Hi Ines, this is a good thing to post to the list since there are others that might know better than me. Also, please include the full terminal output. thanks doug
On 05/18/2012 11:51 AM, Inês Violante wrote:
Thanks a lot!
Just another question: I get this message for one of my subjects using the previous command:
ERROR: Too many out-of-range vertex indices in MRISreadAnnotationIntoArray!
I must have done something wrong. Is there a way to correct this without having to run the whole recon-all again?
All the best,
ines
On Fri, May 18, 2012 at 4:46 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
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, Inęs 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, Inęs 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
-- 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
Hi,
It repeats this several times and
MRISreadAnnotationIntoArray: vertex index out of range: 775162420 i=2E340A34, in_array_size=157940 annot file: CS/label/lh.aparc.annot MRISreadAnnotationIntoArray: vertex index out of range: 775162420 i=2E340A34, in_array_size=157940 annot file: CS/label/lh.aparc.annot MRISreadAnnotationIntoArray: vertex index out of range: 775162420 i=2E340A34, in_array_size=157940 annot file: CS/label/lh.aparc.annot
(...)
ERROR: Too many out-of-range vertex indices in MRISreadAnnotationIntoArray!
On Fri, May 18, 2012 at 4:53 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Hi Ines, this is a good thing to post to the list since there are others that might know better than me. Also, please include the full terminal output. thanks doug
On 05/18/2012 11:51 AM, Inês Violante wrote:
Thanks a lot!
Just another question: I get this message for one of my subjects using the previous command:
ERROR: Too many out-of-range vertex indices in MRISreadAnnotationIntoArray!
I must have done something wrong. Is there a way to correct this without having to run the whole recon-all again?
All the best,
ines
On Fri, May 18, 2012 at 4:46 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
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, Inęs 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, Inęs 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
-- 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
hmmm, something seems badly wrong here. You shouldn't have any vertex indices over 150K or so. If you load that annot file onto the surface in tksurfer does it look right? Does tksurfer complain when you try to load it?
On Fri, 18 May 2012, Inês Violante wrote:
Hi,
It repeats this several times and
MRISreadAnnotationIntoArray: vertex index out of range: 775162420 i=2E340A34, in_array_size=157940 annot file: CS/label/lh.aparc.annot MRISreadAnnotationIntoArray: vertex index out of range: 775162420 i=2E340A34, in_array_size=157940 annot file: CS/label/lh.aparc.annot MRISreadAnnotationIntoArray: vertex index out of range: 775162420 i=2E340A34, in_array_size=157940 annot file: CS/label/lh.aparc.annot
(...)
ERROR: Too many out-of-range vertex indices in MRISreadAnnotationIntoArray!
On Fri, May 18, 2012 at 4:53 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Hi Ines, this is a good thing to post to the list since there are others that might know better than me. Also, please include the full terminal output. thanks doug
On 05/18/2012 11:51 AM, Inês Violante wrote:
Thanks a lot!
Just another question: I get this message for one of my subjects using the previous command:
ERROR: Too many out-of-range vertex indices in MRISreadAnnotationIntoArray!
I must have done something wrong. Is there a way to correct this without having to run the whole recon-all again?
All the best,
ines
On Fri, May 18, 2012 at 4:46 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
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, In?s 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, In?s 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
-- 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas N Greve -
Inês Violante