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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
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CIFTI Pipeline .surf.gii larger than .dtseries.nii #3190

Open amirhusseinab opened 8 months ago

amirhusseinab commented 8 months ago

What happened?

Hi,

After running the CIFTI pipeline with --project-goodvoxels, I tried to load the sub-###_ses-###_task-rest_space-fsLR_den-91k_bold.dtseries.nii on Left and right midthickness surface files inside Workbench View. I got this error:

The CIFTI file contains 32492 nodes for structure CortexLeft but the corresponding surface brain structure contains 232669 nodes.

It seems the surfaces are not in 91k resolution.

Also, an additional question: Does that "den" indicate denoised? So, there is no need for further denoising (e.g., with XCP-D)?

What command did you use?

fmriprep-v23.2.0a3.simg /input/ /output/ --skip_bids_validation \
--fs-license-file toolboxes/license.txt \
participant --participant-label 3749 \
--output-spaces T1w fsLR MNI152NLin6Asym:res-2 MNI152NLin2009cAsym \
--stop-on-first-crash --nthreads 20 --cifti-output 91k --project-goodvoxels

What version of fMRIPrep are you running?

23.2.0a3

How are you running fMRIPrep?

Singularity

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

No

Please copy and paste any relevant log output.

No response

Additional information / screenshots

No response

effigies commented 7 months ago

The .surf.gii files here are the subject native surfaces. You will need to use fsLR surfaces with .dtseries.nii.

amirhusseinab commented 7 months ago

Thanks for the reply. The only .surf.gii files with fsLR in the analyzed /anat folder are sub-##_ses-001_hemi-L/R_space-fsLR_desc-reg_sphere.surf.gii, sub-##_ses-001_hemi-L/R_space-fsLR_desc-msmsulc_sphere.surf.gii

There are no midthickness/pial/white surf.gii files in "fsLR". Even though loading fsLR.dtseries.nii on the above-mentioned sphere surfaces also results in the same previous error. Of note, fmriprep's log file has no errors.

jAchtzehn commented 2 months ago

I am having the same issue, could you find a fix @amirhusseinab?

amirhusseinab commented 2 months ago

I dropped it that time as it was not a priority, but will be glad to hear any solutions. I have not also tried with the latest versions of fmriprep (24.0.0) and xcp-d.