Add script.

nipreps · Sep 3, 2024 · 73a735f · 73a735f
1 parent 9ff6be3
commit 73a735f
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diff --git a/Dockerfile b/Dockerfile
@@ -40,7 +40,7 @@ RUN python -m build /src
 #
 
 # Utilities for downloading packages
-FROM ${BASE_IMAGE} as downloader
+FROM ${BASE_IMAGE} AS downloader
 # Bump the date to current to refresh curl/certificates/etc
 RUN echo "2023.07.20"
 RUN apt-get update && \
@@ -53,7 +53,7 @@ RUN apt-get update && \
     apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 # AFNI
-FROM downloader as afni
+FROM downloader AS afni
 # Bump the date to current to update AFNI
 RUN echo "2023.07.20"
 RUN mkdir -p /opt/afni-latest \
@@ -70,7 +70,7 @@ RUN mkdir -p /opt/afni-latest \
     && find /opt/afni-latest -type f -not -name "3dTshift" -delete
 
 # Connectome Workbench 1.5.0
-FROM downloader as workbench
+FROM downloader AS workbench
 RUN mkdir /opt/workbench && \
     curl -sSLO https://www.humanconnectome.org/storage/app/media/workbench/workbench-linux64-v1.5.0.zip && \
     unzip workbench-linux64-v1.5.0.zip -d /opt && \
@@ -79,7 +79,7 @@ RUN mkdir /opt/workbench && \
     strip --remove-section=.note.ABI-tag /opt/workbench/libs_linux64/libQt5Core.so.5
 
 # Micromamba
-FROM downloader as micromamba
+FROM downloader AS micromamba
 
 # Install a C compiler to build extensions when needed.
 # traits<6.4 wheels are not available for Python 3.11+, but build easily.
@@ -108,7 +108,7 @@ RUN npm install -g svgo@^3.2.0 bids-validator@^1.14.0 && \
 #
 # Main stage
 #
-FROM ${BASE_IMAGE} as fmripost_rapidtide
+FROM ${BASE_IMAGE} AS fmripost_rapidtide
 
