On 02/20/2018 05:54 PM, Sahil Bajaj wrote:
> Dear Dr. Greve,
>
> I have following follow-up questions ('red' colored) for you and would
> really appreciate any help.
>
> On Tue, Feb 20, 2018 at 2:59 PM, Douglas N Greve
> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> 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.br...@gmail.com
> <mailto:sahil.br...@gmail.com> <mailto:sahil.br...@gmail.com
> <mailto:sahil.br...@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>
> > <mailto: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>
> >
> <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.
>
>
> Thanks for the clarification Dr. Greve. Could you please tell me how
> can I find number of vertices for each cluster (subjectwise) so that I
> can multiple that with mean volume values.
This will be in the csdbase.sig.cluster.summary file.
>
> >
> > (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.
>
>
> Just to confirm volumestack is the file (lh.X_vol.10.mgh) generated
> after following steps, correct?
> mris_preproc --fsgd X.fsgd --target fsaverage --hemi lh --meas volume
> --out X/lh.X_vol.mgh
> mri_surf2surf --hemi lh --s fsaverage --sval X/lh.X_vol.mgh --fwhm 10
> --cortex --tval X/lh.X_vol.10.mgh
>
> Could you please confirm if that's correct?
Yes.
> If that's correct, then mri_segstats command as you described above
> gives mean volume values again, so again I need number of vertices
> here and I am not sure how to get number of vertices for
> corresponding clusters.
You can get them from the above. In this case, you can also add
--accumulate to the mri_segstats command line
>
> Thanks a lot.
> Sahil
>
>
> >
> > 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>
> >
> <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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>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358 <tel:617-724-2358>
> Fax: 617-726-7422 <tel:617-726-7422>
>
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--
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
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