Thanks Bruce! However, as you suspected this does not seem to work: mri_extract_label mri/aseg.mgz 24 mri/mask_code24.mgz gives a tiny volume of a couple of hundred voxels in the middle of the brain (part of 3rd ventricle). I assume here that code 24 is the correct code for all CSF in aseg.mgz.
I guess an alternative would be to take the volume of inner skull minus the volume of everything including and below pial surface. How would one go about doing that? Or would you suggest other ways? Bests, Tommi > Hi Tommi > > you can use mri_extract_label to pull out the labels you want, but the > sulcal CSF labels may not be great since the manual labeling that is the > basis of the aseg was done on only T1 images. > > cheers > Bruce > > On Wed, 8 Dec 2010 > r...@nmr.mgh.harvard.edu wrote: > >> >> Hi, >> >> We are trying to create a CSF volume mask from structural MEMPRAGE T1 >> data >> (we also have ME FLASH 5/30 ->PD if needed). We are interested in two >> CSF >> compartments: >> >> - "superficial" CSF outside grey matter and inside inner skull >> - "deep" CSF inside ventricles >> >> Is there a way to simply extract these from aseg.mgz or how should we go >> about this? >> >> Thanks! >> >> -Tommi >> >> --- >> Tommi Raij, M.D., Ph.D. >> MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging >> Bldg 149, 13th St >> Charlestown, MA 02129 >> U.S.A. >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
