09:06,944 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:06.944294: >> # 4mm scale\n",
      "220610-10:09:06,944 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:06.944294: >> setscale 4\n",
      "220610-10:09:06,958 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:06.958420: >> # 4mm scale\n",
      "220610-10:09:06,958 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:06.958420: >> setscale 4\n",
      "220610-10:09:07,8 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.008288: >> # 4mm scale\n",
      "220610-10:09:07,8 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.008288: >> setscale 4\n",
      "220610-10:09:07,17 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.016940: >> # 4mm scale\n",
      "220610-10:09:07,17 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.016940: >> setscale 4\n",
      "220610-10:09:07,51 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.051749: >> # 4mm scale\n",
      "220610-10:09:07,51 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.051749: >> setscale 4\n",
      "220610-10:09:07,98 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.098625: >> # 4mm scale\n",
      "220610-10:09:07,98 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.098625: >> setscale 4\n",
      "220610-10:09:07,139 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.139182: >> # 4mm scale\n",
      "220610-10:09:07,139 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.139182: >> setscale 4\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "220610-10:09:07,235 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.235000: >> # 4mm scale\n",
      "220610-10:09:07,235 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.235000: >> setscale 4\n",
      "220610-10:09:07,339 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.339908: >> setoption smoothing 4\n",
      "220610-10:09:07,340 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.339908: >> clear U\n",
      "220610-10:09:07,340 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.339908: >> clear UA \n",
      "220610-10:09:07,340 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.339908: >> clear UB\n",
      "220610-10:09:07,340 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.339908: >> clear US\n",
      "220610-10:09:07,340 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.339908: >> clear UP\n",
      "220610-10:09:07,340 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.339908: >> # remeasure costs at this scale\n",
      "220610-10:09:07,340 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.340403: >> measurecost 7 S 0 0 0 0 0 0 rel\n",
      "220610-10:09:07,349 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.348981: >> copy U US\n",
      "220610-10:09:07,349 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.348981: >> clear U\n",
      "220610-10:09:07,349 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.348981: >> measurecost 7 P 0 0 0 0 0 0 rel\n",
      "220610-10:09:07,352 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.352066: >> copy U UP\n",
      "220610-10:09:07,352 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.352066: >> dualsort US UP\n",
      "220610-10:09:07,352 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.352298: >> # optimise best 3 candidates (pre and post 8mm optimisations)\n",
      "220610-10:09:07,352 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.352298: >> clear U\n",
      "220610-10:09:07,352 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.352298: >> optimise 7 US:1-3  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:07,356 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.356180: >> setoption smoothing 4\n",
      "220610-10:09:07,356 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.356180: >> clear U\n",
      "220610-10:09:07,356 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.356180: >> clear UA \n",
      "220610-10:09:07,356 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.356180: >> clear UB\n",
      "220610-10:09:07,356 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.356180: >> clear US\n",
      "220610-10:09:07,356 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.356180: >> clear UP\n",
      "220610-10:09:07,356 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.356180: >> # remeasure costs at this scale\n",
      "220610-10:09:07,356 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.356180: >> measurecost 7 S 0 0 0 0 0 0 rel\n",
      "220610-10:09:07,363 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.363576: >> copy U US\n",
      "220610-10:09:07,363 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.363576: >> clear U\n",
      "220610-10:09:07,363 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.363576: >> measurecost 7 P 0 0 0 0 0 0 rel\n",
      "220610-10:09:07,365 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.365945: >> copy U UP\n",
      "220610-10:09:07,366 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.365945: >> dualsort US UP\n",
      "220610-10:09:07,366 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.365945: >> # optimise best 3 candidates (pre and post 8mm optimisations)\n",
      "220610-10:09:07,366 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.365945: >> clear U\n",
      "220610-10:09:07,366 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.366241: >> optimise 7 US:1-3  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:07,417 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.417319: >> setoption smoothing 4\n",
      "220610-10:09:07,417 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.417319: >> clear U\n",
      "220610-10:09:07,417 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.417319: >> clear UA \n",
      "220610-10:09:07,417 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.417319: >> clear UB\n",
      "220610-10:09:07,417 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.417319: >> clear US\n",
      "220610-10:09:07,417 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.417319: >> clear UP\n",
      "220610-10:09:07,417 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.417319: >> # remeasure costs at this scale\n",
      "220610-10:09:07,417 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.417319: >> measurecost 7 S 0 0 0 0 0 0 rel\n",
      "220610-10:09:07,419 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.419415: >> setoption smoothing 4\n",
      "220610-10:09:07,419 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.419415: >> clear U\n",
      "220610-10:09:07,419 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.419415: >> clear UA \n",
      "220610-10:09:07,419 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.419415: >> clear UB\n",
      "220610-10:09:07,419 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.419415: >> clear US\n",
      "220610-10:09:07,419 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.419415: >> clear UP\n",
      "220610-10:09:07,419 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.419415: >> # remeasure costs at this scale\n",
      "220610-10:09:07,419 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.419921: >> measurecost 7 S 0 0 0 0 0 0 rel\n",
      "220610-10:09:07,421 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.421079: >> copy U US\n",
      "220610-10:09:07,421 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.421079: >> clear U\n",
      "220610-10:09:07,421 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.421079: >> measurecost 7 P 0 0 0 0 0 0 rel\n",
      "220610-10:09:07,422 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.422485: >> copy U US\n",
      "220610-10:09:07,422 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.422485: >> clear U\n",
      "220610-10:09:07,422 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.422485: >> measurecost 7 P 0 0 0 0 0 0 rel\n",
      "220610-10:09:07,423 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.423902: >> copy U UP\n",
      "220610-10:09:07,424 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.423902: >> dualsort US UP\n",
      "220610-10:09:07,424 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.423902: >> # optimise best 3 candidates (pre and post 8mm optimisations)\n",
      "220610-10:09:07,424 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.423902: >> clear U\n",
      "220610-10:09:07,424 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.423902: >> optimise 7 US:1-3  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:07,425 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.425848: >> copy U UP\n",
      "220610-10:09:07,426 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.426025: >> dualsort US UP\n",
      "220610-10:09:07,426 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.426025: >> # optimise best 3 candidates (pre and post 8mm optimisations)\n",
      "220610-10:09:07,426 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.426025: >> clear U\n",
      "220610-10:09:07,426 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.426025: >> optimise 7 US:1-3  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:07,447 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.446973: >> optimise 7 UP:1-3  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:07,460 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.460751: >> optimise 7 UP:1-3  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:07,479 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.479026: >> setoption smoothing 4\n",
      "220610-10:09:07,479 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.479026: >> clear U\n",
      "220610-10:09:07,479 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.479026: >> clear UA \n",
      "220610-10:09:07,479 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.479026: >> clear UB\n",
      "220610-10:09:07,479 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.479026: >> clear US\n",
      "220610-10:09:07,479 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.479026: >> clear UP\n",
      "220610-10:09:07,479 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.479026: >> # remeasure costs at this scale\n",
      "220610-10:09:07,479 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.479026: >> measurecost 7 S 0 0 0 0 0 0 rel\n",
      "220610-10:09:07,483 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.483233: >> copy U US\n",
      "220610-10:09:07,483 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.483390: >> clear U\n",
      "220610-10:09:07,483 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.483390: >> measurecost 7 P 0 0 0 0 0 0 rel\n",
      "220610-10:09:07,485 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.485507: >> copy U UP\n",
      "220610-10:09:07,485 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.485507: >> dualsort US UP\n",
      "220610-10:09:07,485 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.485507: >> # optimise best 3 candidates (pre and post 8mm optimisations)\n",
      "220610-10:09:07,485 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.485507: >> clear U\n",
      "220610-10:09:07,485 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.485789: >> optimise 7 US:1-3  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:07,524 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.524586: >> setoption smoothing 4\n",
      "220610-10:09:07,524 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.524586: >> clear U\n",
      "220610-10:09:07,524 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.524586: >> clear UA \n",
      "220610-10:09:07,524 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.524586: >> clear UB\n",
      "220610-10:09:07,524 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.524586: >> clear US\n",
      "220610-10:09:07,525 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.524586: >> clear UP\n",
      "220610-10:09:07,525 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.524586: >> # remeasure costs at this scale\n",
      "220610-10:09:07,525 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.524586: >> measurecost 7 S 0 0 0 0 0 0 rel\n",
      "220610-10:09:07,529 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.528959: >> copy U US\n",
      "220610-10:09:07,529 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.528959: >> clear U\n",
      "220610-10:09:07,529 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.528959: >> measurecost 7 P 0 0 0 0 0 0 rel\n",
      "220610-10:09:07,533 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.533843: >> copy U UP\n",
      "220610-10:09:07,533 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.533843: >> dualsort US UP\n",
      "220610-10:09:07,534 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.533843: >> # optimise best 3 candidates (pre and post 8mm optimisations)\n",
      "220610-10:09:07,534 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.534093: >> clear U\n",
      "220610-10:09:07,534 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.534093: >> optimise 7 US:1-3  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:07,535 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.535836: >> optimise 7 UP:1-3  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:07,547 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.547802: >> optimise 7 UP:1-3  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:07,568 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.568422: >> # also try the identity transform as a starting point at this resolution\n",
      "220610-10:09:07,568 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.568422: >> clear UQ\n",
      "220610-10:09:07,568 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.568422: >> setrow UQ  1 0 0 0  0 1 0 0  0 0 1 0  0 0 0 1\n",
      "220610-10:09:07,568 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.568847: >> optimise 7 UQ  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:07,574 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.574618: >> setoption smoothing 4\n",
      "220610-10:09:07,574 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.574618: >> clear U\n",
      "220610-10:09:07,574 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.574618: >> clear UA \n",
      "220610-10:09:07,575 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.574618: >> clear UB\n",
      "220610-10:09:07,575 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.574618: >> clear US\n",
      "220610-10:09:07,575 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.574618: >> clear UP\n",
      "220610-10:09:07,575 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.574618: >> # remeasure costs at this scale\n",
      "220610-10:09:07,575 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.574618: >> measurecost 7 S 0 0 0 0 0 0 rel\n",
      "220610-10:09:07,577 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.577594: >> copy U US\n",
      "220610-10:09:07,577 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.577782: >> clear U\n",
      "220610-10:09:07,577 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.577782: >> measurecost 7 P 0 0 0 0 0 0 rel\n",
      "220610-10:09:07,577 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.577818: >> # also try the identity transform as a starting point at this resolution\n",
      "220610-10:09:07,577 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.577818: >> clear UQ\n",
      "220610-10:09:07,578 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.577818: >> setrow UQ  1 0 0 0  0 1 0 0  0 0 1 0  0 0 0 1\n",
      "220610-10:09:07,578 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.578658: >> optimise 7 UQ  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:07,580 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.580625: >> copy U UP\n",
      "220610-10:09:07,580 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.580799: >> dualsort US UP\n",
      "220610-10:09:07,580 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.580799: >> # optimise best 3 candidates (pre and post 8mm optimisations)\n",
      "220610-10:09:07,580 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.580799: >> clear U\n",
      "220610-10:09:07,580 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.580799: >> optimise 7 US:1-3  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:07,595 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.595568: >> optimise 7 UP:1-3  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:07,639 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.639332: >> optimise 7 UP:1-3  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:07,643 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.643706: >> # also try the identity transform as a starting point at this resolution\n",
      "220610-10:09:07,643 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.643706: >> clear UQ\n",
      "220610-10:09:07,643 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.643706: >> setrow UQ  1 0 0 0  0 1 0 0  0 0 1 0  0 0 0 1\n",
      "220610-10:09:07,644 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.643983: >> optimise 7 UQ  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "220610-10:09:07,658 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.658271: >> # also try the identity transform as a starting point at this resolution\n",
      "220610-10:09:07,658 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.658271: >> clear UQ\n",
      "220610-10:09:07,658 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.658271: >> setrow UQ  1 0 0 0  0 1 0 0  0 0 1 0  0 0 0 1\n",
      "220610-10:09:07,658 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.658590: >> optimise 7 UQ  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:07,664 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.664598: >> sort U\n",
      "220610-10:09:07,664 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.664598: >> copy U UA\n",
      "220610-10:09:07,664 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.664598: >> # select best 4 optimised solutions and try perturbations of these\n",
      "220610-10:09:07,664 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.664598: >> clear U\n",
      "220610-10:09:07,664 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.664934: >> copy UA:1-4 U\n",
      "220610-10:09:07,665 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.664934: >> optimise 7 UA:1-4  1.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:07,695 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.695845: >> sort U\n",
      "220610-10:09:07,696 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.695845: >> copy U UA\n",
      "220610-10:09:07,696 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.695845: >> # select best 4 optimised solutions and try perturbations of these\n",
      "220610-10:09:07,696 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.696160: >> clear U\n",
      "220610-10:09:07,696 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.696160: >> copy UA:1-4 U\n",
      "220610-10:09:07,696 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.696160: >> optimise 7 UA:1-4  1.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:07,699 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.699908: >> optimise 7 UP:1-3  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:07,704 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.704855: >> setoption smoothing 4\n",
      "220610-10:09:07,705 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.704855: >> clear U\n",
      "220610-10:09:07,705 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.704855: >> clear UA \n",
      "220610-10:09:07,705 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.704855: >> clear UB\n",
      "220610-10:09:07,705 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.704855: >> clear US\n",
      "220610-10:09:07,705 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.704855: >> clear UP\n",
      "220610-10:09:07,705 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.704855: >> # remeasure costs at this scale\n",
      "220610-10:09:07,705 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.705434: >> measurecost 7 S 0 0 0 0 0 0 rel\n",
      "220610-10:09:07,707 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.707195: >> # also try the identity transform as a starting point at this resolution\n",
      "220610-10:09:07,707 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.707195: >> clear UQ\n",
      "220610-10:09:07,707 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.707195: >> setrow UQ  1 0 0 0  0 1 0 0  0 0 1 0  0 0 0 1\n",
      "220610-10:09:07,708 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.708097: >> optimise 7 UQ  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:07,709 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.709536: >> copy U US\n",
      "220610-10:09:07,709 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.709536: >> clear U\n",
      "220610-10:09:07,709 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.709536: >> measurecost 7 P 0 0 0 0 0 0 rel\n",
      "220610-10:09:07,711 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.711438: >> copy U UP\n",
      "220610-10:09:07,711 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.711438: >> dualsort US UP\n",
      "220610-10:09:07,711 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.711438: >> # optimise best 3 candidates (pre and post 8mm optimisations)\n",
      "220610-10:09:07,711 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.711438: >> clear U\n",
      "220610-10:09:07,711 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.711822: >> optimise 7 US:1-3  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:07,798 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.798372: >> # also try the identity transform as a starting point at this resolution\n",
      "220610-10:09:07,798 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.798372: >> clear UQ\n",
      "220610-10:09:07,799 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.799653: >> setrow UQ  1 0 0 0  0 1 0 0  0 0 1 0  0 0 0 1\n",
      "220610-10:09:07,799 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.799808: >> optimise 7 UQ  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:07,806 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.805950: >> sort U\n",
      "220610-10:09:07,806 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.805950: >> copy U UA\n",
      "220610-10:09:07,806 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.805950: >> # select best 4 optimised solutions and try perturbations of these\n",
      "220610-10:09:07,806 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.805950: >> clear U\n",
      "220610-10:09:07,806 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.805950: >> copy UA:1-4 U\n",
      "220610-10:09:07,806 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.805950: >> optimise 7 UA:1-4  1.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:07,823 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.823749: >> sort U\n",
      "220610-10:09:07,823 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.823749: >> copy U UA\n",
      "220610-10:09:07,824 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.824021: >> # select best 4 optimised solutions and try perturbations of these\n",
      "220610-10:09:07,824 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.824021: >> clear U\n",
      "220610-10:09:07,824 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.824021: >> copy UA:1-4 U\n",
      "220610-10:09:07,824 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.824021: >> optimise 7 UA:1-4  1.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:07,850 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.850143: >> optimise 7 UP:1-3  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:07,855 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.855226: >> sort U\n",
      "220610-10:09:07,855 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.855304: >> # also try the identity transform as a starting point at this resolution\n",
      "220610-10:09:07,855 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.855226: >> copy U UA\n",
      "220610-10:09:07,855 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.855226: >> # select best 4 optimised solutions and try perturbations of these\n",
      "220610-10:09:07,855 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.855226: >> clear U\n",
      "220610-10:09:07,855 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.855576: >> copy UA:1-4 U\n",
      "220610-10:09:07,855 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.855576: >> optimise 7 UA:1-4  1.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:07,857 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.857059: >> clear UQ\n",
      "220610-10:09:07,857 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.857059: >> setrow UQ  1 0 0 0  0 1 0 0  0 0 1 0  0 0 0 1\n",
      "220610-10:09:07,857 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.857394: >> optimise 7 UQ  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:07,903 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.903068: >> sort U\n",
      "220610-10:09:07,909 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.908978: >> copy U UA\n",
      "220610-10:09:07,909 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.908978: >> # select best 4 optimised solutions and try perturbations of these\n",
      "220610-10:09:07,909 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.908978: >> clear U\n",
      "220610-10:09:07,909 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.908978: >> copy UA:1-4 U\n",
      "220610-10:09:07,909 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.908978: >> optimise 7 UA:1-4  1.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:07,965 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.965537: >> sort U\n",
      "220610-10:09:07,965 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.965537: >> copy U UA\n",
      "220610-10:09:07,965 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.965537: >> # select best 4 optimised solutions and try perturbations of these\n",
      "220610-10:09:07,965 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.965852: >> clear U\n",
      "220610-10:09:07,965 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.965852: >> copy UA:1-4 U\n",
      "220610-10:09:07,965 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.965852: >> optimise 7 UA:1-4  1.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:07,973 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.973270: >> # also try the identity transform as a starting point at this resolution\n",
      "220610-10:09:07,973 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.973270: >> clear UQ\n",
      "220610-10:09:07,973 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.973270: >> setrow UQ  1 0 0 0  0 1 0 0  0 0 1 0  0 0 0 1\n",
      "220610-10:09:07,973 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:07.973598: >> optimise 7 UQ  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:08,38 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:08.038039: >> optimise 7 UA:1-4 -1.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:08,60 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:08.060791: >> optimise 7 UA:1-4 -1.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:08,64 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:08.064316: >> sort U\n",
      "220610-10:09:08,64 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:08.064559: >> copy U UA\n",
      "220610-10:09:08,64 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:08.064559: >> # select best 4 optimised solutions and try perturbations of these\n",
      "220610-10:09:08,64 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:08.064559: >> clear U\n",
      "220610-10:09:08,64 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:08.064559: >> copy UA:1-4 U\n",
