Hi all,
I haven't had any answer to my post, so I give another try. Hope it doesn't bother you.
I am trying to overlay a map on a specific subcortical structure (the caudate).
-I obtained the surface of the structure using the command:
mri_tessellate structure.nii.gz 1 lh.structure.surf
-then I projected my map on the surface using:
mri_vol2surf --mov map.nii --regheader structure --hemi lh --surf structure.surf --projdist 0 --fwhm 5 --out projected_map.mgz --interp trilinear
Everything seems to work properly. I am able to see the result using tksurfer.
However, when I try to overlay projected_map.mgz on lh.structure.surf using freeview I experience a segmentation fault issue. It seems that the software looks for the WM, the pial, the curv, etc surfaces. Obviously I don't have these information, since I am projecting the map only on the caudate nucleus.
Is it mandatory to have these inputs? Could you give me an advice about that?
Thanks Maria
Hi Maria,
I've tested the files you sent me and were able to replicate the problem. Will work on it asap. Sorry about the delay.
Ruopeng
On 06/27/2011 12:13 PM, iacono@nmr.mgh.harvard.edu wrote:
Hi all,
I haven't had any answer to my post, so I give another try. Hope it doesn't bother you.
I am trying to overlay a map on a specific subcortical structure (the caudate).
-I obtained the surface of the structure using the command:
mri_tessellate structure.nii.gz 1 lh.structure.surf
-then I projected my map on the surface using:
mri_vol2surf --mov map.nii --regheader structure --hemi lh --surf structure.surf --projdist 0 --fwhm 5 --out projected_map.mgz --interp trilinear
Everything seems to work properly. I am able to see the result using tksurfer.
However, when I try to overlay projected_map.mgz on lh.structure.surf using freeview I experience a segmentation fault issue. It seems that the software looks for the WM, the pial, the curv, etc surfaces. Obviously I don't have these information, since I am projecting the map only on the caudate nucleus.
Is it mandatory to have these inputs? Could you give me an advice about that?
Thanks Maria
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Maria,
The fix is done and should be available in tomorrow's dev build.
Ruopeng
On 06/27/2011 12:13 PM, iacono@nmr.mgh.harvard.edu wrote:
Hi all,
I haven't had any answer to my post, so I give another try. Hope it doesn't bother you.
I am trying to overlay a map on a specific subcortical structure (the caudate).
-I obtained the surface of the structure using the command:
mri_tessellate structure.nii.gz 1 lh.structure.surf
-then I projected my map on the surface using:
mri_vol2surf --mov map.nii --regheader structure --hemi lh --surf structure.surf --projdist 0 --fwhm 5 --out projected_map.mgz --interp trilinear
Everything seems to work properly. I am able to see the result using tksurfer.
However, when I try to overlay projected_map.mgz on lh.structure.surf using freeview I experience a segmentation fault issue. It seems that the software looks for the WM, the pial, the curv, etc surfaces. Obviously I don't have these information, since I am projecting the map only on the caudate nucleus.
Is it mandatory to have these inputs? Could you give me an advice about that?
Thanks Maria
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
iacono＠nmr.mgh.harvard.edu -
Ruopeng Wang