You can also use mri_binarize with the --match flag. It does the same thing, but you can give it multiple match values. There is also a --ventricles option (excludes 4th ventricle).
doug Bruce Fischl wrote: > Hi Tommi, > > no, you need to also extract the left and right ventricles and the > inferior lateral ventricles. > > cheers > Bruce > > > On Wed, 8 Dec 2010 r...@nmr.mgh.harvard.edu > wrote: > > >> 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 > > > -- 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 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.