      "220610-10:09:08,64 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:08.064559: >> optimise 7 UA:1-4  1.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "220610-10:09:08,139 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:08.139744: >> optimise 7 UA:1-4 -1.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:08,146 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:08.146051: >> optimise 7 UA:1-4 -1.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:08,165 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:08.165685: >> optimise 7 UA:1-4 -1.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:08,215 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:08.215777: >> optimise 7 UA:1-4 -1.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:08,272 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:08.272421: >> optimise 7 UA:1-4 -1.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:08,374 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:08.374767: >> optimise 7 UA:1-4  0.0   1.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:08,388 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:08.388565: >> optimise 7 UA:1-4  0.0   1.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:08,408 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:08.408241: >> optimise 7 UA:1-4 -1.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:08,473 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:08.473065: >> optimise 7 UA:1-4  0.0   1.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:08,482 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:08.481981: >> optimise 7 UA:1-4  0.0   1.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:08,503 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:08.503608: >> optimise 7 UA:1-4  0.0   1.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:08,528 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:08.527927: >> optimise 7 UA:1-4  0.0   1.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:08,610 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:08.610117: >> optimise 7 UA:1-4  0.0   1.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:08,709 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:08.709794: >> optimise 7 UA:1-4  0.0  -1.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:08,735 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:08.735175: >> optimise 7 UA:1-4  0.0  -1.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:08,747 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:08.747623: >> optimise 7 UA:1-4  0.0   1.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:08,830 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:08.830197: >> optimise 7 UA:1-4  0.0  -1.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:08,830 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:08.830620: >> optimise 7 UA:1-4  0.0  -1.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:08,865 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:08.865286: >> optimise 7 UA:1-4  0.0  -1.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:08,898 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:08.898609: >> optimise 7 UA:1-4  0.0  -1.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:08,968 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:08.968682: >> optimise 7 UA:1-4  0.0  -1.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:09,71 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:09.070940: >> optimise 7 UA:1-4  0.0   0.0   1.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:09,87 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:09.087622: >> optimise 7 UA:1-4  0.0   0.0   1.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:09,95 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:09.095657: >> optimise 7 UA:1-4  0.0  -1.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:09,174 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:09.174167: >> optimise 7 UA:1-4  0.0   0.0   1.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:09,175 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:09.175435: >> optimise 7 UA:1-4  0.0   0.0   1.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:09,194 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:09.194767: >> optimise 7 UA:1-4  0.0   0.0   1.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:09,228 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:09.228916: >> optimise 7 UA:1-4  0.0   0.0   1.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:09,317 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:09.317143: >> optimise 7 UA:1-4  0.0   0.0   1.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:09,425 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:09.425048: >> optimise 7 UA:1-4  0.0   0.0  -1.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:09,425 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:09.425479: >> optimise 7 UA:1-4  0.0   0.0  -1.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:09,461 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:09.461922: >> optimise 7 UA:1-4  0.0   0.0   1.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:09,525 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:09.525832: >> optimise 7 UA:1-4  0.0   0.0  -1.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:09,549 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:09.549214: >> optimise 7 UA:1-4  0.0   0.0  -1.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:09,554 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:09.553934: >> optimise 7 UA:1-4  0.0   0.0  -1.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:09,589 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:09.589571: >> optimise 7 UA:1-4  0.0   0.0  -1.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:09,664 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:09.664712: >> optimise 7 UA:1-4  0.0   0.0  -1.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:09,752 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:09.752916: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0   0.1  abs 4\n",
      "220610-10:09:09,759 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:09.759416: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0   0.1  abs 4\n",
      "220610-10:09:09,797 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:09.797866: >> optimise 7 UA:1-4  0.0   0.0  -1.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:09,840 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:09.840646: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0   0.1  abs 4\n",
      "220610-10:09:09,868 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:09.867962: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0   0.1  abs 4\n",
      "220610-10:09:09,869 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:09.869342: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0   0.1  abs 4\n",
      "220610-10:09:09,900 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:09.899956: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0   0.1  abs 4\n",
      "220610-10:09:09,960 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:09.960516: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0   0.1  abs 4\n",
      "220610-10:09:10,56 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:10.056615: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0  -0.1  abs 4\n",
      "220610-10:09:10,58 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:10.058374: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0  -0.1  abs 4\n",
      "220610-10:09:10,83 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:10.083140: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0   0.1  abs 4\n",
      "220610-10:09:10,137 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:10.137400: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0  -0.1  abs 4\n",
      "220610-10:09:10,175 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:10.175626: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0  -0.1  abs 4\n",
      "220610-10:09:10,177 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:10.176960: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0  -0.1  abs 4\n",
      "220610-10:09:10,177 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:10.177194: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0  -0.1  abs 4\n",
      "220610-10:09:10,246 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:10.246201: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0  -0.1  abs 4\n",
      "220610-10:09:10,370 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:10.370382: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0   0.2  abs 4\n",
      "220610-10:09:10,377 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:10.377165: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0   0.2  abs 4\n",
      "220610-10:09:10,418 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:10.418075: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0  -0.1  abs 4\n",
      "220610-10:09:10,499 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:10.499386: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0   0.2  abs 4\n",
      "220610-10:09:10,536 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:10.535997: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0   0.2  abs 4\n",
      "220610-10:09:10,546 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:10.546238: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0   0.2  abs 4\n",
      "220610-10:09:10,547 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:10.547290: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0   0.2  abs 4\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "220610-10:09:10,620 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:10.620256: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0   0.2  abs 4\n",
      "220610-10:09:10,737 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:10.737181: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0  -0.2  abs 4\n",
      "220610-10:09:10,748 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:10.747978: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0  -0.2  abs 4\n",
      "220610-10:09:10,789 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:10.789264: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0   0.2  abs 4\n",
      "220610-10:09:10,854 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:10.854130: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0  -0.2  abs 4\n",
      "220610-10:09:10,919 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:10.919193: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0  -0.2  abs 4\n",
      "220610-10:09:10,958 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:10.958170: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0  -0.2  abs 4\n",
      "220610-10:09:10,973 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:10.973800: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0  -0.2  abs 4\n",
      "220610-10:09:11,45 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.045635: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0  -0.2  abs 4\n",
      "220610-10:09:11,156 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.156440: >> sort U\n",
      "220610-10:09:11,157 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.157463: >> copy U UB\n",
      "220610-10:09:11,157 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.157510: >> sort U\n",
      "220610-10:09:11,157 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.157654: >> # 2mm scale\n",
      "220610-10:09:11,157 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.157510: >> copy U UB\n",
      "220610-10:09:11,157 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.157654: >> setscale 2\n",
      "220610-10:09:11,157 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.157846: >> # 2mm scale\n",
      "220610-10:09:11,157 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.157846: >> setscale 2\n",
      "220610-10:09:11,159 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.159196: >> setoption smoothing 2\n",
      "220610-10:09:11,159 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.159196: >> clear U\n",
      "220610-10:09:11,159 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.159326: >> setoption smoothing 2\n",
      "220610-10:09:11,159 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.159196: >> clear UC\n",
      "220610-10:09:11,159 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.159196: >> clear UD\n",
      "220610-10:09:11,159 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.159555: >> clear UE\n",
      "220610-10:09:11,159 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.159555: >> clear UF\n",
      "220610-10:09:11,159 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.159555: >> # remeasure costs at this scale\n",
      "220610-10:09:11,159 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.159555: >> measurecost 7 UB 0 0 0 0 0 0 rel\n",
      "220610-10:09:11,160 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.160457: >> clear U\n",
      "220610-10:09:11,160 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.160457: >> clear UC\n",
      "220610-10:09:11,160 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.160457: >> clear UD\n",
      "220610-10:09:11,160 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.160457: >> clear UE\n",
      "220610-10:09:11,160 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.160457: >> clear UF\n",
      "220610-10:09:11,160 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.160457: >> # remeasure costs at this scale\n",
      "220610-10:09:11,160 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.160881: >> measurecost 7 UB 0 0 0 0 0 0 rel\n",
      "220610-10:09:11,200 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.200792: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0  -0.2  abs 4\n",
      "220610-10:09:11,241 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.241371: >> sort U\n",
      "220610-10:09:11,241 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.241371: >> copy U UC\n",
      "220610-10:09:11,241 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.241689: >> clear U\n",
      "220610-10:09:11,241 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.241689: >> optimise 7  UC:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:11,246 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.246204: >> sort U\n",
      "220610-10:09:11,246 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.246430: >> copy U UC\n",
      "220610-10:09:11,246 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.246430: >> clear U\n",
      "220610-10:09:11,246 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.246430: >> optimise 7  UC:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:11,260 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.260856: >> sort U\n",
      "220610-10:09:11,261 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.261123: >> copy U UB\n",
      "220610-10:09:11,261 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.261123: >> # 2mm scale\n",
      "220610-10:09:11,261 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.261123: >> setscale 2\n",
      "220610-10:09:11,262 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.262495: >> setoption smoothing 2\n",
      "220610-10:09:11,262 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.262495: >> clear U\n",
      "220610-10:09:11,262 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.262495: >> clear UC\n",
