looks ok. you should not need --outdir you can use mri_aparc2aseg to create a nifti file. This is what is used to create aparc+aseg.mgz from the aparc annotation and aseg.mgz. Look in the recon-all.log file for an example command line (just change the output name so you don't overwrite). The aseg.mgz is the volumetric labeling that includes cerebral WM and subcortical gray. It does not include lobes. doug
On 11/19/2013 04:06 PM, Mojdeh Zamyadi wrote: > Thanks a lot for the very quick reply! > > does this look OK? > mri_annotation2label --subject P2 --hemi rh --outdir > freeSurfer_Results/P2/moj_labels/ --lobesStrict > freeSurfer_Results/P2/moj_labels/freeSurfer_lobes > > how can I convert the annotation file to nii.gz?! > > also, could please explain a bit what the "aseg" file contains? because > I though that file had the complete sub-cortical parcellation (including > different parts of different lobes!) > > sorry if my questions are rather basic, I'm very new to freeSurfer > > -M > On 11/19/2013 11:21 AM, Douglas N Greve wrote: >> Try running mri_annotation2label with the --lobesStrict option >> doug >> >> >> On 11/19/2013 11:15 AM, Mojdeh Zamyadi wrote: >>> Hi all, >>> >>> I'm interested in getting a lobar segmentation of the cortex and I've >>> already ran recon-all on my subjects. I'm now confused by the outputs >>> and was wondering if someone could tell me which output file contains >>> segmentation that can be merged to get a 4 lobe parcellation similar to: >>> http://freesurfer.net/fswiki/CorticalParcellation? >>> >>> Thanks a lot, >>> -Mojdeh >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> [email protected] >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list [email protected] 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.
