Yes, you can do this in a few steps. Use mri_binarize to convert the ribbon.mgz into a binary mask of just the cortex (use the --match option). Then use mri_binarize with aseg.mgz to get the hippocampus (17 for left, see $FREESURFER_HOME/FreeSurferColorLUT.txt). Then add them together with fscalc. Then use mri_mask with brain.mgz as the input and the result from above as the mask.

doug

octavian lie wrote:

Dear Bruce and Doug,

I want to clarify what I need. I would need to export to nii.gz a brain volume which has to be :

• T1,
• contain gray and white matter inside the pial surface, without

white-gray segmentation (the source analysis program downstream in the pipeline needs to complete this step in order to function).

• in addition to the pial contents, it should contain

hippocampi/amygdala as per aseg process, but exclude cerebellum

• the volume inside the pial surface has to be "real", not binary.(if

binary, gray should be darker than white, and not sure if this would work with the source analysis program I run).

If I try to export volumes such as brain.mgz, or brain.finalsurf.mgz, the extra dura/scalp *outside* of the pial surface (red line, fig) is also exported. Again, I am working at editing the pial surface to remove extra dura inside the red line; this is a work in progress, including customizing early recon-all steps/ implenting Andre's protocols. My problem is how to exclude tissues* outside* the pial surface/ red line, except hippocampi/amygdala. Can I create a pial/hippocampal mask excluding everything outside the red line/hippocampal/amygdalar volumes, which then I could align to a "real" brain, such as brain.mgz to get the brain inside the calculate pial surface? If so, how you would proceed?

Thank you for your suggestions.

See also my previous message:

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 (red line) 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.

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