      "220610-10:09:11,262 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.262495: >> clear UD\n",
      "220610-10:09:11,262 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.262897: >> clear UE\n",
      "220610-10:09:11,262 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.262897: >> clear UF\n",
      "220610-10:09:11,263 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.262897: >> # remeasure costs at this scale\n",
      "220610-10:09:11,263 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.262897: >> measurecost 7 UB 0 0 0 0 0 0 rel\n",
      "220610-10:09:11,279 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.279571: >> sort U\n",
      "220610-10:09:11,279 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.279571: >> copy U UB\n",
      "220610-10:09:11,279 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.279892: >> # 2mm scale\n",
      "220610-10:09:11,279 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.279892: >> setscale 2\n",
      "220610-10:09:11,280 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.280515: >> setoption smoothing 2\n",
      "220610-10:09:11,280 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.280790: >> clear U\n",
      "220610-10:09:11,280 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.280790: >> clear UC\n",
      "220610-10:09:11,280 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.280972: >> clear UD\n",
      "220610-10:09:11,281 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.280972: >> clear UE\n",
      "220610-10:09:11,281 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.280972: >> clear UF\n",
      "220610-10:09:11,281 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.280972: >> # remeasure costs at this scale\n",
      "220610-10:09:11,281 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.281282: >> measurecost 7 UB 0 0 0 0 0 0 rel\n",
      "220610-10:09:11,328 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.328449: >> copy U UD\n",
      "220610-10:09:11,328 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.328449: >> setoption boundguess 1\n",
      "220610-10:09:11,335 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.335232: >> sort U\n",
      "220610-10:09:11,335 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.335232: >> copy U UB\n",
      "220610-10:09:11,335 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.335536: >> # 2mm scale\n",
      "220610-10:09:11,335 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.335536: >> setscale 2\n",
      "220610-10:09:11,337 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.337162: >> setoption smoothing 2\n",
      "220610-10:09:11,337 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.337162: >> clear U\n",
      "220610-10:09:11,337 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.337162: >> clear UC\n",
      "220610-10:09:11,337 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.337162: >> clear UD\n",
      "220610-10:09:11,337 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.337162: >> clear UE\n",
      "220610-10:09:11,337 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.337162: >> clear UF\n",
      "220610-10:09:11,337 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.337722: >> # remeasure costs at this scale\n",
      "220610-10:09:11,337 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.337722: >> measurecost 7 UB 0 0 0 0 0 0 rel\n",
      "220610-10:09:11,340 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.340050: >> copy U UD\n",
      "220610-10:09:11,340 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.340050: >> setoption boundguess 1\n",
      "220610-10:09:11,340 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.340522: >> if MAXDOF > 7\n",
      "220610-10:09:11,340 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.340522: >>  clear U\n",
      "220610-10:09:11,340 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.340522: >> if MAXDOF > 7\n",
      "220610-10:09:11,340 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.340522: >>  optimise 9  UD:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 1\n",
      "220610-10:09:11,340 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.340522: >> copy U UE\n",
      "220610-10:09:11,340 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.340522: >> if MAXDOF > 9\n",
      "220610-10:09:11,340 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.340522: >>  clear U\n",
      "220610-10:09:11,340 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.340522: >> if MAXDOF > 9\n",
      "220610-10:09:11,341 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.340522: >>  optimise 12 UE:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 2\n",
      "220610-10:09:11,341 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.340522: >> sort U\n",
      "220610-10:09:11,341 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.340522: >> copy U UF\n",
      "220610-10:09:11,341 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.340522: >> # 1mm scale\n",
      "220610-10:09:11,341 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.340522: >> setscale 1\n",
      "220610-10:09:11,341 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.341473: >> setoption smoothing 1\n",
      "220610-10:09:11,341 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.341473: >> setoption boundguess 1\n",
      "220610-10:09:11,341 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.341473: >> clear U\n",
      "220610-10:09:11,341 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.341784: >> # also try the qsform as a starting point at this resolution\n",
      "220610-10:09:11,341 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.341784: >> setrowqsform UF\n",
      "220610-10:09:11,344 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.344888: >> optimise 12 UF:1-2  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 1\n",
      "220610-10:09:11,345 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.345840: >> if MAXDOF > 7\n",
      "220610-10:09:11,346 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.345840: >>  clear U\n",
      "220610-10:09:11,346 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.345840: >> if MAXDOF > 7\n",
      "220610-10:09:11,346 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.345840: >>  optimise 9  UD:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 1\n",
      "220610-10:09:11,346 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.346423: >> copy U UE\n",
      "220610-10:09:11,346 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.346423: >> if MAXDOF > 9\n",
      "220610-10:09:11,346 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.346423: >>  clear U\n",
      "220610-10:09:11,346 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.346423: >> if MAXDOF > 9\n",
      "220610-10:09:11,346 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.346423: >>  optimise 12 UE:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 2\n",
      "220610-10:09:11,346 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.346423: >> sort U\n",
      "220610-10:09:11,346 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.346423: >> copy U UF\n",
      "220610-10:09:11,346 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.346423: >> # 1mm scale\n",
      "220610-10:09:11,346 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.346423: >> setscale 1\n",
      "220610-10:09:11,347 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.347531: >> sort U\n",
      "220610-10:09:11,347 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.347753: >> copy U UB\n",
      "220610-10:09:11,347 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.347753: >> # 2mm scale\n",
      "220610-10:09:11,348 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.347753: >> setscale 2\n",
      "220610-10:09:11,348 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.348747: >> setoption smoothing 2\n",
      "220610-10:09:11,348 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.348747: >> clear U\n",
      "220610-10:09:11,348 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.348747: >> clear UC\n",
      "220610-10:09:11,349 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.348747: >> clear UD\n",
      "220610-10:09:11,349 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.349098: >> clear UE\n",
      "220610-10:09:11,349 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.349098: >> clear UF\n",
      "220610-10:09:11,349 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.349098: >> # remeasure costs at this scale\n",
      "220610-10:09:11,349 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.349098: >> measurecost 7 UB 0 0 0 0 0 0 rel\n",
      "220610-10:09:11,350 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.350927: >> setoption smoothing 1\n",
      "220610-10:09:11,353 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.353136: >> setoption boundguess 1\n",
      "220610-10:09:11,355 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.355324: >> clear U\n",
      "220610-10:09:11,355 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.355324: >> # also try the qsform as a starting point at this resolution\n",
      "220610-10:09:11,355 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.355324: >> setrowqsform UF\n",
      "220610-10:09:11,355 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.355827: >> optimise 12 UF:1-2  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 1\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "220610-10:09:11,374 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.374902: >> sort U\n",
      "220610-10:09:11,375 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.374902: >> copy U UC\n",
      "220610-10:09:11,375 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.375179: >> clear U\n",
      "220610-10:09:11,375 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.375179: >> optimise 7  UC:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:11,392 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.392793: >> sort U\n",
      "220610-10:09:11,393 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.392793: >> copy U UC\n",
      "220610-10:09:11,393 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.393105: >> clear U\n",
      "220610-10:09:11,393 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.393105: >> optimise 7  UC:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:11,410 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.410464: >> sort U\n",
      "220610-10:09:11,414 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.414162: >> copy U UB\n",
      "220610-10:09:11,414 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.414369: >> # 2mm scale\n",
      "220610-10:09:11,414 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.414369: >> setscale 2\n",
      "220610-10:09:11,415 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.415538: >> setoption smoothing 2\n",
      "220610-10:09:11,415 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.415538: >> clear U\n",
      "220610-10:09:11,415 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.415768: >> clear UC\n",
      "220610-10:09:11,415 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.415768: >> clear UD\n",
      "220610-10:09:11,415 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.415768: >> clear UE\n",
      "220610-10:09:11,415 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.415768: >> clear UF\n",
      "220610-10:09:11,415 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.415768: >> # remeasure costs at this scale\n",
      "220610-10:09:11,416 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.415768: >> measurecost 7 UB 0 0 0 0 0 0 rel\n",
      "220610-10:09:11,435 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.435753: >> sort U\n",
      "220610-10:09:11,435 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.435753: >> copy U UC\n",
      "220610-10:09:11,436 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.436064: >> clear U\n",
      "220610-10:09:11,436 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.436064: >> optimise 7  UC:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:11,448 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.448732: >> sort U\n",
      "220610-10:09:11,448 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.448732: >> copy U UC\n",
      "220610-10:09:11,449 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.449025: >> clear U\n",
      "220610-10:09:11,449 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.449025: >> optimise 7  UC:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:11,462 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.462005: >> copy U UD\n",
      "220610-10:09:11,463 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.463830: >> setoption boundguess 1\n",
      "220610-10:09:11,464 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.463830: >> if MAXDOF > 7\n",
      "220610-10:09:11,464 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.463830: >>  clear U\n",
      "220610-10:09:11,464 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.463830: >> if MAXDOF > 7\n",
      "220610-10:09:11,464 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.463830: >>  optimise 9  UD:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 1\n",
      "220610-10:09:11,464 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.464263: >> copy U UE\n",
      "220610-10:09:11,464 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.464263: >> if MAXDOF > 9\n",
      "220610-10:09:11,464 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.464263: >>  clear U\n",
      "220610-10:09:11,464 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.464263: >> if MAXDOF > 9\n",
      "220610-10:09:11,464 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.464263: >>  optimise 12 UE:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 2\n",
      "220610-10:09:11,464 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.464263: >> sort U\n",
      "220610-10:09:11,464 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.464263: >> copy U UF\n",
      "220610-10:09:11,464 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.464263: >> # 1mm scale\n",
      "220610-10:09:11,464 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.464263: >> setscale 1\n",
      "220610-10:09:11,466 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.466860: >> setoption smoothing 1\n",
      "220610-10:09:11,469 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.469895: >> setoption boundguess 1\n",
