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@@ -17,6 +17,7 @@
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# ======================================================================
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# import basic libraries:
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import os
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+import glob
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import sys
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import warnings
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from os.path import join as opj
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@@ -42,7 +43,7 @@ from bids.layout import BIDSLayout
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# import custom functions:
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from highspeed_glm_functions import (
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get_subject_info, plot_stat_maps, leave_one_out)
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-import datalada.api as dl
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+import datalad.api as dl
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# ======================================================================
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# ENVIRONMENT SETTINGS (DEALING WITH ERRORS AND WARNINGS):
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# ======================================================================
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@@ -65,7 +66,7 @@ path_root = None
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sub_list = None
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# path to the project root:
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project_name = 'highspeed-glm'
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-path_root = os.getcwd().split(project_name)[0] + project_name
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+path_root = os.getenv('PWD').split(project_name)[0] + project_name
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if 'darwin' in sys.platform:
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path_spm = '/Users/Shared/spm12'
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path_matlab = '/Applications/MATLAB_R2017a.app/bin/matlab -nodesktop -nosplash'
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@@ -175,20 +176,20 @@ infosource.iterables = [('subject_id', sub_list)]
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# ======================================================================
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# DEFINE SELECTFILES NODE
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# ======================================================================
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-path_confounds = opj(
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- path_root, 'fmriprep', '*', '*',
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- 'func', '*highspeed*confounds_regressors.tsv')
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-path_events = opj(
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- path_root, 'bids', '*', '*', 'func', '*events.tsv')
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-path_func = opj(
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- path_root, 'fmriprep', '*',
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- 'anat', '*highspeed*space-T1w*preproc_bold.nii.gz')
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-path_anat = opj(
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- path_root, 'fmriprep', '*', '*',
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- 'func', '*_desc-preproc_T1w.nii.gz')
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-path_wholemask = opj(
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- path_root, 'fmriprep', '*', '*',
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- 'func', '*highspeed*space-T1w*brain_mask.nii.gz')
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+path_confounds = glob.glob(opj(
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+ path_root, 'fmriprep', 'fmriprep', '*', '*',
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+ 'func', '*highspeed*confounds_regressors.tsv'))
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+path_events = glob.glob(opj(
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+ path_root, 'bids', '*', '*', 'func', '*events.tsv'))
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+path_func = glob.glob(opj(
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+ path_root, 'fmriprep', 'fmriprep', '*', '*',
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+ 'func', '*highspeed*space-T1w*preproc_bold.nii.gz'))
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+path_anat = glob.glob(opj(
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+ path_root, 'fmriprep', 'fmriprep', '*',
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+ 'anat', '*_desc-preproc_T1w.nii.gz'))
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+path_wholemask = glob.glob(opj(
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+ path_root, 'fmriprep', 'fmriprep', '*', '*',
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+ 'func', '*highspeed*space-T1w*brain_mask.nii.gz'))
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dl.get(path_confounds)
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dl.get(path_events)
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dl.get(path_func)
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@@ -196,15 +197,15 @@ dl.get(path_anat)
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dl.get(path_wholemask)
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# define all relevant files paths:
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templates = dict(
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- confounds=opj(path_root, 'derivatives', 'fmriprep', '{subject_id}',
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+ confounds=opj(path_root, 'fmriprep', 'fmriprep', '{subject_id}',
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'*', 'func', '*highspeed*confounds_regressors.tsv'),
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events=opj(path_root, 'bids', '{subject_id}', '*', 'func',
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'*events.tsv'),
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- func=opj(path_root, 'derivatives', 'fmriprep', '{subject_id}', '*',
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+ func=opj(path_root, 'fmriprep', 'fmriprep', '{subject_id}', '*',
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'func', '*highspeed*space-T1w*preproc_bold.nii.gz'),
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- anat=opj(path_root, 'derivatives', 'fmriprep', '{subject_id}',
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+ anat=opj(path_root, 'fmriprep', 'fmriprep', '{subject_id}',
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'anat', '{subject_id}_desc-preproc_T1w.nii.gz'),
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- wholemask=opj(path_root, 'derivatives', 'fmriprep', '{subject_id}',
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+ wholemask=opj(path_root, 'fmriprep', 'fmriprep', '{subject_id}',
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'*', 'func', '*highspeed*space-T1w*brain_mask.nii.gz'),
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)
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# define the selectfiles node:
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