External Email - Use Caution I sent it to your email. Thanks!
Best, Jun On Fri, Oct 7, 2022 at 4:02 PM Wang, Ruopeng <rwa...@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 <wo...@umd.edu> wrote: > > External Email - Use Caution > > 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://secure-web.cisco.com/1XzMKerJeglZz3x3-wrT6B9w3X6pj99LPdLlPJdPdoAKfNMdY6bA8IhZgbdb5Yp6Jtu828I3wbD0MFuWW3xK0R4hU3LcnvFg7LyPQou76ThnG8uxud7Zu3G6TcHiH74hFTHlFDQdL47xb76MXqRBwHjJzuyz1876U2hogHDA2n1tpZScOXAjCfS_MIUBTIqxyNg9MifKP7LXXWUiajtn67_iAiUCNDCAp4S6_0QzJBNwM58D1evD2Rn3zG_VjqsRKhl0zjcQT1qHMWGk9IH6EjF7zktry8CPCreAx9_WfgK29mliJTkMgku4uJBWAewUM/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysis > <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 <rwa...@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 <wo...@umd.edu> wrote: >> >> External Email - Use Caution >> >> 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://secure-web.cisco.com/1kC5DdyBBttyfizE7ked3fdziDdK0MIVn-qrawMrp4rjenxtClAUEfvvHaPU1yFkQVMTCYk4aLyN1JTT4dTSZKY9L9KHGEP40MpuWZYs9kdtb0uMdI3DFprk2HtUlxTCPd3u1AyXlAKJD4rLXrzha_M6bVAgL8MVt7YNuvEtQ1-XIh_jIfVkILo0y_ZM4yhLEg1bN8v3pcgvt3_Jyi8kxnnJM5s4GkzfAqgtj8b90o7DDL-8pmXnKE7N5Hc4-ozUpyGKYc_N2sMW1Z5SPUNqUQAAyo0f2eYRXxquWZldf_mjFyImMnpWQUA3_AJAhg3Qr/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg46328.html >> <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__9Sv7H2PDB5gjqwxh5XykzxR2zONlNldjtFaNS2apS8KGFgbzKkmYuClNFfuMuMkk2anDP3SbhlQRK8NKrVKEXxpovt8wnmOCOrPhnjpUdN6Wi-URZmFVQ0pzVDp8d0whyKUfltuO9Rgf8ebAcFdRQU2Mai7UFBqVR6TEkmA4Si3x32_Iv6j_7ZUr3BF34kN4AsjYAzmmetRmuB8oMNwUVkgROT-H7ef5MHuy-yTf2v1eJoUqM4y5ZB6l3BhmdTAlv15Omsg_dE2NDbjo/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> <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__9Sv7H2PDB5gjqwxh5XykzxR2zONlNldjtFaNS2apS8KGFgbzKkmYuClNFfuMuMkk2anDP3SbhlQRK8NKrVKEXxpovt8wnmOCOrPhnjpUdN6Wi-URZmFVQ0pzVDp8d0whyKUfltuO9Rgf8ebAcFdRQU2Mai7UFBqVR6TEkmA4Si3x32_Iv6j_7ZUr3BF34kN4AsjYAzmmetRmuB8oMNwUVkgROT-H7ef5MHuy-yTf2v1eJoUqM4y5ZB6l3BhmdTAlv15Omsg_dE2NDbjo/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> <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-J6F8XZudnUgy1ilh6gEQimEr4mssG51ko9HEPfwGLeFHxGpnAdaHQwA4JUMlpdq19ZY6vEZ8OqHqsip_kONEC5GmXHAIQ9RHdBRLrkUwLArUmS1sZdtdLRmCf47-A3FVSTlL9NmbrrtZB8KdLlnaQCyTPuEY0Uj5h8_41wnXeaDQAsD9dLJ3i8L94FkeHuc0OMW3Iw7mHy1Ubt32OyPDVMrFIhPEru5QrSbDS1SmP3eaRGSLO-Q7g0zRhGIjaMcI8ok9Vl9zNfqwn-F1xWNEs-8G2/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline >> <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-J6F8XZudnUgy1ilh6gEQimEr4mssG51ko9HEPfwGLeFHxGpnAdaHQwA4JUMlpdq19ZY6vEZ8OqHqsip_kONEC5GmXHAIQ9RHdBRLrkUwLArUmS1sZdtdLRmCf47-A3FVSTlL9NmbrrtZB8KdLlnaQCyTPuEY0Uj5h8_41wnXeaDQAsD9dLJ3i8L94FkeHuc0OMW3Iw7mHy1Ubt32OyPDVMrFIhPEru5QrSbDS1SmP3eaRGSLO-Q7g0zRhGIjaMcI8ok9Vl9zNfqwn-F1xWNEs-8G2/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline >> <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). 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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . 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.
