[Freesurfer] labels to lobes
Hello, Is there a lookup table I can use to convert free surfer labels to lobes? Either label nos (1006, 2006 etc) or label names (ctx-rh-superiorfrontal)? I have 86 labels and want an easy way to differentiate them into the corresponding lobes. Thanks, S ___ 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] labels to lobes
Also, is there a way to associate these labels with motor/auditory/visual cortices? Or do I have to use the specific parcellations? On Feb 28, 2013, at 9:25 AM, Sudhin A. Shah sut2...@med.cornell.edu wrote: Hello, Is there a lookup table I can use to convert free surfer labels to lobes? Either label nos (1006, 2006 etc) or label names (ctx-rh-superiorfrontal)? I have 86 labels and want an easy way to differentiate them into the corresponding lobes. Thanks, S ___ 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] labels to lobes
After a conventional FS run you can do the following: $mri_annotation2label --subject subj --hemi hemi --lobesStrict hemi.lobesStrict.annot Which will create an annotation file hemi.lobesStrict.annot containing the lobar labels. To extract these into their own individual label files, do $mri_annotation2label --subject subj --hemi hemi --annotation lobesStrict --outdir subj/label This will populate the subj/label directory with files: hemi.frontal.label hemi.parietal.label hemi.temporal.label hemi.occiptal.label hemi.cingulate.label So, to be pendantic, if you want the lobar labels for the left hemisphere of a subject called 'sub1', you would $mri_annotation2label --subject sub1 --hemi lh --lobesStrict lh.lobesStrict.annot $mri_annotation2label --subject sub1 --hemi lh --annotation lobesStrict --outdir sub1/label HTH -=R On Thu Feb 28 09:24:58 2013, Sudhin A. Shah wrote: Hello, Is there a lookup table I can use to convert free surfer labels to lobes? Either label nos (1006, 2006 etc) or label names (ctx-rh-superiorfrontal)? I have 86 labels and want an easy way to differentiate them into the corresponding lobes. Thanks, S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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] labels to lobes
Thank you! Is there something similar to assign labels to functional cortices eg. motor, visual, auditory? Thanks S On Feb 28, 2013, at 10:47 AM, Rudolph Pienaar wrote: After a conventional FS run you can do the following: $mri_annotation2label --subject subj --hemi hemi --lobesStrict hemi.lobesStrict.annot Which will create an annotation file hemi.lobesStrict.annot containing the lobar labels. To extract these into their own individual label files, do $mri_annotation2label --subject subj --hemi hemi --annotation lobesStrict --outdir subj/label This will populate the subj/label directory with files: hemi.frontal.label hemi.parietal.label hemi.temporal.label hemi.occiptal.label hemi.cingulate.label So, to be pendantic, if you want the lobar labels for the left hemisphere of a subject called 'sub1', you would $mri_annotation2label --subject sub1 --hemi lh --lobesStrict lh.lobesStrict.annot $mri_annotation2label --subject sub1 --hemi lh --annotation lobesStrict --outdir sub1/label HTH -=R On Thu Feb 28 09:24:58 2013, Sudhin A. Shah wrote: Hello, Is there a lookup table I can use to convert free surfer labels to lobes? Either label nos (1006, 2006 etc) or label names (ctx-rh-superiorfrontal)? I have 86 labels and want an easy way to differentiate them into the corresponding lobes. Thanks, S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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 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
Re: [Freesurfer] labels to lobes
Hi I got an error -lobesStrict unknown. I am running mri_annotation2label version stable5. Is there a workaround? On Feb 28, 2013, at 10:47 AM, Rudolph Pienaar wrote: After a conventional FS run you can do the following: $mri_annotation2label --subject subj --hemi hemi --lobesStrict hemi.lobesStrict.annot Which will create an annotation file hemi.lobesStrict.annot containing the lobar labels. To extract these into their own individual label files, do $mri_annotation2label --subject subj --hemi hemi --annotation lobesStrict --outdir subj/label This will populate the subj/label directory with files: hemi.frontal.label hemi.parietal.label hemi.temporal.label hemi.occiptal.label hemi.cingulate.label So, to be pendantic, if you want the lobar labels for the left hemisphere of a subject called 'sub1', you would $mri_annotation2label --subject sub1 --hemi lh --lobesStrict lh.lobesStrict.annot $mri_annotation2label --subject sub1 --hemi lh --annotation lobesStrict --outdir sub1/label HTH -=R On Thu Feb 28 09:24:58 2013, Sudhin A. Shah wrote: Hello, Is there a lookup table I can use to convert free surfer labels to lobes? Either label nos (1006, 2006 etc) or label names (ctx-rh-superiorfrontal)? I have 86 labels and want an easy way to differentiate them into the corresponding lobes. Thanks, S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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 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
Re: [Freesurfer] labels to lobes
