sorry for the delay, thanks for reposting


On 02/20/2018 11:33 AM, Sahil Bajaj wrote:
> Hello everyone,
>
> I was wondering if someone could please help me in figuring out
> following issues.
>
> Thanks a lot,
> Sahil
> ---------- Forwarded message ----------
> From: *Sahil Bajaj* <sahil.brain@gmail.com <mailto:sahil.brain@gmail.com>>
> Date: Thu, Feb 15, 2018 at 3:50 PM
> Subject: Subjectwise extraction from ROIs
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
>
>
> Hello experts,
>
> I identified two clusters (X for thickness and Y for volume) showing
> significant association between cortical measures (thickness and
> volume) and motor-performance. I followed steps from here:
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
> <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>
> and got several output files same as mentioned at the bottom of this
> page i.e. cache*.*
>
> I am interested in getting subject-wise thickness and volume values
> from these two clusters X and Y.
>
> From previous posts, I found that these subjectwise cluster values
> (e.g. thickness and volume) are saved in *.ocn.dat file. If that's
> correct, I have following questions:
>
> (1). When I look at *.ocn.dat file, subjectwise thickness values range
> between 2-3 and volume values are in the range between 0-2. I am not
> sure if that makes sense and what are the units of thickness and
> volume here?
Thickness is mm and the value is mean thickness, so that makes sense.
Volume is mm3, and the value is "mean" volume, which makes less sense.
You can multiply the mean volume by the number of vertices to get total
volume.

>
> (2). Since *.ocn.dat file for X gives subjectwise thickness value for
> cluster X and *.ocn.dat file for Y gives subjectwise volume values for
> cluster Y, so how can I get volume values for cluster X and thickness
> values for cluster Y?
Assuming that they are different cluster maps, you can run
mri_segstats --seg thicknessglm/contrast/csdbase.sig.ocn.mgh --exclude 0
--i  volumestack.mgh --avgwf volume.thickness-clusters.dat --sum
deleteme.sum
where volumestack would be the input to the volume-based glm.

>
> From pervious FS discussion, I found that it can be done using
> *.ocn.annot files e.g. to extract volume values from X, *.ocn.annot
> for X can be used in mris_anatomical_stats file. To make sure and
> confirm that this is the correct approach, I calculated thickness
> values for X using this approach, expecting that these should match
> with *.ocn.dat for X but it's not matching.
> I also converted *.annot to *.label in native space following steps
> from
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg53591.html
> <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg53591.html>
> but still values are not matching with *.ocn.dat.
Use the mri_segstats command above
>
> I would really appreciate any help.
>
> Thanks,
> Sahil
>
>
>
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