 # Configure apt
 ENV DEBIAN_FRONTEND="noninteractive" \

diff --git a/scripts/fetch_templates.py b/scripts/fetch_templates.py
@@ -0,0 +1,140 @@
+#!/usr/bin/env python
+"""
+Standalone script to facilitate caching of required TemplateFlow templates.
+
+To download and view how to use this script, run the following commands inside a terminal:
+1. wget https://raw.githubusercontent.com/nipreps/fmriprep-aroma/main/scripts/fetch_templates.py
+2. python fetch_templates.py -h
+"""
+
+import argparse
+import os
+
+
+def fetch_MNI2009():
+    """
+    Expected templates:
+
+    tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz
+    tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_T1w.nii.gz
+    tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_desc-brain_mask.nii.gz
+    tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz
+    tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_desc-carpet_dseg.nii.gz
+    tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz
+    tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_label-brain_probseg.nii.gz
+    """
+    template = 'MNI152NLin2009cAsym'
+
+    # tf.get(template, resolution=(1, 2), desc=None, suffix='T1w')
+    # tf.get(template, resolution=(1, 2), desc='brain', suffix='mask')
+    tf.get(template, resolution=1, atlas=None, desc='carpet', suffix='dseg')
+    # tf.get(template, resolution=2, desc='fMRIPrep', suffix='boldref')
+    # tf.get(template, resolution=1, label='brain', suffix='probseg')
+
+
+def fetch_MNI6():
+    """
+    Expected templates:
+
+    tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-01_T1w.nii.gz
+    tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-02_T1w.nii.gz
+    tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-01_desc-brain_mask.nii.gz
+    tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-02_desc-brain_mask.nii.gz
+    tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-02_atlas-HCP_dseg.nii.gz
+    """
+    template = 'MNI152NLin6Asym'
+
+    tf.get(template, resolution=(1, 2), desc=None, suffix='T1w')
+    tf.get(template, resolution=(1, 2), desc='brain', suffix='mask')
+    # CIFTI
+    tf.get(template, resolution=2, atlas='HCP', suffix='dseg')
+    # Transform from MNI152NLin2009cAsym to MNI152NLin6Asym
+    tf.get(
+        template, mode='image', suffix='xfm', extension='.h5', **{'from': 'MNI152NLin2009cAsym'}
+    )
+
+
+def fetch_OASIS():
+    """
+    Expected templates:
+
+    tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz
+    tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_label-WM_probseg.nii.gz
+    tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_label-BS_probseg.nii.gz
+    tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_label-brain_probseg.nii.gz
+    tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-brain_mask.nii.gz
+    tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz
+    """
+    template = 'OASIS30ANTs'
+
+    tf.get(template, resolution=1, desc=None, label=None, suffix='T1w')
+    tf.get(template, resolution=1, label='WM', suffix='probseg')
+    tf.get(template, resolution=1, label='BS', suffix='probseg')
+    tf.get(template, resolution=1, label='brain', suffix='probseg')
+    tf.get(template, resolution=1, label='brain', suffix='mask')
+    tf.get(template, resolution=1, desc='BrainCerebellumExtraction', suffix='mask')
+
+
+def fetch_fsaverage():
+    """
+    Expected templates:
+
+    tpl-fsaverage/tpl-fsaverage_hemi-L_den-164k_desc-std_sphere.surf.gii
+    tpl-fsaverage/tpl-fsaverage_hemi-R_den-164k_desc-std_sphere.surf.gii
+    tpl-fsaverage/tpl-fsaverage_hemi-L_den-164k_desc-vaavg_midthickness.shape.gii
+    tpl-fsaverage/tpl-fsaverage_hemi-R_den-164k_desc-vaavg_midthickness.shape.gii
+    tpl-fsaverage/tpl-fsaverage_hemi-L_den-164k_midthickness.surf.gii
+    tpl-fsaverage/tpl-fsaverage_hemi-R_den-164k_midthickness.surf.gii
+    tpl-fsaverage/tpl-fsaverage_hemi-L_den-164k_sulc.shape.gii
+    tpl-fsaverage/tpl-sfaverage_hemi-R_den-164k_sulc.shape.gii
+    """
+    template = 'fsaverage'
+
+    tf.get(template, density='164k', desc='std', suffix='sphere')
+    tf.get(template, density='164k', suffix='midthickness')
+    tf.get(template, density='164k', suffix='sulc')
+
+
+def fetch_fsLR():
+    """
+    Expected templates:
+
+    tpl-fsLR/tpl-fsLR_hemi-L_den-32k_desc-nomedialwall_dparc.label.gii
+    tpl-fsLR/tpl-fsLR_hemi-L_den-32k_desc-vaavg_midthickness.shape.gii
+    tpl-fsLR/tpl-fsLR_hemi-L_den-32k_sphere.surf.gii
+    tpl-fsLR/tpl-fsLR_hemi-R_den-32k_desc-nomedialwall_dparc.label.gii
+    tpl-fsLR/tpl-fsLR_hemi-R_den-32k_desc-vaavg_midthickness.shape.gii
+    tpl-fsLR/tpl-fsLR_hemi-R_den-32k_sphere.surf.gii
+    tpl-fsLR/tpl-fsLR_space-fsaverage_hemi-L_den-32k_sphere.surf.gii
+    tpl-fsLR/tpl-fsLR_space-fsaverage_hemi-R_den-32k_sphere.surf.gii
+    """
+    tf.get('fsLR', density='32k')
+
+
+def fetch_all():
+    fetch_MNI2009()
+    fetch_MNI6()
+    # fetch_OASIS()
+    # fetch_fsaverage()
+    # fetch_fsLR()
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(
+        description='Helper script for pre-caching required templates to run fMRIPost-AROMA',
+    )
+    parser.add_argument(
+        '--tf-dir',
+        type=os.path.abspath,
+        help='Directory to save templates in. If not provided, templates will be saved to'
+        ' `${HOME}/.cache/templateflow`.',
+    )
+    opts = parser.parse_args()
+
+    # set envvar (if necessary) prior to templateflow import
+    if opts.tf_dir is not None:
+        os.environ['TEMPLATEFLOW_HOME'] = opts.tf_dir
+
+    import templateflow.api as tf
+
+    fetch_all()