Would it be possible to send me the overlay file?
On Oct 7, 2022, at 1:27 PM, Jun Yeon Won <won25@umd.edumailto: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/GroupAnalysishttps://secure-web.cisco.com/1GtdxN3OBQUG-GAQeHnvyIEHYFqFakZTImx2fOZLeWBHrbeeD5eHeJNCNdcRnHDFlzKC4C6WqiSc1P6sVBdo2LOAFE49Rwe2LOipeR4A5RrWeILCZiNICXMCdMi4A7igYMhCM67ZBs9bHRCHqLvIair3rqIDAEtpO7qO3nSnTcFO7kNs--7M7CczPJsfsyGcGnLx4t_98XrAAJLZ0GVzjH_XBSJv01OA-vuPn9MSB4hCXo1kLUBqmNhuQYOPk-Xpnd11wgFzXieOqRiSpPFD408-YUiFo21kUgn5nwWyCtHKkh-_Voz_1E8Wj3gZ9mz-w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysis) 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.edumailto: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.edumailto: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.htmlhttps://secure-web.cisco.com/1OHcN_bRSEDk0roNAjIAfufCwrh4xf7rzgQtoclY3flDVpCe2znW_Z-NEpNRC5ahFScfL8n7RZ7746EG5EibldfK0DyeuD8DOWxlEyzUiN6n_d2y4MRqLtRR8U2w2JQKD1dWyZjSMMQFhQKdnQGw_18koHPTGIRMmENF2G45P9aleWGnIh9S5DkSuIB8fqjPlWZZf9mEfzCdZl1dfoU5zRunt_p6sTDDJbI1pdAK_fiffsZyrD7IoVFSicGxBcz_6P8d2ROKxTtCbnNCmdL3Cw_CbU505e2Yr2rrdrRUWeHs1bWHNGTWzCNfcxGeiA2Zd/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg46328.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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