From 99b66bcd44b8cea541474def85394cff3180ab32 Mon Sep 17 00:00:00 2001
From: GalKepler <galkepler@gmail.com>
Date: Thu, 25 Jul 2024 17:09:13 +0300
Subject: [PATCH] updated usage

---
 docs/usage.rst       | 67 +++++++++++++++++++++++++++++++++++++++++++-
 src/keprep/config.py |  1 +
 2 files changed, 67 insertions(+), 1 deletion(-)

diff --git a/docs/usage.rst b/docs/usage.rst
index e984b15..53867c6 100644
--- a/docs/usage.rst
+++ b/docs/usage.rst
@@ -12,7 +12,72 @@ There are two main ways to customize the configuration of the pipeline:
 1. By modifying the `keprep.config` module directly.::
 
     from keprep import config
-    from keprep.workflows
+    config.execution.bids_dir = '/path/to/bids/dataset' # path to the BIDS dataset
+    config.execution.output_dir = '/path/to/output/directory' # path to the output directory
+    config.execution.participant_label = ['01', '02', '03'] # list of participant labels to process
+
+2. By passing a dictionary of options to the `from_dict` method.::
+
+    from keprep import config
+
+    inputs = {
+        "bids_dir": "/path/to/bids/dataset", # path to the BIDS dataset
+        "output_dir": "/path/to/output/directory", # path to the output directory
+        "participant_label": ["01", "02", "03"] # list of participant labels to process
+    }
+
+    config.from_dict(inputs)
+
+Configuration Options
+----------------------
+
+Execution Settings
+------------------
+* **bids_dir**: Path to the BIDS dataset.
+* **output_dir**: Path to the output directory.
+* **participant_label**: List of participant identifiers to be preprocessed.
+* **anat_derivatives**: Path where anatomical derivatives are found.
+* **bids_database_dir**: Directory containing SQLite database indices for the input BIDS dataset.
+* **reset_database**: Reset the SQLite database (default: True).
+* **fs_license_file**: Path to the FreeSurfer license file.
+* **fs_subjects_dir**: FreeSurfer's subjects directory.
+* **log_dir**: Path to the directory containing execution logs.
+* **log_level**: Output verbosity (default: 25).
+* **work_dir**: Path to the working directory where intermediate results will be available.
+
+Nipype Settings
+----------------
+* **nprocs**: Number of processes (compute tasks) that can be run in parallel (multiprocessing only).
+* **omp_nthreads**: Number of CPUs a single process can access for multithreaded execution.
+* **stop_on_first_crash**: Whether the workflow should stop or continue after the first error (default: True).
+
+Workflow Settings
+-----------------
+* **anat_only**: Execute the anatomical preprocessing only (default: False).
+* **dwi2t1w_dof**: Degrees of freedom of the DWI-to-T1w registration steps (default: 6).
+* **dwi2t1w_init**: Initialization method for DWI-to-T1w coregistration (default: register).
+* **cifti_output**: Generate HCP Grayordinates (accepts 91k or 170k).
+* **do_reconall**: Whether to perform FreeSurfer's recon-all (default: False).
+* **longitudinal**: Run FreeSurfer recon-all with the -logitudinal flag (default: False).
+* **skull_strip_fixed_seed**: Fix a seed for skull-stripping (default: False).
+* **skull_strip_template**: Change default brain extraction template (default: OASIS30ANTs).
+* **hires**: Run FreeSurfer recon-all with the -hires flag.
+* **skull_strip_t1w**: Skip brain extraction of the T1w image (default: force).
+* **response_algorithm**: Algorithm to estimate the response function (default: dhollander).
+* **fod_algorithm**: Algorithm to estimate the fiber orientation distribution (default: msmt_csd).
+* **n_raw_tracts**: Number of streamlines to generate in the tractography (default: 400000).
+* **n_tracts**: Number of streamlines to keep after filtering (default: 40000).
+* **tracking_algorithm**: Algorithm to perform tractography (default: SD_Stream).
+* **tracking_max_angle**: Maximum angle between steps in the tractography (default: 45).
+* **tracking_lenscale_min**: Minimum length scale for the tractography (default: 30).
+* **tracking_lenscale_max**: Maximum length scale for the tractography (default: 500).
+* **tracking_stepscale**: Step scale for the tractography (default: 0.2).
+* **tracking_minvol**: Minimum volume for the tractography (default: 259209).
+* **fs_scale_gm**: Heuristically downsize the fiber density estimates based on the presence of GM in the voxel (default: True).
+* **five_tissue_type_algorithm**: Algorithm to generate the five-tissue-type segmentation (default: hsvs).
+* **debug_sift**: Enable debugging mode for SIFT (default: False).
+
+
 
 
 .. _BIDS: https://bids.neuroimaging.io
diff --git a/src/keprep/config.py b/src/keprep/config.py
index 69dbefa..e80b4b3 100644
--- a/src/keprep/config.py
+++ b/src/keprep/config.py
@@ -602,6 +602,7 @@ def initialize(x):
     seeds.load(settings, init=initialize("seeds"), ignore=ignore)
 
     loggers.init()
+    init_spaces()
 
 
 def load(filename, skip=None, init=True):