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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http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
<http://secure-web.cisco.com/1OQ80xn8YGeWjUO2KyO4RDGDpL87LZ0EBpX6Z7_yDHTAQnUvI_i-ZbX3oYGnWNGBEv3FGrWEfu7Q0-EGZNpUg5oWefQhW2PyflL-E_EDawtfFyF3JoxX9ejxMQcJ_IO4g-glHmBjogdC6b5ZDBj12aMiOPktjP3Q4et2CD9zxjZvyHw4RmulypFF1W7xr921ryGHf1Xcg23EWcl4SQf5PZRnflYvp9NMjHufQ237e-27rWqRrlssP2RVE8NKaUYSS1jXZXdgg9PzheIilaEj7MQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsAnat-to-NativeAnat>
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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