Hi Fariha

The number of regions is based on the anatomy. You can combine them if you like. The volume to use is probably the aparc+aseg.mgz, which is easily convertible to .nii with mri_convert.

Also, you should use freeview not tkmedit (tkmedit has been deprecated for many years)

cheers Bruce On Fri, 14 Dec 2018, Fariha Muazzam wrote:

External Email - Use Caution

Hi Bruce I am working on segmentation of brain regions. I wanted to know:

1. If it is possible that I could get brain segmented into 8 regions or maybe 20, because when I

segmented using recon-all command, I got segmentation of 45 regions ? 2. I was looking at the capability of generating my own atlas using tkmedit, but I was stuck at that as well. 3. Plus I don't understand which is the label image. I use the command tkmedit subject_name image -aseg command to view the segmentations. The aseg.mgz alone volume does not show all the segmented regions. If I want a single volume that has the labels, how would I get that. I eventually want a .nii label volume and .nii original volume

Thank You

On Thu, Dec 13, 2018 at 8:13 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Fariha

  can give us more details? How would you like to customize them? I think the
  answer is probably no, but I'm not sure I understand what you are trying to
  do
  cheers
  Bruce


  On Wed,
  12 Dec 2018, Fariha Muazzam wrote:

  >
  >         External Email - Use Caution        
  >
  > Hi
  >
  > I am working in Freesurfer for subcortical segmentation of brain, I did segmentation of
  a volume and
  > I got around 45 regions. Is it possible that I could customize the regions I want or
  number of
  > segments that I want?
  >
  > Thank You
  > Regards
  >
  > Fariha Muazzam
  > Research Officer
  >
  > --------------------------------------------------------------------------
  > Al-Khawarizmi Institute of Computer Science (KICS)
  >
  > University of Engineering and Technology (UET), Lahore
  >
  > Email: fariha.muazzam@kics.edu.pk  | Web: www.kics.edu.pk 
  >
  >
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