It looks like you might be running a too-old version of mri_annotation2label. What FS build/version are you running? On Thu Feb 28 11:36:50 2013, Sudhin A. Shah wrote: Hi I got an error -lobesStrict unknown. I am running mri_annotation2label version stable5. Is there a workaround? On Feb 28, 2013, at 10:47 AM, Rudolph Pienaar wrote: After a conventional FS run you can do the following: $mri_annotation2label --subject subj --hemi hemi --lobesStrict hemi.lobesStrict.annot Which will create an annotation file hemi.lobesStrict.annot containing the lobar labels. To extract these into their own individual label files, do $mri_annotation2label --subject subj --hemi hemi --annotation lobesStrict --outdir subj/label This will populate the subj/label directory with files: hemi.frontal.label hemi.parietal.label hemi.temporal.label hemi.occiptal.label hemi.cingulate.label So, to be pendantic, if you want the lobar labels for the left hemisphere of a subject called 'sub1', you would $mri_annotation2label --subject sub1 --hemi lh --lobesStrict lh.lobesStrict.annot $mri_annotation2label --subject sub1 --hemi lh --annotation lobesStrict --outdir sub1/label HTH -=R On Thu Feb 28 09:24:58 2013, Sudhin A. Shah wrote: Hello, Is there a lookup table I can use to convert free surfer labels to lobes? Either label nos (1006, 2006 etc) or label names (ctx-rh-superiorfrontal)? I have 86 labels and want an easy way to differentiate them into the corresponding lobes. Thanks, S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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 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. -- 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
Re: [Freesurfer] labels to lobes
freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 On Feb 28, 2013, at 12:12 PM, Rudolph Pienaar wrote: It looks like you might be running a too-old version of mri_annotation2label. What FS build/version are you running? On Thu Feb 28 11:36:50 2013, Sudhin A. Shah wrote: Hi I got an error -lobesStrict unknown. I am running mri_annotation2label version stable5. Is there a workaround? On Feb 28, 2013, at 10:47 AM, Rudolph Pienaar wrote: After a conventional FS run you can do the following: $mri_annotation2label --subject subj --hemi hemi --lobesStrict hemi.lobesStrict.annot Which will create an annotation file hemi.lobesStrict.annot containing the lobar labels. To extract these into their own individual label files, do $mri_annotation2label --subject subj --hemi hemi --annotation lobesStrict --outdir subj/label This will populate the subj/label directory with files: hemi.frontal.label hemi.parietal.label hemi.temporal.label hemi.occiptal.label hemi.cingulate.label So, to be pendantic, if you want the lobar labels for the left hemisphere of a subject called 'sub1', you would $mri_annotation2label --subject sub1 --hemi lh --lobesStrict lh.lobesStrict.annot $mri_annotation2label --subject sub1 --hemi lh --annotation lobesStrict --outdir sub1/label HTH -=R On Thu Feb 28 09:24:58 2013, Sudhin A. Shah wrote: Hello, Is there a lookup table I can use to convert free surfer labels to lobes? Either label nos (1006, 2006 etc) or label names (ctx-rh-superiorfrontal)? I have 86 labels and want an easy way to differentiate them into the corresponding lobes. Thanks, S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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 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. -- 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] labels to lobes
v5.0.0 is too old. I'd suggest grabbing the current 5.1.0 build and then just using the 'mri_annotation2label' from that. On Thu Feb 28 12:17:02 2013, Sudhin A. Shah wrote: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 On Feb 28, 2013, at 12:12 PM, Rudolph Pienaar wrote: It looks like you might be running a too-old version of mri_annotation2label. What FS build/version are you running? On Thu Feb 28 11:36:50 2013, Sudhin A. Shah wrote: Hi I got an error -lobesStrict unknown. I am running mri_annotation2label version stable5. Is there a workaround? On Feb 28, 2013, at 10:47 AM, Rudolph Pienaar wrote: After a conventional FS run you can do the following: $mri_annotation2label --subject subj --hemi hemi --lobesStrict hemi.lobesStrict.annot Which will create an annotation file hemi.lobesStrict.annot containing the lobar labels. To extract these into their own individual label files, do $mri_annotation2label --subject subj --hemi hemi --annotation lobesStrict --outdir subj/label This will populate the subj/label directory with files: hemi.frontal.label hemi.parietal.label hemi.temporal.label hemi.occiptal.label hemi.cingulate.label So, to be pendantic, if you want the lobar labels for the left hemisphere of a subject called 'sub1', you would $mri_annotation2label --subject sub1 --hemi lh --lobesStrict lh.lobesStrict.annot $mri_annotation2label --subject sub1 --hemi lh --annotation lobesStrict --outdir sub1/label HTH -=R On Thu Feb 28 09:24:58 2013, Sudhin A. Shah wrote: Hello, Is there a lookup table I can use to convert free surfer labels to lobes? Either label nos (1006, 2006 etc) or label names (ctx-rh-superiorfrontal)? I have 86 labels and want an easy way to differentiate them into the corresponding lobes. Thanks, S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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 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. -- 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 -- 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
