I tried this, but something is going wrong. Here's what I did: 1. I ran $ mri_binarize --i subjid/mri/aparc+asec.mgz --match xx --match yy --o lobe.mgz - this produces a nice binary mask of, say, the left frontal lobe. 2. Then I ran $ mri_surf2vol --mkmask --surf pial --hemi lh --template lobe.mgz --identity subjid --o lobe_surface.mgz - this produces a nice binary image of the pial surface, but it contains the whole surface, not only the intersection with lobe.mgz. What am I doing wrong?

Thanks, Martin

Douglas N Greve wrote:

Use mri_surf2vol to create volumes. You can binarize aparc+aseg.mgz to give a mask of an area (use --match), then take the intersection of the mask with the surface-in-volume.

doug

Martin Ystad wrote:

...

Hi, I'm working on a fractal dimension analysis of the pial- and white-matter surface. The matlab script that calculates the fractal dimension needs binary nifti-files as input. Since FreeSurfer creates the surfaces I need, here's what I want to do: I'd like to convert the pial and white-matter surfaces (separately) to .nii-volumes (e.g. 256x256) where the voxels intersected by the respective surfaces are white, and everything else is black. Furthermore, I'd like to do this for individual subregions of each surface; for example only the precentral gyrus or the whole frontal lobe, so that only the voxels intersected by the surface belonging to the specific label I choose appear white, and everything else is black. How do I get this output from FreeSurfer?

Thanks, Martin Ystad PhD-candidate, University of Bergen, Norway _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Hi, thanks for the answer. Sorry for my delayed response. I tried the mris_calc command, but it didn't work. Here's the error message I got:

"mris_calc: curvature file 'lobe.mgz' has wrong magic number."

The multiplication was easily done i Matlab, but is there any way to do this with FreeSurfer?

Thanks, Martin

Douglas N Greve wrote:

The 2nd step only creates a mask of the entire surface. You need a step 3 in which you multiply them together:

3. mris_calc -o product.mgz lobe.mgz mul lobe_surface.mgz

Martin Ystad wrote:

...

I tried this, but something is going wrong. Here's what I did:

1. I ran $ mri_binarize --i subjid/mri/aparc+asec.mgz --match xx

--match yy --o lobe.mgz

• this produces a nice binary mask of, say, the left frontal lobe.

2. Then I ran $ mri_surf2vol --mkmask --surf pial --hemi lh

--template lobe.mgz --identity subjid --o lobe_surface.mgz

• this produces a nice binary image of the pial surface, but it

contains the whole surface, not only the intersection with lobe.mgz. What am I doing wrong?

Thanks, Martin

Douglas N Greve wrote:

...

Use mri_surf2vol to create volumes. You can binarize aparc+aseg.mgz to give a mask of an area (use --match), then take the intersection of the mask with the surface-in-volume.

doug

Martin Ystad wrote:

...

Hi, I'm working on a fractal dimension analysis of the pial- and white-matter surface. The matlab script that calculates the fractal dimension needs binary nifti-files as input. Since FreeSurfer creates the surfaces I need, here's what I want to do: I'd like to convert the pial and white-matter surfaces (separately) to .nii-volumes (e.g. 256x256) where the voxels intersected by the respective surfaces are white, and everything else is black. Furthermore, I'd like to do this for individual subregions of each surface; for example only the precentral gyrus or the whole frontal lobe, so that only the voxels intersected by the surface belonging to the specific label I choose appear white, and everything else is black. How do I get this output from FreeSurfer?

Thanks, Martin Ystad PhD-candidate, University of Bergen, Norway _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer