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Thank you, Douglas. Then, fsroi as a work around is also right solution? I do not know what causes the issue: initial conversion of T1W from NIFTI to mgz, segmentation itself or transfer back to NIFTI. I do not know if other files (say brain mask) have the same issue. Looking into these.

Roman
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Tuesday, February 23, 2021 10:04 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] segmentation is shifted with respect to NIFTI T1W
 
Those commands look right

On 2/23/2021 9:27 AM, Roman Fleysher wrote:

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Dear FreeSurfers,

I am working with version 6, starting point is T1W image in NIFTI format. I typically transform segmentations back to native space in NIFTI format to be able to use other software (FSL and such). I noticed that segmentation is shifted by 1 pixel in one axis (y-axis). Mapping of segmentation is a two step process based on description in:

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Specific commands are (schematically) :

# realign to original MGZ

mri_label2vol --seg inputSegmentationInMGZ --temp mri/orig/001.mgz --o outputSegmentationInOrigMGZ --regheader inputSegmentationInMGZ


# convert to NIFTI (*.nii.gz)

mri_convert --in_type mgz --out_type nii outputSegmentationInOrigMGZ outputSegmentationInOrigNIFTI.nii.gz

Are these steps correct? I can shift NIFTI by one pixel using fslroi, but I want to be sure nothing else is happening and that this shift is the correct work around.

Thank you,

Roman



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