I am trying to use nilearn.interfaces.fmriprep.load_confounds but without luck. The .nii and the confounds.tsv coexist in the same directory but load_confounds() is not finding it.
files[0]:
‘**/dartfs-hpc/rc/lab/C/CANlab/labdata/data/WASABI/derivatives/fmriprep-try2/sub-SID000002/ses-01/func/**sub-SID000002_ses-01_task-movemap_acq-mb8_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz’
--------------------------------------------------------------------------- ValueError Traceback (most recent call last) Cell In[78], line 1 ----> 1 confounds_minimal_no_gsr, sample_mask = load_confounds( 2 files[0], 3 strategy=[“high_pass”, “motion”, “wm_csf”, “global_signal”], 4 motion=“basic”, 5 wm_csf=“basic”, 6 global_signal=“basic”, 7 ) 8 print(“The shape of the confounds matrix is:”, confounds_minimal_no_gsr.shape) 9 print(confounds_minimal_no_gsr.columns) File ~/miniconda3/envs/physio/biopac/lib/python3.9/site-packages/nilearn/interfaces/fmriprep/load_confounds.py:279, in load_confounds(img_files, strategy, motion, scrub, fd_threshold, std_dvars_threshold, wm_csf, global_signal, compcor, n_compcor, ica_aroma, demean) 277 sample_mask_out = 278 for file in img_files: → 279 sample_mask, conf = _load_confounds_for_single_image_file( 280 file, strategy, demean, 281 motion=motion, 282 scrub=scrub, 283 fd_threshold=fd_threshold, 284 std_dvars_threshold=std_dvars_threshold, 285 wm_csf=wm_csf, 286 global_signal=global_signal, 287 compcor=compcor, n_compcor=n_compcor,
…
126 ) 127 elif len(confounds_raw) != 1: 128 raise ValueError(“Found more than one confound file.”) ValueError: Could not find associated confound file. The functional derivatives should exist under the same parent directory.
You can see in my directory that both files are there as expected:
(/dartfs-hpc/rc/home/j/f003z4j/miniconda3/envs/physio/biopac) [f003z4j@polaris func]$ ls
sub-SID000002_ses-01_task-movemap_acq-mb8_run-1_AROMAnoiseICs.csv
sub-SID000002_ses-01_task-movemap_acq-mb8_run-1_desc-confounds_timeseries.json
sub-SID000002_ses-01_task-movemap_acq-mb8_run-1_desc-confounds_timeseries.tsv
sub-SID000002_ses-01_task-movemap_acq-mb8_run-1_desc-MELODIC_mixing.tsv
sub-SID000002_ses-01_task-movemap_acq-mb8_run-1_from-scanner_to-T1w_mode-image_xfm.txt
sub-SID000002_ses-01_task-movemap_acq-mb8_run-1_from-T1w_to-scanner_mode-image_xfm.txt
sub-SID000002_ses-01_task-movemap_acq-mb8_run-1_space-MNI152NLin2009cAsym_boldref.nii
sub-SID000002_ses-01_task-movemap_acq-mb8_run-1_space-MNI152NLin2009cAsym_boldref.nii.gz
sub-SID000002_ses-01_task-movemap_acq-mb8_run-1_space-MNI152NLin2009cAsym_desc-brain_mask.json
sub-SID000002_ses-01_task-movemap_acq-mb8_run-1_space-MNI152NLin2009cAsym_desc-brain_mask.nii
sub-SID000002_ses-01_task-movemap_acq-mb8_run-1_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
sub-SID000002_ses-01_task-movemap_acq-mb8_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold.json
sub-SID000002_ses-01_task-movemap_acq-mb8_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold.nii
sub-SID000002_ses-01_task-movemap_acq-mb8_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz