Hello all,
I sent this last week but I think it may have slipped through the cracks.
I have recently run a cluster correction on some data, and was hoping to use these clusters as ROIs and pull stats from them. What is the best way to do so? Thank you in advance for your help,
Nathan
what kind of stats? It will create labels of the clusters, and you can map those labels back to the individual subjects, then run mris_anatomical_stats to pull out, eg, thickness for each subject.
doug
Dankner, Nathan (NIH/NIMH) [F] wrote:
Hello all,
I sent this last week but I think it may have slipped through the cracks.
I have recently run a cluster correction on some data, and was hoping to use these clusters as ROIs and pull stats from them. What is the best way to do so? Thank you in advance for your help,
Nathan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Doug,
I'm mostly looking to pull out cortical thickness. Could you give me an example of the command line which I would use to map the labels back to the individual subjects and pull the stats? Thanks,
Nathan
On 11/9/09 12:03 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
what kind of stats? It will create labels of the clusters, and you can map those labels back to the individual subjects, then run mris_anatomical_stats to pull out, eg, thickness for each subject.
doug
Dankner, Nathan (NIH/NIMH) [F] wrote:
Hello all,
I sent this last week but I think it may have slipped through the cracks.
I have recently run a cluster correction on some data, and was hoping to use these clusters as ROIs and pull stats from them. What is the best way to do so? Thank you in advance for your help,
Nathan
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 greve@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
Use mri_label2label to map from one subject to another. See the help for how to do this. then
cd subject/surf mris_anatomical_stats -l yourlabel.label -t lh.thickness -f table.dat subject lh
doug
Dankner, Nathan (NIH/NIMH) [F] wrote:
Doug,
I'm mostly looking to pull out cortical thickness. Could you give me an example of the command line which I would use to map the labels back to the individual subjects and pull the stats? Thanks,
Nathan
On 11/9/09 12:03 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
what kind of stats? It will create labels of the clusters, and you can map those labels back to the individual subjects, then run mris_anatomical_stats to pull out, eg, thickness for each subject.
doug
Dankner, Nathan (NIH/NIMH) [F] wrote:
Hello all,
I sent this last week but I think it may have slipped through the cracks.
I have recently run a cluster correction on some data, and was hoping to use these clusters as ROIs and pull stats from them. What is the best way to do so? Thank you in advance for your help,
Nathan
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 greve@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
Doug,
I have a follow-up to this question that I asked a while back. The cluster correction only outputs a .annot file, not label files, which doesn't seem to work with mri_label2label. Is there a way around this? Thanks,
Nathan
On 11/9/09 12:20 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
Use mri_label2label to map from one subject to another. See the help for how to do this. then
cd subject/surf mris_anatomical_stats -l yourlabel.label -t lh.thickness -f table.dat subject lh
doug
Dankner, Nathan (NIH/NIMH) [F] wrote:
Doug,
I'm mostly looking to pull out cortical thickness. Could you give me an example of the command line which I would use to map the labels back to the individual subjects and pull the stats? Thanks,
Nathan
On 11/9/09 12:03 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
what kind of stats? It will create labels of the clusters, and you can map those labels back to the individual subjects, then run mris_anatomical_stats to pull out, eg, thickness for each subject.
doug
Dankner, Nathan (NIH/NIMH) [F] wrote:
Hello all,
I sent this last week but I think it may have slipped through the cracks.
I have recently run a cluster correction on some data, and was hoping to use these clusters as ROIs and pull stats from them. What is the best way to do so? Thank you in advance for your help,
Nathan
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 greve@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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
You can use mri_surf2surf to map annotations, or you can use mri_annotation2label to convert the annot to labels, then use mri_label2label.
doug
Dankner, Nathan (NIH/NIMH) [F] wrote:
Doug,
I have a follow-up to this question that I asked a while back. The cluster correction only outputs a .annot file, not label files, which doesn't seem to work with mri_label2label. Is there a way around this? Thanks,
Nathan
On 11/9/09 12:20 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
Use mri_label2label to map from one subject to another. See the help for how to do this. then
cd subject/surf mris_anatomical_stats -l yourlabel.label -t lh.thickness -f table.dat subject lh
doug
Dankner, Nathan (NIH/NIMH) [F] wrote:
Doug,
I'm mostly looking to pull out cortical thickness. Could you give me an example of the command line which I would use to map the labels back to the individual subjects and pull the stats? Thanks,
Nathan
On 11/9/09 12:03 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
what kind of stats? It will create labels of the clusters, and you can map those labels back to the individual subjects, then run mris_anatomical_stats to pull out, eg, thickness for each subject.
doug
Dankner, Nathan (NIH/NIMH) [F] wrote:
Hello all,
I sent this last week but I think it may have slipped through the cracks.
I have recently run a cluster correction on some data, and was hoping to use these clusters as ROIs and pull stats from them. What is the best way to do so? Thank you in advance for your help,
Nathan
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 greve@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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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@nmr.mgh.harvard.edu
-
Dankner, Nathan (NIH/NIMH) [F] -
Douglas N Greve