Would it be possible to send me the overlay file?

On Oct 7, 2022, at 1:27 PM, Jun Yeon Won <won25@umd.edu> wrote:

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Hi  Ruopeng,

I tried to adjust overlay thresholds in the Configure Overlay window, but I think it still looks weird. The gray part should be blue and the blue part should be gray since when I clicked the gray part it showed -1.6 and the blue 0. Could you please let me know how to flip this?

<image.png>

I also tried to overlay annot file according to the instruction on this page (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis) using the below script.

freeview -f $SUBJECTS_DIR/fsaverage/surf/rh.inflated:overlay=cache.th20.abs.sig.cluster.mgh:overlay_threshold=2,5:annot=cache.th20.abs.sig.ocn.annot -viewport 3d

<image.png>

So this result shows the gray part in the first photo should be blue. Could you please advise?

Best,

Jun

On Thu, Oct 6, 2022 at 4:38 PM Wang, Ruopeng <RWANG4@mgh.harvard.edu> wrote:

You can adjust overlay thresholds in Configure Overlay window.

Ruopeng

On Oct 6, 2022, at 10:49 AM, Jun Yeon Won <won25@umd.edu> wrote:

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Dear Freesurfer experts,

I am running a linear regression analysis and found a significant result showing below (cache.th20.abs.sig.cluster.summary file). 

 

<image.png>

I ran the below script to get this result. Right hemisphere was focused for this analysis.

          mri_glmfit-sim --glmdir rh.thickness.10.glmdir \
          --cache 2 abs \
          --cwp 0.05 

 

But, when visualizing the cache.th20.abs.sig.cluster.mgh file, it shows below - the hemisphere is in yellow. 

 

<image.png>

The below is a visualization of sig.mgh. The underlay should be gray but I am not sure why the underlay looks yellow when overlaying the thresholded result.

 

<image.png>

 I saw somebody posted the same issue here (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg46328.html), but I was not able to find the solution from here.  Could you please let me know what is an issue and how to resolve this?

Best,

Jun

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