Hi Bruce

   
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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
>
>

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