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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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