________________________________________ Von: Fellhauer, Iven Gesendet: Donnerstag, 15. März 2012 10:29 Bis: Douglas N Greve Betreff: AW: [Freesurfer] WG: Save segmentation results as nifi files
Dear all, in which space are the output files stored? If they are not stored in MNI space, which steps are necessary to convert these images into MNI space. Best regards, Iven Fellhauer ________________________________________ Von: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Gesendet: Dienstag, 31. Januar 2012 18:33 Bis: Fellhauer, Iven Cc: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] WG: Save segmentation results as nifi files 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
