Dear Freesurfers,

What would be the best approach to sub-segment the subcortical structures (using mri_divide_parcellation) to anatomically relevant sub-segments similar to Thalamus sub-segments in FreeSurferColorLUT.txt (SegID 8001 to 80014).

Thank you, Nasim

mris_preproc will generate a concatentation of all subjects. It won't compute the average unless you add --mean.

doug

Jeff Sadino wrote:

Hello,

I ran mris_preproc on 56 subjects and then graphed the concatenated image. I also read this image into matlab and did the averaging using matlab, and then graphed the resulting image. When I did this, the two average pictures were slightly different. I thought that mris_preproc just simply averages all the subjects into common space. I noticed that its vector in matlab keeps the thickness value for all vertex's for all 56 subjects. I want to have the matlab capability for some custom processing I am doing, but the discrepancy leads me to think that mris_preproc is not a simple average. Can anyone elucidate this for me? Thank you!

Matlab script. Only place I would suspect a wrong assumption is when I throw out the rest of the subjects at curv4=curv3(1,:,:,1) %Select your input thickness file path='/mnt/users/Jeff/fs/lc/HIV/pass2pics/416/diff/nc.rh.ave.mgh';

%Read the thickness file curv=MRIread(path);

%Select the volume attribute curv2=curv.vol;

%Create a duplicate thickness array for manipulation curv3=curv2;

%Get the number of concatanated subjects tmp=size(curv2); m=tmp(4) clear 'tmp'

%Sum each vertex for all your subjects for im=2:m for in=1:7 curv3(1,:,in,1)=curv3(1,:,in,1)+curv2(1,:,in,im); end end

%Select just the first frame curv4=curv3(1,:,:,1);

%Compute the average thickness curv.vol=curv4/m;

%Write to thickness file MRIwrite(curv,'nc.rh.ave1.tmp.mgh');

---

Rediscover Hotmail®: Get quick friend updates right in your inbox. Check it out. http://windowslive.com/RediscoverHotmail?ocid=TXT_TAGLM_WL_HM_Rediscover_Updates2_042009

---

---

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