External Email - Use Caution
I sent it to your email. Thanks!
Best, Jun
On Fri, Oct 7, 2022 at 4:02 PM Wang, Ruopeng RWANG4@mgh.harvard.edu wrote:
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:
External Email - Use CautionHi 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://secure-web.cisco.com/1XzMKerJeglZz3x3-wrT6B9w3X6pj99LPdLlPJdPdoAKfNM... https://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.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:
External Email - Use CautionDear 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 0.05But, 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://secure-web.cisco.com/1kC5DdyBBttyfizE7ked3fdziDdK0MIVn-qrawMrp4rjenx... https://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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1wbwFcKICiaPMpvMX0Rpf-oSDktZAM4yQ0Jlzc-aunC3x9I... https://secure-web.cisco.com/13NEvITjKAgurs-U1UnvIfWvlvqnLo9_QMysNMNzDnZZ_-r9hApfR8XVvFxDK4dm91A_n7ksKt1BVI4PmdQ0Aotow7HfHIVPvfo0blahKmEWwPpWC0ISlL_BVdwkaUPX_HSLCHINhCn1ilpBs7hzwUXkKLHxwO4fkNbq7xHdqvlFeLbacf-SOj9xFNNBktBWPwFBcDEJoUkEFTujdahsDNruGsWUQOlGIGkL9E9RcjLSRdvFl2rJHLJif3mU_63F81KvU8xZpWcfXdSOSaP8bzRGohuouOWydO4KVIVpLcY6v1cILJq1svy4rvHInImo-/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1wbwFcKICiaPMpvMX0Rpf-oSDktZAM4yQ0Jlzc-aunC3x9I... https://secure-web.cisco.com/13NEvITjKAgurs-U1UnvIfWvlvqnLo9_QMysNMNzDnZZ_-r9hApfR8XVvFxDK4dm91A_n7ksKt1BVI4PmdQ0Aotow7HfHIVPvfo0blahKmEWwPpWC0ISlL_BVdwkaUPX_HSLCHINhCn1ilpBs7hzwUXkKLHxwO4fkNbq7xHdqvlFeLbacf-SOj9xFNNBktBWPwFBcDEJoUkEFTujdahsDNruGsWUQOlGIGkL9E9RcjLSRdvFl2rJHLJif3mU_63F81KvU8xZpWcfXdSOSaP8bzRGohuouOWydO4KVIVpLcY6v1cILJq1svy4rvHInImo-/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1-yLAbQF-2O5NFn65pKqGE4i9kXvPwPLj15qw-N-J6F8XZu... https://secure-web.cisco.com/19sMtHybNLtCo8ojm1GWpSoKA174P5ZeBhE92krel4HQl9DKGAGSbKgJqHNSNFGgMKPxmU1wCYP8yoI3V9alARe-fvEZ1n3oDZ1YMowtpxcpb-AOvvlbeQ_O6QDsqoCUnZN0HuwvOJYof1LP3RwR6CpkMkur4NaHmxwweydu00YvUF0HIPsdRv9vx2S6L3gbCM2WyqbBQOjhb7xMmOazriFOPAGWyazNi3YXmczWyD6r0WVIKdhG6WL5RJT22TBH3iZ1N78XQ_8ZWe13HEk5mc_4-dOQEhF0Gl6i1tke8Nwm5yxF_FSnXSedUdc1oZPa6/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1-yLAbQF-2O5NFn65pKqGE4i9kXvPwPLj15qw-N-J6F8XZu... https://secure-web.cisco.com/19sMtHybNLtCo8ojm1GWpSoKA174P5ZeBhE92krel4HQl9DKGAGSbKgJqHNSNFGgMKPxmU1wCYP8yoI3V9alARe-fvEZ1n3oDZ1YMowtpxcpb-AOvvlbeQ_O6QDsqoCUnZN0HuwvOJYof1LP3RwR6CpkMkur4NaHmxwweydu00YvUF0HIPsdRv9vx2S6L3gbCM2WyqbBQOjhb7xMmOazriFOPAGWyazNi3YXmczWyD6r0WVIKdhG6WL5RJT22TBH3iZ1N78XQ_8ZWe13HEk5mc_4-dOQEhF0Gl6i1tke8Nwm5yxF_FSnXSedUdc1oZPa6/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1wbwFcKICiaPMpvMX0Rpf-oSDktZAM4yQ0Jlzc-aunC3x9I...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1wbwFcKICiaPMpvMX0Rpf-oSDktZAM4yQ0Jlzc-aunC3x9I... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1-yLAbQF-2O5NFn65pKqGE4i9kXvPwPLj15qw-N-J6F8XZu... < https://secure-web.cisco.com/1-yLAbQF-2O5NFn65pKqGE4i9kXvPwPLj15qw-N-J6F8XZu... . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.