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:
- 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 > > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer