update part-ma tag

courtois-neuromod · Jan 17, 2025 · 6bb10bd · 6bb10bd
1 parent 17bf80d
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diff --git a/code/glmsingle/GLMsingle_cleanmask.py b/code/glmsingle/GLMsingle_cleanmask.py
@@ -35,7 +35,7 @@
     out_path = f"{args.things_dir}/glmsingle"
 
     sub_list = ['01', '02', '03', '06']
-    suffix = '_space-T1w_desc-preproc_part-mag_bold.nii.gz'
+    suffix = '_part-mag_space-T1w_desc-preproc_bold.nii.gz'
 
     for sub_num in sub_list:
         mask_path = f'{out_path}/sub-{sub_num}/glmsingle/input'

diff --git a/code/glmsingle/GLMsingle_preprocBOLD.py b/code/glmsingle/GLMsingle_preprocBOLD.py
@@ -49,11 +49,11 @@ def compile_maskedBOLD_hdf5(data_path, out_path, sub_num, mni=False):
     Generate a mask from the union of brain voxels across sessions and runs
     '''
     if mni:
-        mask_suffix = '_space-MNI152NLin2009cAsym_desc-brain_part-mag_mask.nii.gz'
-        mspace = 'T1w'
-    else:
-        mask_suffix = '_space-T1w_desc-brain_part-mag_mask.nii.gz'
+        mask_suffix = '_part-mag_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz'
         mspace = 'MNI'
+    else:
+        mask_suffix = '_part-mag_space-T1w_desc-brain_mask.nii.gz'
+        mspace = 'T1w'
 
     mask_list = sorted(
         glob.glob(f'{data_path}/sub-{sub_num}/ses-*/func/*{mask_suffix}')
@@ -73,9 +73,9 @@ def compile_maskedBOLD_hdf5(data_path, out_path, sub_num, mni=False):
     Time is in TR (1.49s)
     '''
     if mni:
-        suffix = '_space-MNI152NLin2009cAsym_desc-preproc_part-mag_bold.nii.gz'
+        suffix = '_part-mag_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz'
     else:
-        suffix = '_space-T1w_desc-preproc_part-mag_bold.nii.gz'
+        suffix = '_part-mag_space-T1w_desc-preproc_bold.nii.gz'
 
     bold_files = sorted(
         glob.glob(f'{data_path}/sub-{sub_num}/ses-*/func/*{suffix}')

diff --git a/code/glmsingle/README.md b/code/glmsingle/README.md
@@ -55,7 +55,7 @@ python GLMsingle_preprocBOLD.py --data_dir="${DATADIR}" --out_dir="${OUTDIR}" --
 
 **Input**:
 - All of a subject's ``*_bold.nii.gz`` files, for all sessions (~36) and runs (6 per session)
-(e.g., ``sub-03_ses-10_task-things_run-1_space-T1w_desc-preproc_part-mag_bold.nii.gz``).
+(e.g., ``sub-03_ses-10_task-things_run-1_part-mag_space-T1w_desc-preproc_bold.nii.gz``).
 Note that the script can process scans in MNI or T1w space (default is T1w; use default).
 
 **Output**:
@@ -145,7 +145,7 @@ python GLMsingle_cleanmask.py --things_dir="${DATADIR}"
 
 **Input**:
 - All 4 subject's ``*bold.nii.gz`` files, for all sessions (~36) and runs (6 per session) \
-(e.g., ``sub-03_ses-10_task-things_run-1_space-T1w_desc-preproc_part-mag_bold.nii.gz``)
+(e.g., ``sub-03_ses-10_task-things_run-1_part-mag_space-T1w_desc-preproc_bold.nii.gz``)
 - ``sub-{sub_num}_task-things_space-T1w_label-brain_desc-union_mask.nii``, the
 functional mask generated from the union of the functional masks of every run in Step 2.
 

diff --git a/code/qc/README.md b/code/qc/README.md
@@ -16,7 +16,7 @@ python compile_headmotion.py --data_dir="${DATADIR}" --out_dir="${OUTDIR}" --sub
 
 *Input*:
 
-- A subject's ``desc-confounds`` files outputed by fmriprep for each run. E.g., ``sub-06_ses-30_task-things_run-5_desc-confounds_part-mag_timeseries.tsv``
+- A subject's ``desc-confounds`` files outputed by fmriprep for each run. E.g., ``sub-06_ses-30_task-things_run-5_part-mag_desc-confounds_timeseries.tsv``
 
 *Output*:
 

diff --git a/code/qc/compile_headmotion.py b/code/qc/compile_headmotion.py
@@ -18,7 +18,7 @@ def get_arguments():
         required=True,
         type=str,
         help='absolute path to root dataset directory that contains '
-        'desc-confounds_part-mag_timeseries.tsv files',
+        '_part-mag_desc-confounds_timeseries.tsv files',
     )
     parser.add_argument(
         '--out_dir',
@@ -45,7 +45,7 @@ def extract_motion(
     extract head motion metrics and concatenate in dataframe.
     Export as .tsv
     '''
-    suffix = '_desc-confounds_part-mag_timeseries.tsv'
+    suffix = '_part-mag_desc-confounds_timeseries.tsv'
     confound_files = sorted(glob.glob(
         f"{data_path}/sub-{sub_num}/ses-*/func/*{suffix}"))