Hi Atira

what was your mri_convert command line? Make sure to specify no scaling of the intensity volume. Can you try adding:

-ns 1

to the mri_convert command line, and if that doesn't work send us the full command line and full screen output from it? This is always a good thing to do as it gives us enough information to help

cheers Bruce

On Sun, 26 Apr 2020, atira gan-zvi bick wrote:

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Hi I'm new to freesurfer.

I used freesurfer to preform Thalamus segmentation, and can see the segmented volume in freeview. I would like to export the segmented volume to nii to continue analysis in MRvista. I was able to do this using mri_convert - however the values in the nifti are not those on the label list (as seen in  freeview). The number of different values is similar but not the same, and the values themselves  are totally different (8103-8233 in freeview, 16384 - 32767). It is possible to compare regions based on visual inspection - however that is tedious and might lead to mistakes. How can I export the labels of each region in the segmented mgz?

Any suggestions? I'd appreciate to learn fro your experience

Thanks Atira

-- ד"ר עתירה גן-צבי ביק יחידת ההדמיה התפקודית הדסה עין-כרם האוניברסיטה העברית

Atira Bick (Phd) fMRI unit Hadassah medical center, Hebrew University Jerusalem