Dear All,
I am increasingly fascinated by freesurfer. Here is a rookie issue: I use a source imaging program that is rather simple-minded in its MRI processing steps. To be able to use the inverse solution tools of that program, I need to use 2 volumes: - a head MRI to be used to electrode coregistration - a skull-stripped brain MR without cerebellum, including both the gray and white matter; the program needs to perform its own white matter extraction to generate the gray matter volume to be used as source space. - both MRs have to be subject to the same transforms, if any, and have to have the same origin and coordinate systems (like real head/brain pairs).
So first, I am in the search of the "best" brain extraction possible, with as little dura included as possible. Besides trying to implement Andre's dura protocols, and editing the pial surface for brainmask.mgz, then running the rest of the recon-all steps, I need to be able to export in nii.gz format a volume having its pial surface as calculated by freesurfer. When exporting brain.finalsurfs.mgz with mri_convert, it looks that the calculated pial surface as visualized with tkmedit subjid brain.finalsurfs.mgz -surfs is ignored in the nii.gz file. When the output nii volume is imported in programs such as Bioimage Suite, I essentially see what looks like the outside (surface) brainmask.mgz volume as in tekmedit but not accounting for the calculated pial surface. How can I export brain.finalsurfs.mgz with its calculated pial surface as a nii volume? In other words, I would need a ribbon.mgz type volume to include the white matter on the inside. I suppose it comes down to adding options to the mri_convert brain.finalsurfs.mgz step after surfaces have been generated, but I would need some guidance Please advise.
Octavian.
Hi Octavian
try using mris_fill with the pial surface to generate a binary volume that is 1 in the interior of the pial and 0 outside of it.
cheers Bruce On Sun, 4 Mar 2012, octavian lie wrote:
Dear All, I am increasingly fascinated by freesurfer. Here is a rookie issue: I use a source imaging program that is rather simple-minded in its MRI processing steps. To be able to use the inverse solution tools of that program, I need to use 2 volumes:
- a head MRI to be used to electrode coregistration
- a skull-stripped brain MR without cerebellum, including both the gray and white matter; the program needs to perform its own white
matter extraction to generate the gray matter volume to be used as source space.
- both MRs have to be subject to the same transforms, if any, and have to have the same origin and coordinate systems (like real
head/brain pairs). So first, I am in the search of the "best" brain extraction possible, with as little dura included as possible. Besides trying to implement Andre's dura protocols, and editing the pial surface for brainmask.mgz, then running the rest of the recon-all steps, I need to be able to export in nii.gz format a volume having its pial surface as calculated by freesurfer. When exporting brain.finalsurfs.mgz with mri_convert, it looks that the calculated pial surface as visualized with tkmedit subjid brain.finalsurfs.mgz -surfs is ignored in the nii.gz file. When the output nii volume is imported in programs such as Bioimage Suite, I essentially see what looks like the outside (surface) brainmask.mgz volume as in tekmedit but not accounting for the calculated pial surface. How can I export brain.finalsurfs.mgz with its calculated pial surface as a nii volume? In other words, I would need a ribbon.mgz type volume to include the white matter on the inside. I suppose it comes down to adding options to the mri_convert brain.finalsurfs.mgz step after surfaces have been generated, but I would need some guidance Please advise. Octavian.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
octavian lie