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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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resampling from the 1mm isotropic .mgz file to T1 space issue #2654

Open lhocke0o opened 2 years ago

lhocke0o commented 2 years ago

What happened?

When the data are resampled from the 1mm isotropic .mgz file to T1 space, the interpolation causes voxels on the boundary regions to be replaced by values intermediate between the values of the two regions.

For example: PATHTOPROCESSEDANATFILES/sub-XXX_desc-aparcaseg_dseg.nii.gz or PATHTOPROCESSEDANATFILES/sub-XXX_desc-aseg_dseg.nii.gz I found that when I want to extract certain values corresponding to the cerebellum (values 7,8,46 and 47 from the original freesurfer output aparc+aseg.mgz) I find various voxels outside the cerebellum which have the values 7,8,46 and 47. The voxels seem to lie between prior voxels that would average to the new value (e.g. there are values of 2 and 12 in aparc+aseg.mgz around the voxel which is now 7 )

Screen Shot 2021-12-07 at 2 17 08 PM

. Screenshot attached. Blue is where the values 7,8 and 46,47 of the cerebellum all appear in my PATHTOPROCESSEDANATFILES/sub-XXX_desc-aparcaseg_dseg.nii.gz and PATHTOPROCESSEDANATFILES/sub-XXX_desc-aseg_dseg.nii.gz.

What command did you use?

NA

What version of fMRIPrep are you running?

Version is 20.2.1.

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.

N/A

Additional information / screenshots

N/A

effigies commented 2 years ago

Can you please update to the latest release in the series (20.2.6)? I believe this has been fixed.