      "220610-10:09:11,470 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.469895: >> clear U\n",
      "220610-10:09:11,470 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.469895: >> # also try the qsform as a starting point at this resolution\n",
      "220610-10:09:11,470 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.469895: >> setrowqsform UF\n",
      "220610-10:09:11,470 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.470259: >> optimise 12 UF:1-2  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 1\n",
      "220610-10:09:11,480 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.480208: >> # in addition, try qsform as the final transformation, not just an initialisation\n",
      "220610-10:09:11,480 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.480208: >> clear UG\n",
      "220610-10:09:11,480 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.480208: >> setrowqsform UG\n",
      "220610-10:09:11,480 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.480537: >> measurecost 12 UG:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 1\n",
      "220610-10:09:11,483 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.483145: >> # in addition, try qsform as the final transformation, not just an initialisation\n",
      "220610-10:09:11,483 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.483145: >> clear UG\n",
      "220610-10:09:11,483 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.483145: >> setrowqsform UG\n",
      "220610-10:09:11,483 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.483489: >> measurecost 12 UG:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 1\n",
      "220610-10:09:11,489 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.489947: >> sort U\n",
      "220610-10:09:11,490 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.490904: >> sort U\n",
      "220610-10:09:11,492 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.492788: >> copy U UD\n",
      "220610-10:09:11,492 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.492788: >> setoption boundguess 1\n",
      "220610-10:09:11,493 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.492788: >> if MAXDOF > 7\n",
      "220610-10:09:11,493 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.492788: >>  clear U\n",
      "220610-10:09:11,493 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.492788: >> if MAXDOF > 7\n",
      "220610-10:09:11,493 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.493259: >>  optimise 9  UD:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 1\n",
      "220610-10:09:11,493 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.493259: >> copy U UE\n",
      "220610-10:09:11,493 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.493259: >> if MAXDOF > 9\n",
      "220610-10:09:11,493 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.493259: >>  clear U\n",
      "220610-10:09:11,493 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.493259: >> if MAXDOF > 9\n",
      "220610-10:09:11,493 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.493259: >>  optimise 12 UE:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 2\n",
      "220610-10:09:11,493 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.493259: >> sort U\n",
      "220610-10:09:11,493 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.493259: >> copy U UF\n",
      "220610-10:09:11,493 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.493259: >> # 1mm scale\n",
      "220610-10:09:11,493 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.493259: >> setscale 1\n",
      "220610-10:09:11,495 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.495706: >> setoption smoothing 1\n",
      "220610-10:09:11,495 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.495706: >> setoption boundguess 1\n",
      "220610-10:09:11,495 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.495963: >> clear U\n",
      "220610-10:09:11,496 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.495963: >> # also try the qsform as a starting point at this resolution\n",
      "220610-10:09:11,496 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.495963: >> setrowqsform UF\n",
      "220610-10:09:11,496 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.495963: >> optimise 12 UF:1-2  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 1\n",
      "220610-10:09:11,509 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.509620: >> sort U\n",
      "220610-10:09:11,509 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.509620: >> copy U UC\n",
      "220610-10:09:11,509 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.509905: >> clear U\n",
      "220610-10:09:11,509 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.509905: >> optimise 7  UC:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:11,523 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.523829: >> copy U UD\n",
      "220610-10:09:11,524 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.523829: >> setoption boundguess 1\n",
      "220610-10:09:11,524 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.523829: >> if MAXDOF > 7\n",
      "220610-10:09:11,524 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.524178: >>  clear U\n",
      "220610-10:09:11,524 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.524178: >> if MAXDOF > 7\n",
      "220610-10:09:11,524 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.524178: >>  optimise 9  UD:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 1\n",
      "220610-10:09:11,524 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.524178: >> copy U UE\n",
      "220610-10:09:11,524 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.524178: >> if MAXDOF > 9\n",
      "220610-10:09:11,524 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.524178: >>  clear U\n",
      "220610-10:09:11,524 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.524178: >> if MAXDOF > 9\n",
      "220610-10:09:11,524 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.524178: >>  optimise 12 UE:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 2\n",
      "220610-10:09:11,524 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.524178: >> sort U\n",
      "220610-10:09:11,524 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.524178: >> copy U UF\n",
      "220610-10:09:11,524 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.524178: >> # 1mm scale\n",
      "220610-10:09:11,524 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.524178: >> setscale 1\n",
      "220610-10:09:11,526 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.526061: >> setoption smoothing 1\n",
      "220610-10:09:11,526 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.526061: >> setoption boundguess 1\n",
      "220610-10:09:11,526 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.526061: >> clear U\n",
      "220610-10:09:11,526 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.526061: >> # also try the qsform as a starting point at this resolution\n",
      "220610-10:09:11,526 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.526420: >> setrowqsform UF\n",
      "220610-10:09:11,526 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.526420: >> optimise 12 UF:1-2  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 1\n",
      "220610-10:09:11,531 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.531389: >> copy U UD\n",
      "220610-10:09:11,531 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.531389: >> setoption boundguess 1\n",
      "220610-10:09:11,531 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.531389: >> if MAXDOF > 7\n",
      "220610-10:09:11,531 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.531389: >>  clear U\n",
      "220610-10:09:11,531 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.531389: >> if MAXDOF > 7\n",
      "220610-10:09:11,531 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.531858: >>  optimise 9  UD:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 1\n",
      "220610-10:09:11,531 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.531858: >> copy U UE\n",
      "220610-10:09:11,531 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.531858: >> if MAXDOF > 9\n",
      "220610-10:09:11,532 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.531858: >>  clear U\n",
      "220610-10:09:11,532 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.531858: >> if MAXDOF > 9\n",
      "220610-10:09:11,532 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.531858: >>  optimise 12 UE:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 2\n",
      "220610-10:09:11,532 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.531858: >> sort U\n",
      "220610-10:09:11,532 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.531858: >> copy U UF\n",
      "220610-10:09:11,532 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.531858: >> # 1mm scale\n",
      "220610-10:09:11,532 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.531858: >> setscale 1\n",
      "220610-10:09:11,533 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.533913: >> setoption smoothing 1\n",
      "220610-10:09:11,534 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.533913: >> setoption boundguess 1\n",
      "220610-10:09:11,534 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.533913: >> clear U\n",
      "220610-10:09:11,534 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.533913: >> # also try the qsform as a starting point at this resolution\n",
      "220610-10:09:11,534 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.534269: >> setrowqsform UF\n",
      "220610-10:09:11,534 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.534269: >> optimise 12 UF:1-2  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 1\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "220610-10:09:11,588 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.588110: >> copy U UD\n",
      "220610-10:09:11,588 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.588110: >> setoption boundguess 1\n",
      "220610-10:09:11,588 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.588428: >> if MAXDOF > 7\n",
      "220610-10:09:11,588 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.588428: >>  clear U\n",
      "220610-10:09:11,588 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.588428: >> if MAXDOF > 7\n",
      "220610-10:09:11,588 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.588428: >>  optimise 9  UD:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 1\n",
      "220610-10:09:11,588 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.588428: >> copy U UE\n",
      "220610-10:09:11,588 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.588428: >> if MAXDOF > 9\n",
      "220610-10:09:11,588 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.588428: >>  clear U\n",
      "220610-10:09:11,588 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.588428: >> if MAXDOF > 9\n",
      "220610-10:09:11,588 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.588428: >>  optimise 12 UE:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 2\n",
      "220610-10:09:11,588 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.588428: >> sort U\n",
      "220610-10:09:11,588 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.588428: >> copy U UF\n",
      "220610-10:09:11,588 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.588428: >> # 1mm scale\n",
      "220610-10:09:11,589 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.588428: >> setscale 1\n",
      "220610-10:09:11,590 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.590619: >> sort U\n",
      "220610-10:09:11,591 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.591761: >> copy U UB\n",
      "220610-10:09:11,592 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.591969: >> # 2mm scale\n",
      "220610-10:09:11,592 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.591969: >> setscale 2\n",
      "220610-10:09:11,593 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.593270: >> setoption smoothing 2\n",
      "220610-10:09:11,593 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.593270: >> clear U\n",
      "220610-10:09:11,593 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.593270: >> clear UC\n",
      "220610-10:09:11,593 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.593270: >> clear UD\n",
      "220610-10:09:11,593 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.593627: >> clear UE\n",
      "220610-10:09:11,593 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.593627: >> clear UF\n",
      "220610-10:09:11,593 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.593627: >> # remeasure costs at this scale\n",
      "220610-10:09:11,593 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.593627: >> measurecost 7 UB 0 0 0 0 0 0 rel\n",
      "220610-10:09:11,597 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.597877: >> setoption smoothing 1\n",
      "220610-10:09:11,599 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.599685: >> setoption boundguess 1\n",
      "220610-10:09:11,602 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.602344: >> clear U\n",
      "220610-10:09:11,602 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.602527: >> # also try the qsform as a starting point at this resolution\n",
      "220610-10:09:11,603 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.603652: >> setrowqsform UF\n",
      "220610-10:09:11,603 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.603837: >> optimise 12 UF:1-2  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 1\n",
      "220610-10:09:11,608 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.607999: >> # in addition, try qsform as the final transformation, not just an initialisation\n",
      "220610-10:09:11,608 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.607999: >> clear UG\n",
      "220610-10:09:11,608 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.607999: >> setrowqsform UG\n",
      "220610-10:09:11,608 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.607999: >> measurecost 12 UG:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 1\n",
      "220610-10:09:11,610 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.610589: >> sort U\n",
      "220610-10:09:11,622 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.622258: >> # in addition, try qsform as the final transformation, not just an initialisation\n",
