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Hi Bruce
It worked! how simple... Thank you so much.
Atira
Message: 2 Date: Sun, 26 Apr 2020 12:04:36 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] exporting segmented mgz file To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.2004261203210.6647@gate.nmr.mgh.harvard.edu Content-Type: text/plain; charset="utf-8"
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:
????????External Email - Use Caution????????
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
-- ?"? ????? ??-??? ??? ????? ?????? ???????? ???? ???-??? ??????????? ??????
Atira Bick (Phd) fMRI unit Hadassah medical center, Hebrew University Jerusalem