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
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" sut2006@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.
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: rudolph@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA
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: rudolph@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.
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: rudolph@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.
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: rudolph@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: rudolph@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA
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: rudolph@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: rudolph@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
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: rudolph@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: rudolph@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: rudolph@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA
freesurfer@nmr.mgh.harvard.edu
-
Rudolph Pienaar -
Sudhin A. Shah