      "220610-10:09:11,622 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.622258: >> clear UG\n",
      "220610-10:09:11,622 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.622258: >> setrowqsform UG\n",
      "220610-10:09:11,622 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.622622: >> measurecost 12 UG:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 1\n",
      "220610-10:09:11,625 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.625577: >> sort U\n",
      "220610-10:09:11,665 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.665580: >> # in addition, try qsform as the final transformation, not just an initialisation\n",
      "220610-10:09:11,665 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.665580: >> clear UG\n",
      "220610-10:09:11,665 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.665857: >> setrowqsform UG\n",
      "220610-10:09:11,665 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.665857: >> measurecost 12 UG:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 1\n",
      "220610-10:09:11,667 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.667270: >> # in addition, try qsform as the final transformation, not just an initialisation\n",
      "220610-10:09:11,667 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.667270: >> clear UG\n",
      "220610-10:09:11,667 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.667270: >> setrowqsform UG\n",
      "220610-10:09:11,667 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.667598: >> measurecost 12 UG:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 1\n",
      "220610-10:09:11,667 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.667725: >> sort U\n",
      "220610-10:09:11,669 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.669579: >> sort U\n",
      "220610-10:09:11,674 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.674640: >> sort U\n",
      "220610-10:09:11,674 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.674868: >> copy U UC\n",
      "220610-10:09:11,674 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.674868: >> clear U\n",
      "220610-10:09:11,675 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.674868: >> optimise 7  UC:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:11,717 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.717784: >> # in addition, try qsform as the final transformation, not just an initialisation\n",
      "220610-10:09:11,717 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.717784: >> clear UG\n",
      "220610-10:09:11,718 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.717784: >> setrowqsform UG\n",
      "220610-10:09:11,718 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.718117: >> measurecost 12 UG:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 1\n",
      "220610-10:09:11,719 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.719949: >> sort U\n",
      "220610-10:09:11,756 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.756276: >> copy U UD\n",
      "220610-10:09:11,756 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.756492: >> setoption boundguess 1\n",
      "220610-10:09:11,756 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.756492: >> if MAXDOF > 7\n",
      "220610-10:09:11,756 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.756492: >>  clear U\n",
      "220610-10:09:11,756 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.756492: >> if MAXDOF > 7\n",
      "220610-10:09:11,756 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.756492: >>  optimise 9  UD:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 1\n",
      "220610-10:09:11,756 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.756492: >> copy U UE\n",
      "220610-10:09:11,756 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.756492: >> if MAXDOF > 9\n",
      "220610-10:09:11,756 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.756492: >>  clear U\n",
      "220610-10:09:11,756 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.756492: >> if MAXDOF > 9\n",
      "220610-10:09:11,757 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.756492: >>  optimise 12 UE:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 2\n",
      "220610-10:09:11,757 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.756492: >> sort U\n",
      "220610-10:09:11,757 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.756492: >> copy U UF\n",
      "220610-10:09:11,757 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.756492: >> # 1mm scale\n",
      "220610-10:09:11,757 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.756492: >> setscale 1\n",
      "220610-10:09:11,759 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.759261: >> setoption smoothing 1\n",
      "220610-10:09:11,759 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.759460: >> setoption boundguess 1\n",
      "220610-10:09:11,759 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.759460: >> clear U\n",
      "220610-10:09:11,759 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.759460: >> # also try the qsform as a starting point at this resolution\n",
      "220610-10:09:11,759 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.759460: >> setrowqsform UF\n",
      "220610-10:09:11,759 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.759460: >> optimise 12 UF:1-2  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 1\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "220610-10:09:11,876 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.876808: >> # in addition, try qsform as the final transformation, not just an initialisation\n",
      "220610-10:09:11,876 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.876808: >> clear UG\n",
      "220610-10:09:11,877 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.877118: >> setrowqsform UG\n",
      "220610-10:09:11,877 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.877225: >> measurecost 12 UG:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 1\n",
      "220610-10:09:11,879 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:11.879681: >> sort U\n",
      "220610-10:09:12,241 nipype.workflow INFO:\n",
      "\t [Node] Finished \"flirt\", elapsed time 8.99053s.\n",
      "220610-10:09:12,254 nipype.workflow INFO:\n",
      "\t [Node] Finished \"flirt\", elapsed time 9.018707s.\n",
      "220610-10:09:12,359 nipype.workflow INFO:\n",
      "\t [Node] Finished \"flirt\", elapsed time 9.139271s.\n",
      "220610-10:09:12,372 nipype.workflow INFO:\n",
      "\t [Node] Finished \"flirt\", elapsed time 9.009829s.\n",
      "220610-10:09:12,427 nipype.workflow INFO:\n",
      "\t [Node] Finished \"flirt\", elapsed time 9.242053s.\n",
      "220610-10:09:12,434 nipype.workflow INFO:\n",
      "\t [Node] Finished \"flirt\", elapsed time 9.291133s.\n",
      "220610-10:09:12,530 nipype.workflow INFO:\n",
      "\t [Node] Finished \"flirt\", elapsed time 9.07241s.\n",
      "220610-10:09:12,659 nipype.workflow INFO:\n",
      "\t [Node] Finished \"flirt\", elapsed time 9.291766s.\n",
      "220610-10:09:13,442 nipype.workflow INFO:\n",
      "\t [Node] Setting-up \"flirt\" in \"/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmp4_x59b1o/Nipype1Task_2685df55f97181e4c73283e7178f690eabd1ad1e07842ffa68d2d83cddb255ab/flirt\".\n",
      "220610-10:09:13,449 nipype.workflow INFO:\n",
      "\t [Node] Executing \"flirt\" <nipype.interfaces.fsl.preprocess.FLIRT>\n",
      "220610-10:09:13,472 nipype.workflow INFO:\n",
      "\t [Node] Setting-up \"flirt\" in \"/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmp4_x59b1o/Nipype1Task_9d2cffa493224fb10a8963b5a5f65d93038c09daa1c37e24d55d400b185e279c/flirt\".\n",
      "220610-10:09:13,477 nipype.workflow INFO:\n",
      "\t [Node] Executing \"flirt\" <nipype.interfaces.fsl.preprocess.FLIRT>\n",
      "220610-10:09:13,577 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:13.577158:The output image will use the sform from the reference image\n",
      "220610-10:09:13,577 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:13.577158:The output image will use the transformed sform from the input image\n",
      "220610-10:09:13,577 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:13.577158:Init Matrix = \n",
      "220610-10:09:13,577 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:13.577158:1.000000 0.000000 0.000000 0.000000 \n",
      "220610-10:09:13,577 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:13.577158:0.000000 1.000000 0.000000 0.000000 \n",
      "220610-10:09:13,578 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:13.577158:0.000000 0.000000 1.000000 0.000000 \n",
      "220610-10:09:13,578 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:13.577158:0.000000 0.000000 0.000000 1.000000 \n",
      "220610-10:09:13,578 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:13.577158:\n",
      "220610-10:09:13,578 nipype.interface INFO:\n",
      "\t stderr 2022-06-10T10:09:13.578192:WARNING: Both reference and input images have an sform matrix set\n",
      "220610-10:09:13,600 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:13.600509:The output image will use the sform from the reference image\n",
      "220610-10:09:13,601 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:13.600509:The output image will use the transformed sform from the input image\n",
      "220610-10:09:13,601 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:13.600509:Init Matrix = \n",
      "220610-10:09:13,602 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:13.600509:1.000000 0.000000 0.000000 0.000000 \n",
      "220610-10:09:13,603 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:13.600509:0.000000 1.000000 0.000000 0.000000 \n",
      "220610-10:09:13,603 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:13.600509:0.000000 0.000000 1.000000 0.000000 \n",
      "220610-10:09:13,604 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:13.600509:0.000000 0.000000 0.000000 1.000000 \n",
      "220610-10:09:13,605 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:13.600509:\n",
      "220610-10:09:13,605 nipype.interface INFO:\n",
      "\t stderr 2022-06-10T10:09:13.605262:WARNING: Both reference and input images have an sform matrix set\n",
      "220610-10:09:14,52 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:14.052427: >> # 8mm scale\n",
      "220610-10:09:14,52 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:14.052427: >> setscale 8\n",
      "220610-10:09:14,74 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:14.074110: >> # 8mm scale\n",
      "220610-10:09:14,74 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:14.074110: >> setscale 8\n",
      "220610-10:09:14,294 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:14.294822: >> setoption smoothing 8\n",
      "220610-10:09:14,294 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:14.294822: >> clear S\n",
      "220610-10:09:14,295 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:14.294822: >> clear P\n",
      "220610-10:09:14,295 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:14.294822: >> search\n",
      "220610-10:09:14,319 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:14.319447: >> setoption smoothing 8\n",
      "220610-10:09:14,319 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:14.319447: >> clear S\n",
      "220610-10:09:14,319 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:14.319447: >> clear P\n",
      "220610-10:09:14,319 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:14.319447: >> search\n",
      "220610-10:09:15,196 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.196477: >> # 4mm scale\n",
      "220610-10:09:15,196 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.196477: >> setscale 4\n",
      "220610-10:09:15,201 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.201177: >> # 4mm scale\n",
      "220610-10:09:15,201 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.201177: >> setscale 4\n",
      "220610-10:09:15,375 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.375415: >> setoption smoothing 4\n",
      "220610-10:09:15,375 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.375415: >> clear U\n",
      "220610-10:09:15,375 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.375415: >> clear UA \n",
      "220610-10:09:15,375 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.375415: >> clear UB\n",
      "220610-10:09:15,375 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.375415: >> clear US\n",
      "220610-10:09:15,375 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.375415: >> clear UP\n",
      "220610-10:09:15,376 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.375415: >> # remeasure costs at this scale\n",
      "220610-10:09:15,376 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.375415: >> measurecost 7 S 0 0 0 0 0 0 rel\n",
      "220610-10:09:15,377 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.377143: >> copy U US\n",
      "220610-10:09:15,377 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.377143: >> clear U\n",
      "220610-10:09:15,377 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.377143: >> measurecost 7 P 0 0 0 0 0 0 rel\n",
      "220610-10:09:15,378 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.378872: >> copy U UP\n",
      "220610-10:09:15,379 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.378872: >> dualsort US UP\n",
      "220610-10:09:15,379 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.378872: >> # optimise best 3 candidates (pre and post 8mm optimisations)\n",
      "220610-10:09:15,379 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.378872: >> clear U\n",
      "220610-10:09:15,379 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.378872: >> optimise 7 US:1-3  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:15,383 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.383107: >> setoption smoothing 4\n",
      "220610-10:09:15,383 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.383107: >> clear U\n",
      "220610-10:09:15,383 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.383609: >> clear UA \n",
      "220610-10:09:15,383 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.383609: >> clear UB\n",
      "220610-10:09:15,383 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.383609: >> clear US\n",
      "220610-10:09:15,384 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.383609: >> clear UP\n",
      "220610-10:09:15,384 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.383609: >> # remeasure costs at this scale\n",
