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nipreps / fmriprep

fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
https://fmriprep.org
Apache License 2.0
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fails to process short-TR functional data data of only a couple slices #1168

Open nblauch opened 6 years ago

nblauch commented 6 years ago

Hi - I use FMRIPREP regularly and its great software. Thanks for your work on this.

I have some data acquired with an ultra-fast fMRI sequence involving the acquisition of only 2 (oblique) slices. I am having trouble processing this data with FMRIPREP. FMRIPREP fails during "enhance_and_skull_strip".

I can understand if this data will not be able to be robustly registered to the anatomical, but I would like to at least process it in order to extract a series of confounds for nuisance regression.

I tried also using the (deprecated) option --output-grid-reference with a path to the first functional bold file, but the problem was not solved by this, and processing fails at the same steps, failing to output any derivative files for this sequence. Makes sense since the current problem is not co-registration but a rather a skull-stripping procedure which can't be and probably doesn't need to be applied to these two slices.

I attached an example log/crash file for the first run. I have defaced the anatomical and can share data for testing upon request if that is necessary.

thanks in advance, Nick

crash-20180612-222949-root-n4_correct-92a03867-2db8-4fcd-abd0-3918771c0002.txt

oesteban commented 6 years ago

Thanks Nick.

Currently FMRIPREP has some trouble with partial FoV images, and this case is a particularly extreme one. Would you mind confirming whether this mask /work/fmriprep_wf/single_subject_02_wf/func_preproc_ses_02_task_func_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_mask/ref_image_mask.nii.gz is empty?

Thanks!

nblauch commented 6 years ago

Hi Oscar. The mask is indeed filled with zeros.

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