Hi,
I need to know the surface area of the structures in the aparc file but I want to obtain this measurement from the pial surface and not the white matter surface. How can I do that?
Thank you a lot for your help.
ines
The last argument of mris_anatomical_stats allows you to specify the surface to use (pial in your case)
cheers, -MH
NAME mris_anatomical_stats
SYNOPSIS mris_anatomical_stats [options] <subjectname> <hemi> [<surfacename>]
On Fri, 2012-05-18 at 15:18 +0100, Inês Violante wrote:
Hi,
I need to know the surface area of the structures in the aparc file but I want to obtain this measurement from the pial surface and not the white matter surface. How can I do that?
Thank you a lot for your help.
ines _______________________________________________ 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.
Hi,
Thanks Michael. However, when I try to do this using the aparc.annot file:
mris_anatomical_stats -l CS/label/lh.aparc.annot -b CS lh pial
I receive this error:
mris_anatomical_stats: could not scan # of lines from CS/label/lh.aparc.annot
I imagine this happens because the mris_anatomical_stats is waiting for a .label file
What I aim is the output of the aparcstats2table for the surface area using the pial surface.
Perhaps I am not using the correct command....
Thanks for the help.
ines
On Fri, May 18, 2012 at 3:41 PM, Michael Harms mharms@conte.wustl.edu wrote:
The last argument of mris_anatomical_stats allows you to specify the surface to use (pial in your case)
cheers, -MH
NAME mris_anatomical_stats
SYNOPSIS mris_anatomical_stats [options] <subjectname> <hemi> [<surfacename>]
On Fri, 2012-05-18 at 15:18 +0100, Inês Violante wrote:
Hi,
I need to know the surface area of the structures in the aparc file but I want to obtain this measurement from the pial surface and not the white matter surface. How can I do that?
Thank you a lot for your help.
ines _______________________________________________ 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.
You should be able to get the correct syntax by checking the recon- all.log file for an example.
cheers, -MH
On Fri, 2012-05-18 at 15:48 +0100, Inês Violante wrote:
Hi,
Thanks Michael. However, when I try to do this using the aparc.annot file:
mris_anatomical_stats -l CS/label/lh.aparc.annot -b CS lh pial
I receive this error:
mris_anatomical_stats: could not scan # of lines from CS/label/lh.aparc.annot
I imagine this happens because the mris_anatomical_stats is waiting for a .label file
What I aim is the output of the aparcstats2table for the surface area using the pial surface.
Perhaps I am not using the correct command....
Thanks for the help.
ines
On Fri, May 18, 2012 at 3:41 PM, Michael Harms mharms@conte.wustl.edu wrote:
The last argument of mris_anatomical_stats allows you to specify the surface to use (pial in your case)
cheers, -MH
NAME mris_anatomical_stats
SYNOPSIS mris_anatomical_stats [options] <subjectname> <hemi> [<surfacename>]
On Fri, 2012-05-18 at 15:18 +0100, Inês Violante wrote:
Hi,
I need to know the surface area of the structures in the aparc file but I want to obtain this measurement from the pial surface and not the white matter surface. How can I do that?
Thank you a lot for your help.
ines _______________________________________________ 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.
And you can get the full command line from the $subject/scripts/recon-all.log file doug
On 05/18/2012 10:41 AM, Michael Harms wrote:
The last argument of mris_anatomical_stats allows you to specify the surface to use (pial in your case)
cheers, -MH
NAME mris_anatomical_stats
SYNOPSIS mris_anatomical_stats [options]<subjectname> <hemi> [<surfacename>]
On Fri, 2012-05-18 at 15:18 +0100, Inês Violante wrote:
Hi,
I need to know the surface area of the structures in the aparc file but I want to obtain this measurement from the pial surface and not the white matter surface. How can I do that?
Thank you a lot for your help.
ines _______________________________________________ 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
Thank you.
I've tried this command:
mris_anatomical_stats -f AC/stats/lh.aparc.stats -b -a AC/label/lh.aparc.annot -c ./aparc.annot.ctab AC lh pial
Would this be appropriate?
ines
On Fri, May 18, 2012 at 4:32 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
And you can get the full command line from the $subject/scripts/recon-all.log file doug
On 05/18/2012 10:41 AM, Michael Harms wrote:
The last argument of mris_anatomical_stats allows you to specify the surface to use (pial in your case)
cheers, -MH
NAME mris_anatomical_stats
SYNOPSIS mris_anatomical_stats [options]<subjectname> <hemi> [<surfacename>]
On Fri, 2012-05-18 at 15:18 +0100, Inês Violante wrote:
Hi,
I need to know the surface area of the structures in the aparc file but I want to obtain this measurement from the pial surface and not the white matter surface. How can I do that?
Thank you a lot for your help.
ines _______________________________________________ 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
-- 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
yes, but you might want to change the name of the stats file so that you don't overwrite the one that is there doug
On 05/18/2012 11:39 AM, Inês Violante wrote:
Thank you.
I've tried this command:
mris_anatomical_stats -f AC/stats/lh.aparc.stats -b -a AC/label/lh.aparc.annot -c ./aparc.annot.ctab AC lh pial
Would this be appropriate?
ines
On Fri, May 18, 2012 at 4:32 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
And you can get the full command line from the $subject/scripts/recon-all.log file doug
On 05/18/2012 10:41 AM, Michael Harms wrote:
The last argument of mris_anatomical_stats allows you to specify the surface to use (pial in your case)
cheers, -MH
NAME mris_anatomical_stats
SYNOPSIS mris_anatomical_stats [options]<subjectname> <hemi> [<surfacename>]
On Fri, 2012-05-18 at 15:18 +0100, Inês Violante wrote:
Hi,
I need to know the surface area of the structures in the aparc file but I want to obtain this measurement from the pial surface and not the white matter surface. How can I do that?
Thank you a lot for your help.
ines _______________________________________________ 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
-- 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Inês Violante -
Michael Harms