You can do it in matlab with read_curv.m (to read in the thickness) and read_annotation.m (to read in, eg, lh.aparc.annot), then pull out the vertices you want (make sure to account for the 1-based in matlab)
On 04/27/2018 02:35 PM, Bruce Fischl wrote: > oh sorry, I misunderstood. Hmm, that's a bit trickier. I think if you > create the label with the thickness overlaid, then the label file will > contain the thickness at each vertex, but that might only work in dev > in freeview. Perhaps Ruopeng can comment? > > cheers > Bruce > > On Fri, 27 Apr 2018, Fujiwara, Hisako wrote: > >> External Email - Use Caution >> >> Thank you, Bruce for your prompt reply. I used mris_anatomical_stats >> first but this only gave me an averaged thickness and std etc. I'd >> like to get absolute cortical thickness for each vertex within ROIs. >> I do not interested to compute vertex-wise volume using -th3. What >> option should I use to get a list of absolute cortical thickness for >> each vertex within ROI? >> >> Thank you again, >> Hisako >> >> -----Original Message----- >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce >> Fischl >> Sent: Friday, April 27, 2018 2:23 PM >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] vertex wise cortical thickness within ROIs >> >> Hi Hisako >> >> you can use mris_anatomical_stats for this purpose. >> >> cheers >> Bruce >> >> >> On Fri, 27 Apr 2018, Fujiwara, Hisako wrote: >> >>> >>> External Email - Use Caution >>> >>> Hello FreeSurfer Developers, >>> >>> >>> >>> I'm attempting to compute absolute cortical thickness for each >>> vertices within anatomical ROIs using apac.annot. I have >>> successfully output the whole brain vertex wise cortical thickness >>> using: >>> >>> >>> >>> mris_convert –c <subject>/surf/?h.thickness <subject>/surf/?h.org >>> <subject>/surf/?hthickenss.asc >>> >>> >>> >>> Since this creates huge numbers (> e.g., 140,000) for each hemisphere >>> for each participants, I would like to narrow out focus on the >>> specific ROIs for relevant to our study? Is this achievable to add >>> options to do? >>> >>> >>> >>> Thank you for your help in advance. >>> >>> >>> >>> Best regards, >>> >>> Hisako >>> >>> >>> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ 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.
