fmriprep_denoising
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How to use on a functional scan where "run" isn't specified
This code seems super helpful - appreciate your work in it! Trying to run it on a task of mine that doesnt have a run specified in the naming conventions (there is only one)
When I run the script, I get
Traceback (most recent call last):
File "denoise_fmriprep_output.py", line 235, in <module>
curfunc.split('run-')[1].split('_')[0] + '*' + '*space-MNI152NLin2009cAsym*brain*mask.nii*')[0]
IndexError: list index out of range
Presumably because there is no "run-" flags. When i tried to move through the script and edit/comment out any mentions of run, it still crashes, with an error I can't quite parse through.
Traceback (most recent call last):
File "denoise_fmriprep_output.py", line 312, in <module>
wmts = NiftiLabelsMasker(labels_img=tmpAROMAwm , detrend=False, standardize=False).fit_transform(tmpAROMA)
File "/Volumes/conda/sheyn/envs/fmriprep_denoising/lib/python3.6/site-packages/nilearn/input_data/nifti_labels_masker.py", line 226, in fit_transform
return self.fit().transform(imgs, confounds=confounds)
File "/Volumes/conda/sheyn/envs/fmriprep_denoising/lib/python3.6/site-packages/nilearn/input_data/nifti_labels_masker.py", line 176, in fit
self.labels_img_ = _utils.check_niimg_3d(self.labels_img)
File "/Volumes/conda/sheyn/envs/fmriprep_denoising/lib/python3.6/site-packages/nilearn/_utils/niimg_conversions.py", line 316, in check_niimg_3d
return check_niimg(niimg, ensure_ndim=3, dtype=dtype)
File "/Volumes/conda/sheyn/envs/fmriprep_denoising/lib/python3.6/site-packages/nilearn/_utils/niimg_conversions.py", line 251, in check_niimg
raise ValueError("File not found: '%s'" % niimg)
ValueError: File not found: './tmpdir/sub-1018_se/tmpAROMA_task-vext_wm.nii.gz'
Any easy thoughts/ideas? Or should I go through all my subjects and add the run flag into all the names/outputs
Thanks in advance!