Using fslroi to remove volumes

fmriprep
fmri
neuroimaging
fsl
#1

Hi all! I am trying to use the fslroi command to remove the first 22 volumes from a scan. This is the command I am entering (the data has already been preprocessed through fmriprep):

fslroi sub-63_task-rest_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz sub-63_task-rest_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold2.nii.gz 22 218

And this is the error I am receiving:

Cannot open volume sub-63_task-rest_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold for reading!

It is not a permissions error, or at least, it shouldn’t be as all rwx permissions are present! Just wondering if anyone had any insight! Thanks so much.

#2

I’m not really sure. Have you checked the file with something like mricron to be sure that it has contents? Or some CLI tools that might help:

du -sh sub-63_task-rest_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz
nib-ls sub-63_task-rest_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz