[Freesurfer] Creating annotation file for lobar regions...
Hi all -- Is there a simple way to create an annotation for frontal/temporal/occipital/parietal lobes based off the ?h.aparc.annot files in a FS 'label' dir? Ideally speaking, I'd like to have a ?h.lobar.annot with corresponding lobar.annot.ctab. Apologies if this question has come up before... a quick google didn't reveal anything. Many thanks -=R -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA ___ 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.
Re: [Freesurfer] Creating annotation file for lobar regions...
Try running mri_annotation2label with --lobes lh.lobes.annot doug On Thu, 20 May 2010, Rudolph Pienaar wrote: > Hi all -- > > Is there a simple way to create an annotation for > frontal/temporal/occipital/parietal lobes based off the ?h.aparc.annot > files in a FS 'label' dir? Ideally speaking, I'd like to have a > ?h.lobar.annot with corresponding lobar.annot.ctab. > > Apologies if this question has come up before... a quick google didn't > reveal anything. > > Many thanks > -=R > > -- 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.
Re: [Freesurfer] Creating annotation file for lobar regions...
Great -- many thanks, Doug. What are the newly annotated regions named? Basically, once I do a MatLAB [list, label, annot] = read_annotation('lh.lobes.annot'); what are the annot.struct_names? > > Try running mri_annotation2label with --lobes lh.lobes.annot > > doug > > > On Thu, 20 May 2010, Rudolph Pienaar wrote: > >> Hi all -- >> >> Is there a simple way to create an annotation for >> frontal/temporal/occipital/parietal lobes based off the ?h.aparc.annot >> files in a FS 'label' dir? Ideally speaking, I'd like to have a >> ?h.lobar.annot with corresponding lobar.annot.ctab. >> >> Apologies if this question has come up before... a quick google didn't >> reveal anything. >> >> Many thanks >> -=R >> >> > -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA ___ 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.
Re: [Freesurfer] Creating annotation file for lobar regions...
The names are below. Also, I should point out that this is a bit "experimental" in that I chose which ROIs went into each "lobe". I'm not an anatomist, and it would be a good idea for someone to check my definitions. Also, I have a "cingulate" lobe because I originally did this as part of a replication of the FSL thalamus DTI-based segmentation. doug From: int MRISaparc2lobes(MRIS *surf) in annotation.c MRISmergeAnnotations(surf, 10, parcnames, "frontal"); MRISmergeAnnotations(surf, 9, parcnames, "temporal"); MRISmergeAnnotations(surf, 4, parcnames, "parietal"); MRISmergeAnnotations(surf, 4, parcnames, "occipital"); MRISmergeAnnotations(surf, 4, parcnames, "cingulate"); Rudolph Pienaar wrote: > Great -- many thanks, Doug. What are the newly annotated regions named? > > Basically, once I do a MatLAB > > [list, label, annot] = read_annotation('lh.lobes.annot'); > > what are the annot.struct_names? > >> >> Try running mri_annotation2label with --lobes lh.lobes.annot >> >> doug >> >> >> On Thu, 20 May 2010, Rudolph Pienaar wrote: >> >>> Hi all -- >>> >>> Is there a simple way to create an annotation for >>> frontal/temporal/occipital/parietal lobes based off the ?h.aparc.annot >>> files in a FS 'label' dir? Ideally speaking, I'd like to have a >>> ?h.lobar.annot with corresponding lobar.annot.ctab. >>> >>> Apologies if this question has come up before... a quick google didn't >>> reveal anything. >>> >>> Many thanks >>> -=R >>> >>> >> > > -- 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.