I've put a new version of mri_annotation2label here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_annotation2label This is for centos 6. If that does not work for you, let me know what your platform is
doug
On 12/03/2013 12:28 PM, Mojdeh Zamyadi wrote:
Thanks Doug! maybe I'm making this too complicated! What I want is to know which label (number) corresponds to each of the main lobes. Right now my freeSurfer_lobes.nii.gz image has lables in the range of 0-100's (which is WM if not mistaken), and then labels in the range of 1000-1035 for the left and 2000-2035 for the right hemisphere with zero labels in 1002,1008-1035 & 2002,2008-2035! (and these labels correspond to the GM, correct?!)
I tried --ctab option by running the following command:
mri_annotation2label --subject P2 --hemi lh --ctab new_ColorTable.txt --lobesStrict freeSurfer_Results/P2/label/lh.freeSurfer_lobes.annot
but it's not saving anything! Could you please tell me how to properly use this option?
Thanks again, -Mojdeh
On 11/29/2013 04:28 PM, Douglas Greve wrote:
The commands look right and it sounds like you might have the right result. What do you mean you are getting a detailed WM + GM segmentation? If you just load freeSurfer_lobes.nii.gz into tkmedit, the label names will be all messed up because you don't have the proper color table, but you should still only get 7 per hemi. To get the proper color table, run mri_annotation2label with --ctab, then merge the two ctabs you get (lh and rh). You don't need to rerun mri_aparc2aseg doug
On 11/29/13 3:09 PM, Mojdeh Zamyadi wrote:
Hi all,
Since I haven't heard back about my question so far, I'm posting it again! Sorry about this but I really need your help!
As mentioned in my previous posts, I'm interested in having the GM volumetric lobar masks (frontal, parietal, temporal, occipital, and insular) with the final goal of moving them the DTI space to perform thalamic parcellation. I've ran the following commands:
1- a. mri_annotation2label --subject P2 --hemi lh --lobesStrict freeSurfer_Results/P2/label/lh.freeSurfer_lobes.annot b. mri_annotation2label --subject P2 --hemi rh --lobesStrict freeSurfer_Results/P2/label/rh.freeSurfer_lobes.annot
2- mri_aparc2aseg --annot freeSurfer_lobes --s P2 --o freeSurfer_Results/P2/label/freeSurfer_lobes.nii.gz
I thought after doing this I'm going to get the 5 or 6 lobar labels, but instead I'm getting a detailed WM + GM segmentation. I looked at "FreeSurferColorLUT.txt" and tried to manually combine labels in the range of 1000-1035 for the left and 2000-2035 for the right hemisphere to get the lobe masks, but after having a closer look I realised that labels 1002,1008-1035& 2002,2008-2035 are all empty (ie. I only have 7 labels in each hemisphere)! so, I'm now not sure how to manually combine these labels either!
Could someone PLEASE PLEASE clarify this for me! I would really appreciate any help!
Thanks, -Mojdeh
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