[Freesurfer] Labels to annotation

Dear Freesurfer experts, I have made a parcellation of the white matter surface outside of freesurfer in volumes. I convert the volume labels to surface labels. I have now a lot of surface labels (~500 for each hemisphere) which I want to concatenate to an annotation file for easier visualizati

Re: [Freesurfer] mris_make_face_parcellation

don't think so. You could certainly discard parcels that have a substantial non-cortical component to them, but parcellating the remainder of the surface uniformly isn't trivial. cheers Bruce On Tue, 1 Apr 2014, Karen Marie Sandø Ambrosen wrote: Hi Freesurfer experts, I first parce

[Freesurfer] mris_make_face_parcellation

Hi Freesurfer experts, I first parcellated the ?h.aparc.annot using the mris_divide_parcellation and at first glance it seems fine. However, I experienced that the size of the regions varies a lot. I then found the mris_make_face_parcellation, that parcellate the surface in regions of more equ

Re: [Freesurfer] Convert volume label to surface label

close the label N times before writing --paint dmax surfname : map to closest vertex on source surfname if d < dmax the closest surface vertices: what hardware/software environment are you running in? Bruce On Mon, 24 Mar 2014, Karen Marie Sandø Ambrosen wrote: Hi Bruce, Thanks for y

Re: [Freesurfer] Convert volume label to surface label

cause the surface just misses the voxels that have your label in some points. You can either thicken the label in the volume, or use morphological operations like close (in mri_label2label or manually in tksurfer) to fill the holes cheers Bruce On Mon, 24 Mar 2014, Karen Marie Sandø Ambrosen

[Freesurfer] Convert volume label to surface label

Hi Freesurfer experts, I have a volume label only which is only different from zero in the white matter-gray matter boundary. I am trying to convert this volume label to a surface label in order to visualize it in tksurfer. I am using mri_vol2surf: mri_vol2surf --mov volume_label.nii --out vol

Re: [Freesurfer] mris_convert

Hi again, When I convert a surface to .gii with mris_convert, it is shifted compared to the original surface when loaded into freeview (see previous mail). Does anyone know how to solve this? Best, Karen On 02/18/2014 10:01 AM, Karen Marie Sandø Ambrosen wrote: > Hi Freesurfer experts, &g

[Freesurfer] mris_convert

Hi Freesurfer experts, I am trying to run tracktography from freesurfer labels using probtrackx2 in fsl. To convert the labels to surfaces I use the label2surf command as recommended on the fslwiki. To use the label2surf command I need to convert the surface, e.g. lh.white into a fsl-compatibl

[Freesurfer] Whole brain tractography using Freesurfer surfaces as seed and target

Hi Freesurfer experts, I am trying to perform whole brain tractography using FSL's Probtrackx2 with Freesurfer white surfaces as seed and pial surfaces as targets. To obtain a whole brain connectivity graph I need the streamlines between the hemispheres. This means that I need to remove the par