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 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.
