[Freesurfer] segmentation is shifted with respect to NIFTI T1W

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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:

http://secure-web.cisco.com/1OQ80xn8YGeWjUO2KyO4RDGDpL87LZ0EBpX6Z7_yDHTAQnUv...

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