      "220610-10:09:15,384 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.383609: >> measurecost 7 S 0 0 0 0 0 0 rel\n",
      "220610-10:09:15,384 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.384950: >> copy U US\n",
      "220610-10:09:15,385 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.384950: >> clear U\n",
      "220610-10:09:15,385 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.384950: >> measurecost 7 P 0 0 0 0 0 0 rel\n",
      "220610-10:09:15,387 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.387028: >> copy U UP\n",
      "220610-10:09:15,387 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.387028: >> dualsort US UP\n",
      "220610-10:09:15,387 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.387028: >> # optimise best 3 candidates (pre and post 8mm optimisations)\n",
      "220610-10:09:15,387 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.387028: >> clear U\n",
      "220610-10:09:15,387 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.387028: >> optimise 7 US:1-3  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "220610-10:09:15,438 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.438495: >> optimise 7 UP:1-3  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:15,449 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.449888: >> optimise 7 UP:1-3  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:15,490 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.490627: >> # also try the identity transform as a starting point at this resolution\n",
      "220610-10:09:15,490 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.490627: >> clear UQ\n",
      "220610-10:09:15,490 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.490627: >> setrow UQ  1 0 0 0  0 1 0 0  0 0 1 0  0 0 0 1\n",
      "220610-10:09:15,491 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.491046: >> optimise 7 UQ  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:15,502 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.502497: >> # also try the identity transform as a starting point at this resolution\n",
      "220610-10:09:15,502 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.502497: >> clear UQ\n",
      "220610-10:09:15,502 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.502497: >> setrow UQ  1 0 0 0  0 1 0 0  0 0 1 0  0 0 0 1\n",
      "220610-10:09:15,502 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.502497: >> optimise 7 UQ  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:15,539 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.539945: >> sort U\n",
      "220610-10:09:15,540 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.539945: >> copy U UA\n",
      "220610-10:09:15,540 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.539945: >> # select best 4 optimised solutions and try perturbations of these\n",
      "220610-10:09:15,540 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.539945: >> clear U\n",
      "220610-10:09:15,540 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.539945: >> copy UA:1-4 U\n",
      "220610-10:09:15,540 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.539945: >> optimise 7 UA:1-4  1.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:15,553 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.553674: >> sort U\n",
      "220610-10:09:15,553 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.553674: >> copy U UA\n",
      "220610-10:09:15,554 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.553674: >> # select best 4 optimised solutions and try perturbations of these\n",
      "220610-10:09:15,554 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.553674: >> clear U\n",
      "220610-10:09:15,554 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.553674: >> copy UA:1-4 U\n",
      "220610-10:09:15,554 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.553674: >> optimise 7 UA:1-4  1.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:15,690 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.690241: >> optimise 7 UA:1-4 -1.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:15,710 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.710597: >> optimise 7 UA:1-4 -1.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:15,832 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.832560: >> optimise 7 UA:1-4  0.0   1.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:15,862 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.862628: >> optimise 7 UA:1-4  0.0   1.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:15,990 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:15.990052: >> optimise 7 UA:1-4  0.0  -1.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:16,28 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:16.028209: >> optimise 7 UA:1-4  0.0  -1.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:16,136 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:16.136089: >> optimise 7 UA:1-4  0.0   0.0   1.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:16,180 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:16.180557: >> optimise 7 UA:1-4  0.0   0.0   1.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:16,305 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:16.305817: >> optimise 7 UA:1-4  0.0   0.0  -1.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:16,356 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:16.356455: >> optimise 7 UA:1-4  0.0   0.0  -1.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:16,457 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:16.457595: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0   0.1  abs 4\n",
      "220610-10:09:16,519 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:16.519830: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0   0.1  abs 4\n",
      "220610-10:09:16,609 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:16.609900: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0  -0.1  abs 4\n",
      "220610-10:09:16,674 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:16.674160: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0  -0.1  abs 4\n",
      "220610-10:09:16,758 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:16.758929: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0   0.2  abs 4\n",
      "220610-10:09:16,834 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:16.834431: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0   0.2  abs 4\n",
      "220610-10:09:16,905 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:16.905487: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0  -0.2  abs 4\n",
      "220610-10:09:17,3 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.003108: >> optimise 7 UA:1-4  0.0   0.0   0.0   0.0   0.0   0.0  -0.2  abs 4\n",
      "220610-10:09:17,64 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.064543: >> sort U\n",
      "220610-10:09:17,64 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.064543: >> copy U UB\n",
      "220610-10:09:17,64 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.064825: >> # 2mm scale\n",
      "220610-10:09:17,65 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.064825: >> setscale 2\n",
      "220610-10:09:17,65 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.065511: >> setoption smoothing 2\n",
      "220610-10:09:17,65 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.065511: >> clear U\n",
      "220610-10:09:17,65 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.065511: >> clear UC\n",
      "220610-10:09:17,65 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.065511: >> clear UD\n",
      "220610-10:09:17,65 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.065511: >> clear UE\n",
      "220610-10:09:17,65 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.065511: >> clear UF\n",
      "220610-10:09:17,65 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.065511: >> # remeasure costs at this scale\n",
      "220610-10:09:17,65 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.065511: >> measurecost 7 UB 0 0 0 0 0 0 rel\n",
      "220610-10:09:17,105 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.105883: >> sort U\n",
      "220610-10:09:17,106 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.105883: >> copy U UC\n",
      "220610-10:09:17,106 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.105883: >> clear U\n",
      "220610-10:09:17,106 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.105883: >> optimise 7  UC:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:17,149 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.149586: >> copy U UD\n",
      "220610-10:09:17,149 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.149586: >> setoption boundguess 1\n",
      "220610-10:09:17,149 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.149586: >> if MAXDOF > 7\n",
      "220610-10:09:17,149 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.149586: >>  clear U\n",
      "220610-10:09:17,149 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.149586: >> if MAXDOF > 7\n",
      "220610-10:09:17,149 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.149586: >>  optimise 9  UD:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 1\n",
      "220610-10:09:17,150 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.150082: >> copy U UE\n",
      "220610-10:09:17,150 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.150082: >> if MAXDOF > 9\n",
      "220610-10:09:17,150 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.150082: >>  clear U\n",
      "220610-10:09:17,150 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.150082: >> if MAXDOF > 9\n",
      "220610-10:09:17,150 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.150082: >>  optimise 12 UE:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 2\n",
      "220610-10:09:17,150 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.150082: >> sort U\n",
      "220610-10:09:17,150 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.150082: >> copy U UF\n",
      "220610-10:09:17,150 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.150082: >> # 1mm scale\n",
      "220610-10:09:17,150 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.150082: >> setscale 1\n",
      "220610-10:09:17,150 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.150586: >> setoption smoothing 1\n",
      "220610-10:09:17,150 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.150586: >> setoption boundguess 1\n",
      "220610-10:09:17,150 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.150586: >> clear U\n",
      "220610-10:09:17,150 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.150586: >> # also try the qsform as a starting point at this resolution\n",
      "220610-10:09:17,150 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.150586: >> setrowqsform UF\n",
      "220610-10:09:17,150 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.150586: >> optimise 12 UF:1-2  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 1\n",
      "220610-10:09:17,170 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.170056: >> sort U\n",
      "220610-10:09:17,170 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.170056: >> copy U UB\n",
      "220610-10:09:17,170 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.170056: >> # 2mm scale\n",
      "220610-10:09:17,170 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.170442: >> setscale 2\n",
      "220610-10:09:17,171 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.170969: >> setoption smoothing 2\n",
      "220610-10:09:17,171 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.170969: >> clear U\n",
      "220610-10:09:17,171 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.170969: >> clear UC\n",
      "220610-10:09:17,171 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.170969: >> clear UD\n",
      "220610-10:09:17,171 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.170969: >> clear UE\n",
      "220610-10:09:17,171 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.170969: >> clear UF\n",
      "220610-10:09:17,171 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.170969: >> # remeasure costs at this scale\n",
      "220610-10:09:17,171 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.170969: >> measurecost 7 UB 0 0 0 0 0 0 rel\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "220610-10:09:17,260 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.260922: >> sort U\n",
      "220610-10:09:17,261 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.260922: >> copy U UC\n",
      "220610-10:09:17,261 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.260922: >> clear U\n",
      "220610-10:09:17,261 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.260922: >> optimise 7  UC:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4\n",
      "220610-10:09:17,262 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.262064: >> # in addition, try qsform as the final transformation, not just an initialisation\n",
      "220610-10:09:17,262 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.262064: >> clear UG\n",
      "220610-10:09:17,262 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.262064: >> setrowqsform UG\n",
      "220610-10:09:17,262 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.262064: >> measurecost 12 UG:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 1\n",
      "220610-10:09:17,262 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.262064: >> sort U\n",
      "220610-10:09:17,330 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.330684: >> copy U UD\n",
      "220610-10:09:17,330 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.330684: >> setoption boundguess 1\n",
      "220610-10:09:17,330 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.330927: >> if MAXDOF > 7\n",
      "220610-10:09:17,331 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.330927: >>  clear U\n",
      "220610-10:09:17,331 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.330927: >> if MAXDOF > 7\n",
      "220610-10:09:17,331 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.330927: >>  optimise 9  UD:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 1\n",
      "220610-10:09:17,331 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.330927: >> copy U UE\n",
      "220610-10:09:17,331 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.330927: >> if MAXDOF > 9\n",
      "220610-10:09:17,331 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.330927: >>  clear U\n",
