you can use mri_segstats with the --slabel option On 3/5/19 10:35 AM, Bruce Fischl wrote: > Hi Kan > > you can give the surface-based label to mris_anatomical_stats and it > will constrain it's calculations to the label (where it makes sense): > > mris_anatomical_stats -l <path to your label> ... > > you can probably do it with mri_segstats too - Doug will know > > cheers > Bruce > > > On Tue, 5 Mar 2019, 310913949 wrote: > >> >> External Email - Use Caution >> >> Hi bruce?? >> I still have some questions about extracting cortical features of >> a ROI. I used the >> mri_label2label to sample the volumetric label to the surface of the >> subject. But I dont know how to >> do next, as i found that the RAS coordinates do not correspond to >> the coordinates in the >> lh.thickness, and why? >> Besides, I found the web of how to extract cortical thickness >> values for a region-of-interest >> (ROI) defined in volume >> space(https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness).But >> >> it doesn't report >> the coordinates information. How can I get the ROI's coordinates >> information if i use this method? >> Thanks for your help! >> Kan Deng >> >> >> >> ------------------ Original ------------------ >> From: "Bruce Fischl"<fis...@nmr.mgh.harvard.edu>; >> Date: Fri, Jan 25, 2019 10:58 PM >> To: "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>; >> Subject: Re: [Freesurfer] How to extract cortical features of a ROI >> >> Hi Kan >> >> if you draw a volumetric label you first need to sample it to the >> surface >> of that subject (mri_label2label --sample). If all you want are stats >> from >> the subject there is no need to map it to fsaverage - that is only >> necessary if you want to use a group coordinate system. >> >> cheers >> Bruce >> >> >> >> On Fri, 25 Jan 2019, >> 310913949 wrote: >> >> > >> > External Email - Use Caution >> > >> > >> > Dear Freesurfer Experts, >> > I want to extract cortical features of a ROI that I drawn >> manually on the rawavg.mgz in >> Freesurfer, but i >> > don't know how to do that. I think maybe first the lesion mask >> should be registered to the >> standard templates >> > fsaverage, but I don't know what the command line is , could you >> tell me? And secondly, I should >> use >> > mri_label2label to map the label to individual subject and extract >> the cortical features of the >> ROI, am I right? >> > I am looking forward to your reply!Thanks. >> > >> > Best wishes! >> > Kan Deng >> > >> > >> _______________________________________________ >> 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
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