Thanks. I created a video to loop through all my 170+ subjects in template space:

https://drive.google.com/open?id=0BxHeqEv37qqDeGFWVnpSVkVobkk

I see some cases that have dramatic problems. I will need to check those more carefully and probably do an inspection of each one in individual space. Beside those, do you think the variability of values going in and out of the medial wall is normal for most of the subjects? You can point at specific cases with the number of the subject on the overlay menu (left). Thickness values start at 0.001

Thanks for your help so far.

Dorian

On Thu, Mar 9, 2017 at 4:29 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi Dorian

you can load the aparc.annot for each subject and use it to chek if the
spherical registration worked ok. It's easy enough to write a script to
load these for each subject, then write a tif file with a medial view, and
zip through them all with nmovie

cheers
Bruce
On Thu, 9 Mar 2017, Dorian P. wrote:

> 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.
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