Update license and output docs.

LICENSE.md

@@ -29,36 +29,6 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 ## External code
 
-### aslprep.niworkflows (copied from version 1.3.0)
-
-Copyright (c) 2016, the CRN developers team.
-All rights reserved.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
-* Redistributions of source code must retain the above copyright notice, this
-  list of conditions and the following disclaimer.
-
-* Redistributions in binary form must reproduce the above copyright notice,
-  this list of conditions and the following disclaimer in the documentation
-  and/or other materials provided with the distribution.
-
-* Neither the name of niworkflows nor the names of its
-  contributors may be used to endorse or promote products derived from
-  this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
 ### aslprep.utils.misc.estimate_att_pcasl
 
 MIT License

aslprep/data/NOTICE

@@ -1,5 +1,8 @@
-fMRIPrep
-Copyright 2023 The NiPreps Developers.
+ASLPrep
+Copyright 2023 The PennLINC Team and the NiPreps Developers.
+
+This product is primarily developed by the PennLINC team,
+but it is also a part of the NiPreps community.
 
 This product includes software developed by
 the NiPreps Community (https://nipreps.org/).

docs/outputs.rst

@@ -42,7 +42,7 @@ The `BIDS Derivatives RC1`_ specification describes the naming and metadata conv
 that we follow.
 
 
-Anatomical derivatives
+Anatomical Derivatives
 ======================
 
 Anatomical derivatives are placed in each subject's ``anat`` subfolder.
@@ -65,11 +65,11 @@ Additionally, the following transforms are saved::
 
    sub-<label>/[ses-<label>/]
       anat/
-         sub-<label>_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
-         sub-<label>_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
+         sub-<label>_from-<space>_to-T1w_mode-image_xfm.h5
+         sub-<label>_from-T1w_to-<space>_mode-image_xfm.h5
 
 
-ASL and CBF derivatives
+ASL and CBF Derivatives
 =======================
 
 ASL derivatives are stored in the ``perf/`` subfolder.
@@ -78,11 +78,22 @@ these will be indicated with ``[specifiers]``::
 
    sub-<label>/[ses-<label>/]
       perf/
-         <source_entities>[_space-<label>]_aslref.nii.gz  # asl reference image
+         <source_entities>_desc-hmc_aslref.nii.gz  # asl reference image for HMC
+         <source_entities>_desc-coreg_aslref.nii.gz  # asl reference image for coregistration
+         <source_entities>[_space-<label>]_aslref.nii.gz  # asl reference image for normalization
          <source_entities>[_space-<label>]_desc-brain_mask.nii.gz  # asl brain mask
          <source_entities>[_space-<label>]_desc-preproc_asl.nii.gz  # preprocessed asl timeseries
+
+Additionally, the following transforms are saved::
+
+         <source_entities>_from-orig_to-aslref_mode-image_xfm.txt  # HMC transforms from raw ASL to aslref
+         <source_entities>_from-aslref_to-T1w_mode-image_xfm.txt
+
+CBF Outputs::
+
          <source_entities>[_space-<label>]_cbf.nii.gz  # mean CBF
          <source_entities>[_space-<label>]_desc-timeseries_cbf.nii.gz  # computed CBF timeseries
+         <source_entities>[_space-<label>]_att.nii.gz  # arterial transit time (multi-PLD data only)
 
 SCORE and SCRUB Outputs::
 
@@ -135,7 +146,7 @@ with one column for each confound variable.
 
 
 *******************
-CBF quality control
+CBF Quality Control
 *******************
 
 *ASLPrep* produces a quality control (QC) file for each ASL run::
@@ -162,12 +173,12 @@ Parcellated CBF Results
 
 The atlases currently used in *ASLPrep* can be separated into three groups: subcortical, cortical,
 and combined cortical/subcortical.
-The two subcortical atlases are the Tian atlas (desc-Tian; :footcite:t:`tian2020topographic`) and
-the CIFTI subcortical parcellation (desc-HCP).
+The two subcortical atlases are the Tian atlas (``desc-Tian``; :footcite:t:`tian2020topographic`) and
+the CIFTI subcortical parcellation (``desc-HCP``).
 The cortical atlases are the Glasser :footcite:p:`Glasser_2016` and the
 Gordon :footcite:p:`Gordon_2014`.
 The combined cortical/subcortical atlases are 10 different resolutions of the
-4S (Schaefer Supplemented with Subcortical Structures) atlas.
+4S (Schaefer Supplemented with Subcortical Structures) atlas (``desc-4S<*>56Parcels``).
 
 The 4S atlas combines the Schaefer 2018 cortical atlas (version v0143) :footcite:p:`Schaefer_2017`
 at 10 different resolutions (100, 200, 300, 400, 500, 600, 700, 800, 900, and 1000 parcels) with
@@ -189,7 +200,7 @@ as outputting the reference image-space versions would produce too many extra ou
    aslprep/
       atlas-<label>_dseg.json
       atlas-<label>_dseg.tsv
-      space-MNI152NLin6Asym_atlas-<label>_dseg.nii.gz
+      space-<label>_atlas-<label>_dseg.nii.gz
 
       sub-<label>/[ses-<label>/]
          perf/