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
>
>
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