Thank you Bruce, Douglas.

Yes, I think thicknesses were obtained with v 5.3.0. There might be errors as Bruce pointed out, I am going now through all maps to check them. This makes me think of a question. Volumetric template registrations sometimes go wrong. Does this happen also to surface registrations in FS sometimes ???

I am using other statistics, not glm, but thanks for suggesting it. Data are imported and exported in R using some R functions I built myself, nothing fancy, just using intermediate text files to get what I want and put it back for visualization.

Thank you

On Thu, Mar 9, 2017 at 11:23 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:


On 03/08/2017 09:27 PM, Dorian P. wrote:
> Hi Freesurfers,
>
> I am using R to perform thickness analyses. All subjects are
> transformed in fsaverage space and all values are placed in a matrix
> with 327684 columns (163842 for each hemisphere). I put the results
> back in a surface file (.asc format) and then convert it to a binary
> Freesurfer format. I then open the files in Freesurfer to view them.
>
> Overall the results make sense and fall in the right places. But I am
> concerned that some results fall into the corpus callosum, which, if I
> remember correctly should not have any thickness value, and therefore
> no results.
>
> Here is a screenshot:
> Inline image 1
>
> Can someone help my understand what might be wrong? Or, if this is
> normal, why I am finding thickness results where there is no thickness?
Is this 5.3? The thickness may not be 0 in the medial wall, but non-zero
values are meaningless and should be masked out or ignored.
>
> Is there a way to find label numbers for each vertex in fsaverage
> space (i.e. list of parcel number for each vertex). This might be
> useful to exclude certain vertices or compute summery statistics of
> the results directly in R.
You can load the annotation into matlab with read_annotation.m
>
> Third question, is it possible to threshold the above map based on
> minimal cluster area (i.e., in mri_surfcluster). If yes, do I need to
> prepare a binary file with p-values for thresholding (0-1), or can I
> use mri_surfcluster with t-score maps (0-Inf)?
You can use any map you want, you just have to specify the threshold
correctly. Also, you will need to have a FWHM. To get this I would run
an analysis in mri_glmfit using a design similar to what you used in R
(small differences probably won't affect the FWHM measure).
>
> Thank you for your help.
> Dorian
>
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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