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Hi Daliah,
sorry for the late response. In case it's still relevant, I have a few remarks:
a) The results can be viewed on an inflated surface both in Matlab and in Freeview, whatever you prefer.
There is a correspondence between the vertices of the two surfaces, so whatever can be overlaid on 'lh.sphere' can be overlaid on 'lh.inflated' as well.
To view it in Freeview, you would need to export the data from Matlab using the 'fs_write_Y' command. There is an example in the tutorial for a similar case.
To view it in Matlab using the 'patch' command, you'd need to import the (e.g.) lh.inflated file from the fsaverage directory. This can be done as follows:
lhinflated = fs_read_surf('PUT_YOUR_FREESURFER_DIRECTORY_HERE/subjects/fsaverage/surf/lh.inflated');
surfInflated.faces = lhinflated.tri; surfInflated.vertices = lhinflated.coord';
Then use 'surfInflated' instead of 'surf' for plotting with the 'patch' command.
b) This may be the more important remark:
If I am understanding your procedure correctly, then what you are plotting at this stage, i.e. after the 'lme_mass_fit_EMinitÄ and 'lme_mass_RgGrow' commands , are not 'clusters of significant vertices', but just covariance estimates that will be used during the final model fitting step, which is done at a later stage with the 'lme_mass_fit_Rgw' command.
The significance of the effects that you are interested in can only be established after running the 'lme_mass_F' command, followed by a correction for multiple comparisons.
Best,
Kersten
On Mo, 2019-06-10 at 11:56 -0400, Daliah Ross wrote:
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Hello FreeSurfer Developers,
I am working on running a mass-univariate linear mixed effects model with cortical thickness data, and I have a question about the step that segments the initial covariance estimates into homogenous regions. The next step from the LME webpage (figure; p1 = patch(surf); …) creates figures of the left hemisphere projected onto a sphere and shows clusters of the significant vertices. I am having trouble interpreting this spherical figure. Can it be opened in freesurfer, (i.e. in freeview or tksurfer), so that I can see these clusters projected onto, for example, the inflated cortex (e.g. of fsaverage)?
Thank you, Daliah Ross
Daliah Ross | dross3@mail.yu.edumailto:dross3@mail.yu.edu
Ph.D. Student, Clinical Psychology with Health Emphasis Ferkauf Graduate School of Psychology Yeshiva University Albert Einstein College of Medicine
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