There's not a separate GM, WM, and CSF. You can create these from the segmentations with mri_binarize. In general, it is run something like this:
mri_binarize --i aparc+aseg.mgz --match id1 id2 --o output.nii where id1 and id2 are structure codes from $FREESURFER_HOME/FreeSurferColorLUT.txt For all WM use: 2, 41, 77, 7, 46, 251-255 For all ventricular CSF and choroid plexus use: 4, 5, 14, 45, 44, 72, 31, 63, 15 For GM, use all the above plus 0, then add the --inv option to invert the mask (basically creating a mask of everything that is not GM and inverting it). doug Fellhauer, Iven wrote: > Hi Bruce > > And thank you for your hint, but where are the files for GM, WM and CFS > stored in the Freesurfer output directory structur? > > Best regards, > > Iven > > > -----Ursprüngliche Nachricht----- > Von: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] > Gesendet: Montag, 30. Januar 2012 15:20 > An: Fellhauer, Iven > Cc: freesurfer@nmr.mgh.harvard.edu > Betreff: Re: [Freesurfer] Save segmentation results as nifi files > > Hi Ivan > > you can convert any volume to any supported output type using mri_convert. It > will figure out the format from the extension, so: > > mri_convert aseg.mgz aseg.nii.gz > > or > > mri_convert aseg.mgz aseg.nii > > should do the trick > > cheers > Bruce > > > > On Mon, > 30 Jan 2012, Fellhauer, Iven wrote: > > >> Dear all, >> >> >> >> I run recon-all with the ?autorecon1 and ?autorecon2 options. Now I >> want to store the segmentation results in a spm like way. One nifti >> file for each matter. Can I do this with freesurfer? And how can I do >> this with freesurfer? >> >> >> >> Best regards, >> >> >> >> Iven Fellhauer >> >> >> >> ---------------------------------------------------------------- >> >> Universitätsklinikum Heidelberg >> >> Zentrum für Psychosoziale Medizin >> >> Klinik für Allgemeine Psychiatrie >> >> Sektion für Gerontopsychiatrie >> >> Voßstr. 4 >> >> 69115 Heidelberg >> >> Tel.: +49 (0) 6221 - 56 7578 >> >> Email: iven.fellha...@med.uni-heidelberg.de >> >> >> >> >> >> > > > 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. > _______________________________________________ > 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
