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. > > > > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
