you can load the annotation into matlab with read_annotation.m doug Antonella Kis wrote: > Hi Doug, > > Thank you very much for your answer. I need to prepare a table here > to include the number of vertex and the cortical thickness, for some > further studies. Is there a way to do it in MATLAB? How can I run > MATLAB using FS under Linux? I have the startup.m file and a MATLAB > directory installed in the freesurfer folder but I don't know how I > can run MATLAB using FS. > > Thank you very much for your help. > Antonella > > > > ------------------------------------------------------------------------ > *From:* Douglas N Greve <gr...@nmr.mgh.harvard.edu> > *To:* Antonella Kis <ator...@yahoo.com> > *Cc:* Bruce Fischl <fis...@nmr.mgh.harvard.edu>; > "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > *Sent:* Wednesday, August 3, 2011 10:55 AM > *Subject:* Re: [Freesurfer] Error with aparcstats2table > > Hi Antonella, there is not an option for getting the number of > vertices because that is not a meaningful quantity. Why do you want it? > doug > > Antonella Kis wrote: > > > > Hi Bruce, > > > > Sorry to bother you again with the same question. Unfortunately I > did not get any reply from the freesurfer list (from Doug and/or Nick > as you mentioned) so I will really appreciate if you can help me with > the same question: > > in the aparc stats I have for each segmentation the Number of > Vertices, Surface Area, etc. > > I want this data to be exported in a table where in the first ro I > will have the thickness of each segmentation(bankssts , etc) and the > second row I want the Number of Vertices, for each subject. > > > > > > Many thanks, > > Antonella > > *From:* Bruce Fischl <fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>> > > *To:* Antonella Kis <ator...@yahoo.com <mailto:ator...@yahoo.com>> > > *Sent:* Friday, July 29, 2011 5:24 PM > > *Subject:* Re: [Freesurfer] Error with aparcstats2table > > > > doug and nick can help with that > > On Fri, 29 Jul 2011, Antonella Kis wrote: > > > > > Hi Bruce, > > > > > > Thanks again for helping. I mean in the aparc stats I have for > each segmentation the Number of Vertices, Surface Area, etc. I want > this data > > > to be exported in a table where in the first ro I will have the > thickness of each segmentation(bankssts , etc) and the second row I > want the > > > Number of Vertices, for each subject. > > > > > > Thanks. > > > Antonella > > > > > > > _______________________________________________________________________________________________________________________________________________ > > > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu> <mailto:fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>>> > > > To: Antonella Kis <ator...@yahoo.com <mailto:ator...@yahoo.com> > <mailto:ator...@yahoo.com <mailto:ator...@yahoo.com>>> > > > Cc: "freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>" > <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > Sent: Friday, July 29, 2011 3:18 PM > > > Subject: Re: [Freesurfer] Error with aparcstats2table > > > > > > Hi Antonella, > > > > > > what do you mean by no. of vertices? The total # in the surface? > You can get that with mri_info. It's loosely related to surface area, > but not > > > that interested a quantity. > > > > > > Bruce > > > > > > > > > On Fri, 29 Jul 2011, Antonella Kis wrote: > > > > > > > Hello everyone, > > > > > > > > > > > > I was trying to create a table with my statistical results (the > cortical thickness and the number of vertices) and I was running: > > > > > > > > aparcstats2table --hemi lh --subjects bert NPI001 --meas > thickness -t lh.aparcstas.THICKNESS.txt > > > > > > > > When I tried to also get the number of vertices a table by > running: aparcstats2table --hemi lh --subjects bert NPI001 --meas > vertices -t > > > > lh.aparcstas.VERTICES.txt I got the following error: > > > > > > > > aparcstats2table: error: option --measure: invalid choice: > 'Voxels' (choose from 'area', 'volume', 'thickness', 'thicknessstd', > 'meancurv') > > > > > > > > I Why I don't have an option for the no. of vertices? > > > > > > > > Can I get a table with both data: cortical thickness and no. of > vertices? > > > > > > > > Many thanks, > > > > Antonella > > > > > > > > > > > > > > > > > > > > > > > > > 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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@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 gr...@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