      "220610-10:09:17,331 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.330927: >> if MAXDOF > 9\n",
      "220610-10:09:17,331 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.330927: >>  optimise 12 UE:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 2\n",
      "220610-10:09:17,331 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.330927: >> sort U\n",
      "220610-10:09:17,331 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.330927: >> copy U UF\n",
      "220610-10:09:17,331 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.330927: >> # 1mm scale\n",
      "220610-10:09:17,331 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.330927: >> setscale 1\n",
      "220610-10:09:17,333 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.333027: >> setoption smoothing 1\n",
      "220610-10:09:17,333 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.333027: >> setoption boundguess 1\n",
      "220610-10:09:17,333 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.333507: >> clear U\n",
      "220610-10:09:17,334 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.334469: >> # also try the qsform as a starting point at this resolution\n",
      "220610-10:09:17,335 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.335202: >> setrowqsform UF\n",
      "220610-10:09:17,337 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.337070: >> optimise 12 UF:1-2  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 1\n",
      "220610-10:09:17,452 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.452653: >> # in addition, try qsform as the final transformation, not just an initialisation\n",
      "220610-10:09:17,452 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.452653: >> clear UG\n",
      "220610-10:09:17,453 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.452653: >> setrowqsform UG\n",
      "220610-10:09:17,453 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.452653: >> measurecost 12 UG:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 1\n",
      "220610-10:09:17,464 nipype.interface INFO:\n",
      "\t stdout 2022-06-10T10:09:17.464686: >> sort U\n",
      "220610-10:09:17,823 nipype.workflow INFO:\n",
      "\t [Node] Finished \"flirt\", elapsed time 4.343435s.\n",
      "220610-10:09:17,919 nipype.workflow INFO:\n",
      "\t [Node] Finished \"flirt\", elapsed time 4.468275s.\n",
      "220610-10:09:18,718 nipype.workflow INFO:\n",
      "\t [Node] Setting-up \"thres\" in \"/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmp4_x59b1o/Nipype1Task_cd336c784480f43bc48f0292befddf035d1b0cce2dfc2b6810b87a5f51bb8ec0/thres\".\n",
      "220610-10:09:18,724 nipype.workflow INFO:\n",
      "\t [Node] Setting-up \"thres\" in \"/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmp4_x59b1o/Nipype1Task_575baa43f2d071facd1006dc8e0babe7e66087ace1210a648292ce614d110248/thres\".\n",
      "220610-10:09:18,734 nipype.workflow INFO:\n",
      "\t [Node] Executing \"thres\" <nipype.interfaces.fsl.maths.Threshold>\n",
      "220610-10:09:18,737 nipype.workflow INFO:\n",
      "\t [Node] Executing \"thres\" <nipype.interfaces.fsl.maths.Threshold>\n",
      "220610-10:09:18,738 nipype.workflow INFO:\n",
      "\t [Node] Setting-up \"thres\" in \"/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmp4_x59b1o/Nipype1Task_29d2700f17288f1125508491ff8a771f2f72078a1f55805b7b8c0859eb6793a7/thres\".\n",
      "220610-10:09:18,738 nipype.workflow INFO:\n",
      "\t [Node] Setting-up \"thres\" in \"/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmp4_x59b1o/Nipype1Task_1079c68fa2cd7880cfbbff1dc5e4838ce09ed2e55fbbc3b039d6fb02c481c40a/thres\".\n",
      "220610-10:09:18,756 nipype.workflow INFO:\n",
      "\t [Node] Setting-up \"thres\" in \"/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmp4_x59b1o/Nipype1Task_a8cc928ed1f91e0106bdb77a07a4cb17e433b30edcaabeffbec48318862a030d/thres\".\n",
      "220610-10:09:18,767 nipype.workflow INFO:\n",
      "\t [Node] Executing \"thres\" <nipype.interfaces.fsl.maths.Threshold>\n",
      "220610-10:09:18,760 nipype.workflow INFO:\n",
      "\t [Node] Executing \"thres\" <nipype.interfaces.fsl.maths.Threshold>\n",
      "220610-10:09:18,767 nipype.workflow INFO:\n",
      "\t [Node] Executing \"thres\" <nipype.interfaces.fsl.maths.Threshold>\n",
      "220610-10:09:18,795 nipype.workflow INFO:\n",
      "\t [Node] Setting-up \"thres\" in \"/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmp4_x59b1o/Nipype1Task_71fe40ed13b6d2141ec23dd375fd8d9cfddb67dba4d167862402d914e48bbd0d/thres\".\n",
      "220610-10:09:18,800 nipype.workflow INFO:\n",
      "\t [Node] Setting-up \"thres\" in \"/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmp4_x59b1o/Nipype1Task_a899f51d6ee6fd64d8d86318eadfdd01050dd6c6314a5148ba168280ed332dd8/thres\".\n",
      "220610-10:09:18,808 nipype.workflow INFO:\n",
      "\t [Node] Executing \"thres\" <nipype.interfaces.fsl.maths.Threshold>\n",
      "220610-10:09:18,820 nipype.workflow INFO:\n",
      "\t [Node] Executing \"thres\" <nipype.interfaces.fsl.maths.Threshold>\n",
      "220610-10:09:18,901 nipype.workflow INFO:\n",
      "\t [Node] Setting-up \"thres\" in \"/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmp4_x59b1o/Nipype1Task_69b0f4166bc6b0a7d60649b28f37718e2584ed39c5e5378bf3035baba787c7f9/thres\".\n",
      "220610-10:09:18,912 nipype.workflow INFO:\n",
      "\t [Node] Executing \"thres\" <nipype.interfaces.fsl.maths.Threshold>\n",
      "220610-10:09:19,50 nipype.workflow INFO:\n",
      "\t [Node] Finished \"thres\", elapsed time 0.310829s.\n",
      "220610-10:09:19,62 nipype.workflow INFO:\n",
      "\t [Node] Finished \"thres\", elapsed time 0.288046s.\n",
      "220610-10:09:19,76 nipype.workflow INFO:\n",
      "\t [Node] Finished \"thres\", elapsed time 0.302401s.\n",
      "220610-10:09:19,79 nipype.workflow INFO:\n",
      "\t [Node] Finished \"thres\", elapsed time 0.343428s.\n",
      "220610-10:09:19,158 nipype.workflow INFO:\n",
      "\t [Node] Finished \"thres\", elapsed time 0.343203s.\n",
      "220610-10:09:19,161 nipype.workflow INFO:\n",
      "\t [Node] Finished \"thres\", elapsed time 0.33753s.\n",
      "220610-10:09:19,166 nipype.workflow INFO:\n",
      "\t [Node] Finished \"thres\", elapsed time 0.393565s.\n",
      "220610-10:09:19,390 nipype.workflow INFO:\n",
      "\t [Node] Finished \"thres\", elapsed time 0.475674s.\n",
      "220610-10:09:19,596 nipype.workflow INFO:\n",
      "\t [Node] Setting-up \"thres\" in \"/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmp4_x59b1o/Nipype1Task_182071bb1c7be06eb7edb29c035c42d269d8945ff268f6f8378135c3d8af969c/thres\".\n",
      "220610-10:09:19,602 nipype.workflow INFO:\n",
      "\t [Node] Executing \"thres\" <nipype.interfaces.fsl.maths.Threshold>\n",
      "220610-10:09:19,638 nipype.workflow INFO:\n",
      "\t [Node] Setting-up \"thres\" in \"/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmp4_x59b1o/Nipype1Task_381ec34effc4c46a87bb271d89349fb31925d9fca54ee92f5208f8e3bfae1e0e/thres\".\n",
      "220610-10:09:19,644 nipype.workflow INFO:\n",
      "\t [Node] Executing \"thres\" <nipype.interfaces.fsl.maths.Threshold>\n",
      "220610-10:09:19,802 nipype.workflow INFO:\n",
      "\t [Node] Finished \"thres\", elapsed time 0.196685s.\n",
      "220610-10:09:19,840 nipype.workflow INFO:\n",
      "\t [Node] Finished \"thres\", elapsed time 0.193356s.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "220610-10:09:20,205 nipype.workflow INFO:\n",
      "\t [Node] Setting-up \"merge\" in \"/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmp4_x59b1o/Nipype1Task_8e613948eeae8d99bc21cf54a88615a8defd7ddf994d16208c6400a02ac05782/merge\".\n",
      "220610-10:09:20,210 nipype.workflow INFO:\n",
      "\t [Node] Executing \"merge\" <nipype.interfaces.fsl.utils.Merge>\n",
      "220610-10:09:21,158 nipype.workflow INFO:\n",
      "\t [Node] Finished \"merge\", elapsed time 0.946545s.\n",
      "b0_flirt_results:  ({'b0_flirt_workflow.split_moving': [PosixPath('/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmpbwh10bzq/Workflow_1199fb24ddf7b5a08e32c9f3a945607441f30aaf978d98aca3ffcddd92a291ec/vol0000.nii.gz'), PosixPath('/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmpbwh10bzq/Workflow_1199fb24ddf7b5a08e32c9f3a945607441f30aaf978d98aca3ffcddd92a291ec/vol0001.nii.gz'), PosixPath('/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmpbwh10bzq/Workflow_1199fb24ddf7b5a08e32c9f3a945607441f30aaf978d98aca3ffcddd92a291ec/vol0002.nii.gz'), PosixPath('/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmpbwh10bzq/Workflow_1199fb24ddf7b5a08e32c9f3a945607441f30aaf978d98aca3ffcddd92a291ec/vol0003.nii.gz'), PosixPath('/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmpbwh10bzq/Workflow_1199fb24ddf7b5a08e32c9f3a945607441f30aaf978d98aca3ffcddd92a291ec/vol0004.nii.gz'), PosixPath('/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmpbwh10bzq/Workflow_1199fb24ddf7b5a08e32c9f3a945607441f30aaf978d98aca3ffcddd92a291ec/vol0005.nii.gz'), PosixPath('/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmpbwh10bzq/Workflow_1199fb24ddf7b5a08e32c9f3a945607441f30aaf978d98aca3ffcddd92a291ec/vol0006.nii.gz'), PosixPath('/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmpbwh10bzq/Workflow_1199fb24ddf7b5a08e32c9f3a945607441f30aaf978d98aca3ffcddd92a291ec/vol0007.nii.gz'), PosixPath('/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmpbwh10bzq/Workflow_1199fb24ddf7b5a08e32c9f3a945607441f30aaf978d98aca3ffcddd92a291ec/vol0008.nii.gz'), PosixPath('/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmpbwh10bzq/Workflow_1199fb24ddf7b5a08e32c9f3a945607441f30aaf978d98aca3ffcddd92a291ec/vol0009.nii.gz')], 'b0_flirt_workflow.dilate': '/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmpwq_btkfi/Nipype1Task_f6d3ebbd2c958e5e5fe5ba667f9cf310ba108df4cd958220d8c9525c0236f0de/dilate/sub-PREVDEMALS0010025PG_ses-M00_dwi_b0_roi_brain_mask_maths.nii.gz', 'b0_flirt_workflow.fslroi_ref': '/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmpwq_btkfi/Nipype1Task_ab8e8253bfc4959e6cc84b52ab9a3657610a49ba734f9c653db27d3f7cf19379/fslroi_ref/sub-PREVDEMALS0010025PG_ses-M00_dwi_b0_roi.nii.gz'}, Result(output=Output(out_matrix_file=[PosixPath('/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmp4_x59b1o/Workflow_a2d7e1dd3d5dc5e6646584d0133d3828f66bb2cac14d3748e2a3e21432a30ae2/vol0000_flirt.mat'), PosixPath('/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmp4_x59b1o/Workflow_a2d7e1dd3d5dc5e6646584d0133d3828f66bb2cac14d3748e2a3e21432a30ae2/vol0001_flirt.mat'), PosixPath('/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmp4_x59b1o/Workflow_a2d7e1dd3d5dc5e6646584d0133d3828f66bb2cac14d3748e2a3e21432a30ae2/vol0002_flirt.mat'), PosixPath('/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmp4_x59b1o/Workflow_a2d7e1dd3d5dc5e6646584d0133d3828f66bb2cac14d3748e2a3e21432a30ae2/vol0003_flirt.mat'), PosixPath('/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmp4_x59b1o/Workflow_a2d7e1dd3d5dc5e6646584d0133d3828f66bb2cac14d3748e2a3e21432a30ae2/vol0004_flirt.mat'), PosixPath('/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmp4_x59b1o/Workflow_a2d7e1dd3d5dc5e6646584d0133d3828f66bb2cac14d3748e2a3e21432a30ae2/vol0005_flirt.mat'), PosixPath('/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmp4_x59b1o/Workflow_a2d7e1dd3d5dc5e6646584d0133d3828f66bb2cac14d3748e2a3e21432a30ae2/vol0006_flirt.mat'), PosixPath('/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmp4_x59b1o/Workflow_a2d7e1dd3d5dc5e6646584d0133d3828f66bb2cac14d3748e2a3e21432a30ae2/vol0007_flirt.mat'), PosixPath('/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmp4_x59b1o/Workflow_a2d7e1dd3d5dc5e6646584d0133d3828f66bb2cac14d3748e2a3e21432a30ae2/vol0008_flirt.mat'), PosixPath('/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmp4_x59b1o/Workflow_a2d7e1dd3d5dc5e6646584d0133d3828f66bb2cac14d3748e2a3e21432a30ae2/vol0009_flirt.mat')], out_file='/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmp4_x59b1o/FunctionTask_f23a42d113cd5dc23d69bfd396eedc38036c7d778acf9f211e0589f4b2331336/merged_files.nii.gz'), runtime=None, errored=False))\n",
      "out_reference_b0:  /private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmpboapvdzy/FunctionTask_68d893f8c7ad905b9ed96b86f35a746dc71306eb292b767b6554d7d92fb41ef8/merged_files_avg_b0.nii.gz\n",
      "220610-10:09:37,600 nipype.workflow INFO:\n",
      "\t [Node] Setting-up \"bet_2\" in \"/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmpboapvdzy/Nipype1Task_616a6cc4a271db404a7c5b509927dc40c8bdb3d3612f18c553117e275d22cda0/bet_2\".\n",
      "220610-10:09:37,607 nipype.workflow INFO:\n",
      "\t [Node] Executing \"bet_2\" <nipype.interfaces.fsl.preprocess.BET>\n",
      "220610-10:09:39,964 nipype.workflow INFO:\n",
      "\t [Node] Finished \"bet_2\", elapsed time 2.356275s.\n",
      "220610-10:09:42,618 nipype.workflow INFO:\n",
      "\t [Node] Setting-up \"eddy\" in \"/private/var/folders/pf/jc4hflzn2jd71fnht2_2kfm0000w83/T/tmpboapvdzy/Nipype1Task_5650ee0de51d38641122beef2820feb45c111429236fab611c550ecfc5789afb/eddy\".\n",
      "220610-10:09:42,623 nipype.workflow INFO:\n",
      "\t [Node] Executing \"eddy\" <nipype.interfaces.fsl.epi.Eddy>\n"
     ]
    }
   ],
   "source": [
    "## Workflow execution\n",
    "from pydra import Submitter\n",
    "\n",
    "with Submitter(plugin=\"cf\") as submitter:\n",
    "    submitter(workflow)\n",
    "\n",
    "results = workflow.result(return_inputs=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "284e839c",
   "metadata": {},
   "outputs": [],
   "source": [
    "results"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "d30eac8c",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "34e890c1",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "f098e002",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "6eb53809",
   "metadata": {},
   "outputs": [],
   "source": [
    "workflow.set_output([\n",
    "    (\"image_id\", workflow.init_input_node.lzout.image_id),\n",
    "        (\"t1w\",workflow.init_input_node.lzout.t1w),\n",
    "        (\"dwi\",workflow.init_input_node.lzout.dwi),\n",
    "        (\"bvec\",workflow.init_input_node.lzout.bvec),\n",
    "        (\"bval\",workflow.init_input_node.lzout.bval),\n",
    "        (\"total_readout_time\",workflow.init_input_node.lzout.total_readout_time),\n",
    "        (\"phase_encoding_direction\",workflow.init_input_node.lzout.phase_encoding_direction),\n",
    "])"
   ]
  }
 ],
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   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
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