glad to hear that there are simple answers to some questions!

take care Bruce On Sun, 3 May 2020, atira gan-zvi bick wrote:

External Email - Use Caution

  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
  >
  >

  ------------------------------

-- 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