Fmriprep wf.anat_preproc_wf.anat_template_wf.t1_template_dimensions error

fmriprep

#1

I’m getting an error for the T1w images I am using in preprocessing. I’ve loaded the T1w image in FSLView and SPM, and have also checked that it isn’t a zipped file… and nothing seems to be wrong with the T1 image (file opens/image looks fine).

But I get the following error:

[Node] Error on “fmriprep_wf.single_subject_0001_wf.anat_preproc_wf.anat_template_wf.t1_template_dimensions”

nibabel.filebased.images.ImageFileError: Cannot work out file type of “/data/sub-0001/anat/sub-0001_T1w.nii”

Has anyone experienced this before?


#2

My best guess is that sub-0001_T1w.nii is actually a .nii.gz file. Did you run the BIDS Validator on this dataset? It should pick up such things.


#3

I ran BIDS validator prior to running fmriprep and the dataset passed. It is not a .nii.gz file.


#4

Ah yes, sorry - you actually mentioned this in the original post.

Can you open the file using nibabel? If not might be worth opening an issue at https://github.com/nipy/nibabel/issues providing the problematic nifti file.


#5

I can open the file successfully using nibabel


#6

And your input data resides on /net/pizza/BPReward_BIDS/? Is that a remote drive? Could you try copying a subset of the input data to local drive and using that? Maybe the issue is due to some interaction between docker and a remote file system.