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> -----原始邮件----- > 发件人: freesurfer-requ...@nmr.mgh.harvard.edu > 发送时间:2025-01-06 22:12:15 (星期一) > 收件人: freesurfer@nmr.mgh.harvard.edu > 主题: Freesurfer Digest, Vol 251, Issue 6 > > Send Freesurfer mailing list submissions to > freesurfer@nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > > https://secure-web.cisco.com/19u5yrx1hEBh57aEQRnpFtUiQK-dS5rJ76xYC65HhTa_BvN0TGk9Vfi2AeR1OU6jHQ3n-0iZiJTAqEvRy3TEq-i-2b6QbNPEsnT_BcKYzT7qpyOdJJQoDA3rt2sLfg5opm0kQcz53NiimjtO57eoQIuNz8AmCQZ8YhctP2rj1FI5wQuEsFJqGYSLNvd4QO2RphNpOhZktdJI9Qv0nAS6qIAU3Jmf8cHu6icA1Jr86jXgn1FakAP8-K3JBixOxnS44Xy0a1yEoL_aCa3t6DeqGPAZ7iTA901eH9fQjIaZ7GVm1gFI69_KYWTo9Aw-zE3SQb4rmGNK-YO1WfY1Fyd3aiw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-requ...@nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-ow...@nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: [ext] Re: Freeview crash (Tietze, Anna) > 2. How to Plot Surface with ROI Boundaries Using Harvard-Oxford > Brain Atlas? (Zeng, Xinglin) > 3. Re: [ext] Re: Freeview crash (Wang, Ruopeng) > 4. Re: [ext] Re: Freeview crash (Dicamillo, Robert) > 5. registration error (Ramesh Babu) > 6. Re: [External] Re: Assistance with mri_vol2surf: Missing > Surface Values in Output (Douglas N. Greve) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 3 Jan 2025 20:58:14 +0000 > From: "Tietze, Anna" <anna.tie...@charite.de> > Subject: Re: [Freesurfer] [ext] Re: Freeview crash > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <89fa2c60-63ff-4959-8039-0724e56ef...@charite.de> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Hi Ruopeng, > > It works with the app when I move the licence.txt! It doesn?t work from the > terminal so far, but this helps a lot. Thank you very much! > > Best, Anna > > From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Wang, Ruopeng" > <rwa...@mgh.harvard.edu> > Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Date: Friday, 3. January 2025 at 18:17 > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] [ext] Re: Freeview crash > > I mean /Applications/freesurfer/license.txt. > > > On Jan 3, 2025, at 11:36 AM, Tietze, Anna > <anna.tie...@charite.de<mailto:anna.tie...@charite.de>> wrote: > > > It?s there: > licence.txt located in: /Applications/freesurfer/7.4.0/license.txt (can be > read, as recon-all works) > Or do you mean /Applications/freesurfer/license.txt? > > Von: > freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > > <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> > Im Auftrag von Wang, Ruopeng > Gesendet: Freitag, 3. Januar 2025 16:58 > An: Freesurfer support list > <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> > Betreff: Re: [Freesurfer] [ext] Re: Freeview crash > > To run as an app bundle, since there is no global environment settings, you > need to put the license file in /Applications/freesurfer folder. Then you > should be able to load data. > > On Jan 3, 2025, at 12:47 AM, Tietze, Anna > <anna.tie...@charite.de<mailto:anna.tie...@charite.de>> wrote: > > External Email - Use Caution > Yes, I?ve tried that as well. Freeview opens as an app bundle, but it crashes > when I load a file. Interestingly, this is inconsistent?sometimes I can load > a file without any issues, but most of the time, it crashes in the same way. > I?ve this problem on two different Macs: > > * System 1: macOS Sonoma 14.5 with FreeSurfer 7.3.2. > * System 2: macOS Sonoma 14.7.1 with FreeSurfer 7.4.0. > > From: > <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> > on behalf of "Wang, Ruopeng" > <rwa...@mgh.harvard.edu<mailto:rwa...@mgh.harvard.edu>> > Reply-To: Freesurfer support list > <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> > Date: Thursday, 2. January 2025 at 19:04 > To: Freesurfer support list > <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> > Subject: [ext] Re: [Freesurfer] Freeview crash > > Have you tried running freeview as an app bundle? Or can you try running > freeview directly from the binary location? Like this: > > $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview > > On Jan 2, 2025, at 7:14 AM, Tietze, Anna > <anna.tie...@charite.de<mailto:anna.tie...@charite.de>> wrote: > > > Hi, > > When I want to open files with freeview, it crashes immediately. I tried my > own recon-all output and the bert dataset. Can you help me? > > Operating system: Mac, Sonoma 14.7.1 > Fressurfer version 7.4.0 > XQuatz 2.8.5 > licence.txt located in: /Applications/freesurfer/7.4.0/license.txt (can be > read, as recon-all works) > environment is set by FREESURFER_HOME=/Applications/freesurfer/7.4.0 and > source $FREESURFER_HOME/SetUpFreeSurfer.sh > > When I run the command freeview, the following message is given: > /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6615 Segmentation > fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" > > Or trying to open a file: > freeview -v > /Users/annatietze/Documents/freesurfer/freesurfer_subjects/nini_ra/mri/orig/001.mgz > /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6765 Segmentation > fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" > > freeview -v /Applications/freesurfer/7.4.0/subjects/bert/mri/orig/001.mgz > /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6799 Segmentation > fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" > > Attached is a detailed error report. > > What did I overlook?? Thank you so much for help! > > Best, Anna > <problem report freeview.rtf> > External Email - Use Caution > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto: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/1hhsmBghDvdXvV8bIdu3XWLPammaCaGvm3GPUp7fLDRWRr4KujzWNQGEvUK5rd3G-_cXl3PAwnjaYULHKTQELBUcOawcDOJWApoD_fsATRk1tAKcadLeQRW8dJA0AVpl9zdtRMa5ztZ3MPx0CEAmdH40EwZ99OrNoCN-HA6lm1RZUyHRP6CdesneUhhCm1mhGEoyFJQXD6dlMRUa6UuRNu8fVar0zTwISqwEqNg6p2l0LOAbfK1esjbup4bhWhL0SaRrTlUzv322_mgMpzD8C8zJIQB6a2VPSd2F6ZOFW_5RI1izWLJNEjvWTPra_z4RW/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/16k7GeT10xnyGxKgd_FlVZCkydV-RDVkVN5jCKeQIWh34il3jxFy101naM-yIxvXqpP2HyIp-eGB9RvrusOKbKf9XRXAN55tTbtdwTjP9dePStqI5NKRTIAsPPY6kJCfItER09-PaaHsooudqs_kiKeXxx9OrieieJPMPBxG5dmGT1GrY9s8bK8r1SYNmjTW7Z5IckX9mnkBlpxYMS97B8lnTFbjQj_BXa0Ya7vv7IcJqIbM1InBbPxGvF7ToPyG4Rzy-r98xWDbyFexID6H8dkhLe_yHX7HhwFJDKMTfV5ZsfIQ5KGVzR-HCeEIAP5S4_HVTTDoacjsxxjrOd1OcYw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto: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/1hhsmBghDvdXvV8bIdu3XWLPammaCaGvm3GPUp7fLDRWRr4KujzWNQGEvUK5rd3G-_cXl3PAwnjaYULHKTQELBUcOawcDOJWApoD_fsATRk1tAKcadLeQRW8dJA0AVpl9zdtRMa5ztZ3MPx0CEAmdH40EwZ99OrNoCN-HA6lm1RZUyHRP6CdesneUhhCm1mhGEoyFJQXD6dlMRUa6UuRNu8fVar0zTwISqwEqNg6p2l0LOAbfK1esjbup4bhWhL0SaRrTlUzv322_mgMpzD8C8zJIQB6a2VPSd2F6ZOFW_5RI1izWLJNEjvWTPra_z4RW/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/1QJz6xShsji1s-ybZT93kuMT6Br9o_orKDeEAjsEP1AQitVjyVeHTdGRVTyOgmTpiCikQDZWiFccCRyhtW_q_C3nlwIEgjD_S4xBcegNL4wFTlj9DY7PSanZGnfTTMPaigtNE89HaUY3bMazDc2VUtm0-zzcnx5xUYw-BSmO7AIPjOd97McD1sMCWlCXNeqalX98VmbZdCqT1VBdwtam8sY3ZCnp8h4GgZ8CQPmYdAFWhnW8ErSl3nRNKIVT6oflvJ79MigCrt8VcFVJonMLnKXigZ5_wNg_TuteqpSrwrStpy4THTu7x47gf70NU9uz3/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > > <smime.p7s> External Email - Use Caution > External Email - Use Caution > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://secure-web.cisco.com/1hhsmBghDvdXvV8bIdu3XWLPammaCaGvm3GPUp7fLDRWRr4KujzWNQGEvUK5rd3G-_cXl3PAwnjaYULHKTQELBUcOawcDOJWApoD_fsATRk1tAKcadLeQRW8dJA0AVpl9zdtRMa5ztZ3MPx0CEAmdH40EwZ99OrNoCN-HA6lm1RZUyHRP6CdesneUhhCm1mhGEoyFJQXD6dlMRUa6UuRNu8fVar0zTwISqwEqNg6p2l0LOAbfK1esjbup4bhWhL0SaRrTlUzv322_mgMpzD8C8zJIQB6a2VPSd2F6ZOFW_5RI1izWLJNEjvWTPra_z4RW/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. 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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. > > External Email - Use Caution > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://secure-web.cisco.com/1hhsmBghDvdXvV8bIdu3XWLPammaCaGvm3GPUp7fLDRWRr4KujzWNQGEvUK5rd3G-_cXl3PAwnjaYULHKTQELBUcOawcDOJWApoD_fsATRk1tAKcadLeQRW8dJA0AVpl9zdtRMa5ztZ3MPx0CEAmdH40EwZ99OrNoCN-HA6lm1RZUyHRP6CdesneUhhCm1mhGEoyFJQXD6dlMRUa6UuRNu8fVar0zTwISqwEqNg6p2l0LOAbfK1esjbup4bhWhL0SaRrTlUzv322_mgMpzD8C8zJIQB6a2VPSd2F6ZOFW_5RI1izWLJNEjvWTPra_z4RW/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://secure-web.cisco.com/1vaYuel2s3t0nDuGAqtMekQ55VLo0Wx1qKzaAI-Ka6Hq3yQCYPI_Lk1pzwMSswhglakSLnpsc5-RpiI1xag3g8vGP9HXu0cqKS4KoKajsBbpKOAJEnZLuFDwUDvoLUYDeBnhwGPFtWzwCEsold1Oj3GhjhfjvixNZihAVV1tlfBqHJiPpw--6-WURg4Ez0kG7H_5cwV5WP6iAZrmTc1xeC7mCEnXTEqD97wuoLOB7kVh2SRafCXIOvs9fCmBrAgTjjt6qcD3-i72b0p2wUi-E6QTkmVRxwAmNCVxVjtNxhM691OCyRsV-QRWgXY_EiSEnnuVFrqL9D0kzkthCS6gOqw/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20250103%2F4c0ce5aa%2Fattachment-0001.html > > > ------------------------------ > > Message: 2 > Date: Fri, 3 Jan 2025 21:41:10 +0000 > From: "Zeng, Xinglin" <xz...@som.umaryland.edu> > Subject: [Freesurfer] How to Plot Surface with ROI Boundaries Using > Harvard-Oxford Brain Atlas? > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > > <sj0pr03mb62387b0a0fc3fed260418150e4...@sj0pr03mb6238.namprd03.prod.outlook.com> > > Content-Type: text/plain; charset="gb2312" > > External Email - Use Caution > > Dear Community, > I am currently working on visualizing ROI boundaries on the brain surface > using the Harvard-Oxford brain atlas. My goal is to generate a surface plot > that overlays ROI boundaries from the atlas in a clear and accurate manner. > I also tried visualizing in Freeview, connectome_workbench, and I could plot > the surface but I was unable to plot the boundaries correctly. > Specific challenges I?m facing: > I don?t know how to combine the ROI boundaries with a functional surface > overlay while keeping the boundaries visible. > [image]<https://secure-web.cisco.com/1fPE3CB8QmpDeyTgP4PtZ-z8NpAcvN9BTPzZ9KyYFvuwJFdGkBgzzlDbAeHjSiWowHCcdjFYy_0RVY14gTa8kqXTTA13YCutucyc0iAhl2VIiptxBZDfj-6nDULTqrOmDy2y1hp-6RgviwTMG2hlNJJ_JrJW__yC-ps45Vs_pVJortE5NFYQDIvl0OecVj561gcZQy7sHy4ramEkNvcrAYRvEe96Hbzr65cCa8ALg4BWI6gWkqpnNcNz3QUDmcVuD0DEEsQVDX1BmpPA7c6Szb5kSk98nYeTWy56xuPubm2RUQD68e-yo9ftyYe5H10EW/https%3A%2F%2Fneurostars.org%2Fuploads%2Fdefault%2Foriginal%2F2X%2Fc%2Fcbbb2f05337bfed159466379ac2e74a7b160b3a2.jpeg> > image800?330 95 > KB<https://secure-web.cisco.com/1fPE3CB8QmpDeyTgP4PtZ-z8NpAcvN9BTPzZ9KyYFvuwJFdGkBgzzlDbAeHjSiWowHCcdjFYy_0RVY14gTa8kqXTTA13YCutucyc0iAhl2VIiptxBZDfj-6nDULTqrOmDy2y1hp-6RgviwTMG2hlNJJ_JrJW__yC-ps45Vs_pVJortE5NFYQDIvl0OecVj561gcZQy7sHy4ramEkNvcrAYRvEe96Hbzr65cCa8ALg4BWI6gWkqpnNcNz3QUDmcVuD0DEEsQVDX1BmpPA7c6Szb5kSk98nYeTWy56xuPubm2RUQD68e-yo9ftyYe5H10EW/https%3A%2F%2Fneurostars.org%2Fuploads%2Fdefault%2Foriginal%2F2X%2Fc%2Fcbbb2f05337bfed159466379ac2e74a7b160b3a2.jpeg> > I would really appreciate any tips, example commands, or references to > similar workflows. Thank you in advance for your help! > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://secure-web.cisco.com/1EXKmdhIjSQ4dLrzLRqWRnPYTDlhpdUDCDaWaE89dujquQ4_IQH9NWcCwZLBGo699eFw61kdaxPmypwStFkg5FCZ4xMpO-kHdSZibnE_YheG_4QAP76dXB4K6ytZA3141-qtrs8aA5ZuEUcrChEVUVbYbGlcBI0WF3gG2Zq3UP7fYtsKmIrmGlc9PiWkTvpnP2Cv5TBz-VHgfCVcXEqOxNOa7KpsWdci6kbXP5Cm1kp9K7OzETSEH07nrp3nHJHVc8_eT0152GjOFWDLtEiyVasy4q0Tct08aZ22yDXVQ2UyUwTP7W6tRU_RkPeFK1CnLLfUmUq9wS4qKWdGHpD7fgQ/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20250103%2F74077d1f%2Fattachment-0001.html > > > ------------------------------ > > Message: 3 > Date: Fri, 3 Jan 2025 22:32:08 +0000 > From: "Wang, Ruopeng" <rwa...@mgh.harvard.edu> > Subject: Re: [Freesurfer] [ext] Re: Freeview crash > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <5f23557a-5575-4de9-9aa6-24b278431...@mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > You can run freeview from the the command-line by directly calling the binary > in the app bundle, for example: > > $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview > > > On Jan 3, 2025, at 3:58 PM, Tietze, Anna > <anna.tie...@charite.de<mailto:anna.tie...@charite.de>> wrote: > > > External Email - Use Caution > > Hi Ruopeng, > > It works with the app when I move the licence.txt! It doesn?t work from the > terminal so far, but this helps a lot. Thank you very much! > > Best, Anna > > From: > <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> > on behalf of "Wang, Ruopeng" > <rwa...@mgh.harvard.edu<mailto:rwa...@mgh.harvard.edu>> > Reply-To: Freesurfer support list > <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> > Date: Friday, 3. January 2025 at 18:17 > To: Freesurfer support list > <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] [ext] Re: Freeview crash > > I mean /Applications/freesurfer/license.txt. > > > On Jan 3, 2025, at 11:36 AM, Tietze, Anna > <anna.tie...@charite.de<mailto:anna.tie...@charite.de>> wrote: > > > It?s there: > licence.txt located in: /Applications/freesurfer/7.4.0/license.txt (can be > read, as recon-all works) > Or do you mean /Applications/freesurfer/license.txt? > > Von: > freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > > <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> > Im Auftrag von Wang, Ruopeng > Gesendet: Freitag, 3. Januar 2025 16:58 > An: Freesurfer support list > <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> > Betreff: Re: [Freesurfer] [ext] Re: Freeview crash > > To run as an app bundle, since there is no global environment settings, you > need to put the license file in /Applications/freesurfer folder. Then you > should be able to load data. > > On Jan 3, 2025, at 12:47 AM, Tietze, Anna > <anna.tie...@charite.de<mailto:anna.tie...@charite.de>> wrote: > > External Email - Use Caution > Yes, I?ve tried that as well. Freeview opens as an app bundle, but it crashes > when I load a file. Interestingly, this is inconsistent?sometimes I can load > a file without any issues, but most of the time, it crashes in the same way. > I?ve this problem on two different Macs: > > * System 1: macOS Sonoma 14.5 with FreeSurfer 7.3.2. > * System 2: macOS Sonoma 14.7.1 with FreeSurfer 7.4.0. > > > From: > <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> > on behalf of "Wang, Ruopeng" > <rwa...@mgh.harvard.edu<mailto:rwa...@mgh.harvard.edu>> > Reply-To: Freesurfer support list > <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> > Date: Thursday, 2. January 2025 at 19:04 > To: Freesurfer support list > <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> > Subject: [ext] Re: [Freesurfer] Freeview crash > > Have you tried running freeview as an app bundle? Or can you try running > freeview directly from the binary location? Like this: > > $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview > > On Jan 2, 2025, at 7:14 AM, Tietze, Anna > <anna.tie...@charite.de<mailto:anna.tie...@charite.de>> wrote: > > > Hi, > > When I want to open files with freeview, it crashes immediately. I tried my > own recon-all output and the bert dataset. Can you help me? > > Operating system: Mac, Sonoma 14.7.1 > Fressurfer version 7.4.0 > XQuatz 2.8.5 > licence.txt located in: /Applications/freesurfer/7.4.0/license.txt (can be > read, as recon-all works) > environment is set by FREESURFER_HOME=/Applications/freesurfer/7.4.0 and > source $FREESURFER_HOME/SetUpFreeSurfer.sh > > When I run the command freeview, the following message is given: > /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6615 Segmentation > fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" > > Or trying to open a file: > freeview -v > /Users/annatietze/Documents/freesurfer/freesurfer_subjects/nini_ra/mri/orig/001.mgz > /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6765 Segmentation > fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" > > freeview -v /Applications/freesurfer/7.4.0/subjects/bert/mri/orig/001.mgz > /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6799 Segmentation > fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" > > Attached is a detailed error report. > > What did I overlook?? Thank you so much for help! > > Best, Anna > <problem report freeview.rtf> > External Email - Use Caution > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto: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/19u5yrx1hEBh57aEQRnpFtUiQK-dS5rJ76xYC65HhTa_BvN0TGk9Vfi2AeR1OU6jHQ3n-0iZiJTAqEvRy3TEq-i-2b6QbNPEsnT_BcKYzT7qpyOdJJQoDA3rt2sLfg5opm0kQcz53NiimjtO57eoQIuNz8AmCQZ8YhctP2rj1FI5wQuEsFJqGYSLNvd4QO2RphNpOhZktdJI9Qv0nAS6qIAU3Jmf8cHu6icA1Jr86jXgn1FakAP8-K3JBixOxnS44Xy0a1yEoL_aCa3t6DeqGPAZ7iTA901eH9fQjIaZ7GVm1gFI69_KYWTo9Aw-zE3SQb4rmGNK-YO1WfY1Fyd3aiw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/16k7GeT10xnyGxKgd_FlVZCkydV-RDVkVN5jCKeQIWh34il3jxFy101naM-yIxvXqpP2HyIp-eGB9RvrusOKbKf9XRXAN55tTbtdwTjP9dePStqI5NKRTIAsPPY6kJCfItER09-PaaHsooudqs_kiKeXxx9OrieieJPMPBxG5dmGT1GrY9s8bK8r1SYNmjTW7Z5IckX9mnkBlpxYMS97B8lnTFbjQj_BXa0Ya7vv7IcJqIbM1InBbPxGvF7ToPyG4Rzy-r98xWDbyFexID6H8dkhLe_yHX7HhwFJDKMTfV5ZsfIQ5KGVzR-HCeEIAP5S4_HVTTDoacjsxxjrOd1OcYw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto: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/19u5yrx1hEBh57aEQRnpFtUiQK-dS5rJ76xYC65HhTa_BvN0TGk9Vfi2AeR1OU6jHQ3n-0iZiJTAqEvRy3TEq-i-2b6QbNPEsnT_BcKYzT7qpyOdJJQoDA3rt2sLfg5opm0kQcz53NiimjtO57eoQIuNz8AmCQZ8YhctP2rj1FI5wQuEsFJqGYSLNvd4QO2RphNpOhZktdJI9Qv0nAS6qIAU3Jmf8cHu6icA1Jr86jXgn1FakAP8-K3JBixOxnS44Xy0a1yEoL_aCa3t6DeqGPAZ7iTA901eH9fQjIaZ7GVm1gFI69_KYWTo9Aw-zE3SQb4rmGNK-YO1WfY1Fyd3aiw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/1QJz6xShsji1s-ybZT93kuMT6Br9o_orKDeEAjsEP1AQitVjyVeHTdGRVTyOgmTpiCikQDZWiFccCRyhtW_q_C3nlwIEgjD_S4xBcegNL4wFTlj9DY7PSanZGnfTTMPaigtNE89HaUY3bMazDc2VUtm0-zzcnx5xUYw-BSmO7AIPjOd97McD1sMCWlCXNeqalX98VmbZdCqT1VBdwtam8sY3ZCnp8h4GgZ8CQPmYdAFWhnW8ErSl3nRNKIVT6oflvJ79MigCrt8VcFVJonMLnKXigZ5_wNg_TuteqpSrwrStpy4THTu7x47gf70NU9uz3/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > > <smime.p7s> External Email - Use Caution > External Email - Use Caution > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto: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/19u5yrx1hEBh57aEQRnpFtUiQK-dS5rJ76xYC65HhTa_BvN0TGk9Vfi2AeR1OU6jHQ3n-0iZiJTAqEvRy3TEq-i-2b6QbNPEsnT_BcKYzT7qpyOdJJQoDA3rt2sLfg5opm0kQcz53NiimjtO57eoQIuNz8AmCQZ8YhctP2rj1FI5wQuEsFJqGYSLNvd4QO2RphNpOhZktdJI9Qv0nAS6qIAU3Jmf8cHu6icA1Jr86jXgn1FakAP8-K3JBixOxnS44Xy0a1yEoL_aCa3t6DeqGPAZ7iTA901eH9fQjIaZ7GVm1gFI69_KYWTo9Aw-zE3SQb4rmGNK-YO1WfY1Fyd3aiw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/1hhsmBghDvdXvV8bIdu3XWLPammaCaGvm3GPUp7fLDRWRr4KujzWNQGEvUK5rd3G-_cXl3PAwnjaYULHKTQELBUcOawcDOJWApoD_fsATRk1tAKcadLeQRW8dJA0AVpl9zdtRMa5ztZ3MPx0CEAmdH40EwZ99OrNoCN-HA6lm1RZUyHRP6CdesneUhhCm1mhGEoyFJQXD6dlMRUa6UuRNu8fVar0zTwISqwEqNg6p2l0LOAbfK1esjbup4bhWhL0SaRrTlUzv322_mgMpzD8C8zJIQB6a2VPSd2F6ZOFW_5RI1izWLJNEjvWTPra_z4RW/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. 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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. > > External Email - Use Caution > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto: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/19u5yrx1hEBh57aEQRnpFtUiQK-dS5rJ76xYC65HhTa_BvN0TGk9Vfi2AeR1OU6jHQ3n-0iZiJTAqEvRy3TEq-i-2b6QbNPEsnT_BcKYzT7qpyOdJJQoDA3rt2sLfg5opm0kQcz53NiimjtO57eoQIuNz8AmCQZ8YhctP2rj1FI5wQuEsFJqGYSLNvd4QO2RphNpOhZktdJI9Qv0nAS6qIAU3Jmf8cHu6icA1Jr86jXgn1FakAP8-K3JBixOxnS44Xy0a1yEoL_aCa3t6DeqGPAZ7iTA901eH9fQjIaZ7GVm1gFI69_KYWTo9Aw-zE3SQb4rmGNK-YO1WfY1Fyd3aiw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/1hhsmBghDvdXvV8bIdu3XWLPammaCaGvm3GPUp7fLDRWRr4KujzWNQGEvUK5rd3G-_cXl3PAwnjaYULHKTQELBUcOawcDOJWApoD_fsATRk1tAKcadLeQRW8dJA0AVpl9zdtRMa5ztZ3MPx0CEAmdH40EwZ99OrNoCN-HA6lm1RZUyHRP6CdesneUhhCm1mhGEoyFJQXD6dlMRUa6UuRNu8fVar0zTwISqwEqNg6p2l0LOAbfK1esjbup4bhWhL0SaRrTlUzv322_mgMpzD8C8zJIQB6a2VPSd2F6ZOFW_5RI1izWLJNEjvWTPra_z4RW/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://secure-web.cisco.com/19u5yrx1hEBh57aEQRnpFtUiQK-dS5rJ76xYC65HhTa_BvN0TGk9Vfi2AeR1OU6jHQ3n-0iZiJTAqEvRy3TEq-i-2b6QbNPEsnT_BcKYzT7qpyOdJJQoDA3rt2sLfg5opm0kQcz53NiimjtO57eoQIuNz8AmCQZ8YhctP2rj1FI5wQuEsFJqGYSLNvd4QO2RphNpOhZktdJI9Qv0nAS6qIAU3Jmf8cHu6icA1Jr86jXgn1FakAP8-K3JBixOxnS44Xy0a1yEoL_aCa3t6DeqGPAZ7iTA901eH9fQjIaZ7GVm1gFI69_KYWTo9Aw-zE3SQb4rmGNK-YO1WfY1Fyd3aiw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://secure-web.cisco.com/1rDme66yCV7wNijvg3gVQJSRdXxf3gb-6-PlIXxsxlSGPgxIuuuIeyfLhALs_mGxLZzjWzoIhFRHxXNAhm9I4qgwEf3Uzi8bJ6qOTQuPSiMjdc1kj5_PHwA4qAbfWU3G2t_ub2sQJiI3usM69hkEUZCOa-AypQbWCjvExOd9YUFQYrZ1JIjLy3M5_xWFvnVR4aFW39trmjMoR_29Xc7_ZRH_qpkVDiaT8oDWPRLjWyvTxM_eQwzWXNhTtekwB4ANN0cSFHO6XEhN3pHp0-ZgWGCbAufYeF_ba26nfpNqpRIUvz99eMQ9XZ4DuJwaa8Lkb1h8dUaxTHDNZwfQ89ckNbg/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20250103%2F112c364f%2Fattachment-0001.html > > > ------------------------------ > > Message: 4 > Date: Sat, 4 Jan 2025 00:01:36 +0000 > From: "Dicamillo, Robert" <rdicami...@mgh.harvard.edu> > Subject: Re: [Freesurfer] [ext] Re: Freeview crash > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Cc: Robert Dicamillo <rd...@nmr.mgh.harvard.edu> > Message-ID: <8267ff83-f6ce-447f-8d39-598be596d...@mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Hello Ruopeng, > > Just FYI - users should no longer have to put a license.txt under the > freesurfer distribution; that fallback location should remain for backwards > compatibility with old freesurfer setups. Apps/commands should first always > check if FS_LICENSE is set in the environment and test if it points to a > valid license.txt file. We added that so users do not need to sudo, and > add the freesurfer license under the distribution every time they (re)install > freesurfer, or if they want to have multiple versions of freesurfer > installed, so a single license file location pointed to by FS_LICENSE works > for different/multiple installs of freesurfer. > > - rob > > On Jan 3, 2025, at 17:32, Wang, Ruopeng <rwa...@mgh.harvard.edu> wrote: > > You can run freeview from the the command-line by directly calling the binary > in the app bundle, for example: > > $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview > > > On Jan 3, 2025, at 3:58 PM, Tietze, Anna > <anna.tie...@charite.de<mailto:anna.tie...@charite.de>> wrote: > > > External Email - Use Caution > > Hi Ruopeng, > > It works with the app when I move the licence.txt! It doesn?t work from the > terminal so far, but this helps a lot. Thank you very much! > > Best, Anna > > From: > <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> > on behalf of "Wang, Ruopeng" > <rwa...@mgh.harvard.edu<mailto:rwa...@mgh.harvard.edu>> > Reply-To: Freesurfer support list > <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> > Date: Friday, 3. January 2025 at 18:17 > To: Freesurfer support list > <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] [ext] Re: Freeview crash > > I mean /Applications/freesurfer/license.txt. > > > On Jan 3, 2025, at 11:36 AM, Tietze, Anna > <anna.tie...@charite.de<mailto:anna.tie...@charite.de>> wrote: > > > It?s there: > licence.txt located in: /Applications/freesurfer/7.4.0/license.txt (can be > read, as recon-all works) > Or do you mean /Applications/freesurfer/license.txt? > > Von: > freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > > <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> > Im Auftrag von Wang, Ruopeng > Gesendet: Freitag, 3. Januar 2025 16:58 > An: Freesurfer support list > <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> > Betreff: Re: [Freesurfer] [ext] Re: Freeview crash > > To run as an app bundle, since there is no global environment settings, you > need to put the license file in /Applications/freesurfer folder. Then you > should be able to load data. > > On Jan 3, 2025, at 12:47 AM, Tietze, Anna > <anna.tie...@charite.de<mailto:anna.tie...@charite.de>> wrote: > > External Email - Use Caution > Yes, I?ve tried that as well. Freeview opens as an app bundle, but it crashes > when I load a file. Interestingly, this is inconsistent?sometimes I can load > a file without any issues, but most of the time, it crashes in the same way. > I?ve this problem on two different Macs: > > * System 1: macOS Sonoma 14.5 with FreeSurfer 7.3.2. > * System 2: macOS Sonoma 14.7.1 with FreeSurfer 7.4.0. > > > From: > <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> > on behalf of "Wang, Ruopeng" > <rwa...@mgh.harvard.edu<mailto:rwa...@mgh.harvard.edu>> > Reply-To: Freesurfer support list > <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> > Date: Thursday, 2. January 2025 at 19:04 > To: Freesurfer support list > <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> > Subject: [ext] Re: [Freesurfer] Freeview crash > > Have you tried running freeview as an app bundle? Or can you try running > freeview directly from the binary location? Like this: > > $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview > > On Jan 2, 2025, at 7:14 AM, Tietze, Anna > <anna.tie...@charite.de<mailto:anna.tie...@charite.de>> wrote: > > > Hi, > > When I want to open files with freeview, it crashes immediately. I tried my > own recon-all output and the bert dataset. Can you help me? > > Operating system: Mac, Sonoma 14.7.1 > Fressurfer version 7.4.0 > XQuatz 2.8.5 > licence.txt located in: /Applications/freesurfer/7.4.0/license.txt (can be > read, as recon-all works) > environment is set by FREESURFER_HOME=/Applications/freesurfer/7.4.0 and > source $FREESURFER_HOME/SetUpFreeSurfer.sh > > When I run the command freeview, the following message is given: > /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6615 Segmentation > fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" > > Or trying to open a file: > freeview -v > /Users/annatietze/Documents/freesurfer/freesurfer_subjects/nini_ra/mri/orig/001.mgz > /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6765 Segmentation > fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" > > freeview -v /Applications/freesurfer/7.4.0/subjects/bert/mri/orig/001.mgz > /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6799 Segmentation > fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" > > Attached is a detailed error report. > > What did I overlook?? Thank you so much for help! > > Best, Anna > <problem report freeview.rtf> > External Email - Use Caution > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto: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/19u5yrx1hEBh57aEQRnpFtUiQK-dS5rJ76xYC65HhTa_BvN0TGk9Vfi2AeR1OU6jHQ3n-0iZiJTAqEvRy3TEq-i-2b6QbNPEsnT_BcKYzT7qpyOdJJQoDA3rt2sLfg5opm0kQcz53NiimjtO57eoQIuNz8AmCQZ8YhctP2rj1FI5wQuEsFJqGYSLNvd4QO2RphNpOhZktdJI9Qv0nAS6qIAU3Jmf8cHu6icA1Jr86jXgn1FakAP8-K3JBixOxnS44Xy0a1yEoL_aCa3t6DeqGPAZ7iTA901eH9fQjIaZ7GVm1gFI69_KYWTo9Aw-zE3SQb4rmGNK-YO1WfY1Fyd3aiw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/16k7GeT10xnyGxKgd_FlVZCkydV-RDVkVN5jCKeQIWh34il3jxFy101naM-yIxvXqpP2HyIp-eGB9RvrusOKbKf9XRXAN55tTbtdwTjP9dePStqI5NKRTIAsPPY6kJCfItER09-PaaHsooudqs_kiKeXxx9OrieieJPMPBxG5dmGT1GrY9s8bK8r1SYNmjTW7Z5IckX9mnkBlpxYMS97B8lnTFbjQj_BXa0Ya7vv7IcJqIbM1InBbPxGvF7ToPyG4Rzy-r98xWDbyFexID6H8dkhLe_yHX7HhwFJDKMTfV5ZsfIQ5KGVzR-HCeEIAP5S4_HVTTDoacjsxxjrOd1OcYw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto: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/19u5yrx1hEBh57aEQRnpFtUiQK-dS5rJ76xYC65HhTa_BvN0TGk9Vfi2AeR1OU6jHQ3n-0iZiJTAqEvRy3TEq-i-2b6QbNPEsnT_BcKYzT7qpyOdJJQoDA3rt2sLfg5opm0kQcz53NiimjtO57eoQIuNz8AmCQZ8YhctP2rj1FI5wQuEsFJqGYSLNvd4QO2RphNpOhZktdJI9Qv0nAS6qIAU3Jmf8cHu6icA1Jr86jXgn1FakAP8-K3JBixOxnS44Xy0a1yEoL_aCa3t6DeqGPAZ7iTA901eH9fQjIaZ7GVm1gFI69_KYWTo9Aw-zE3SQb4rmGNK-YO1WfY1Fyd3aiw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/1QJz6xShsji1s-ybZT93kuMT6Br9o_orKDeEAjsEP1AQitVjyVeHTdGRVTyOgmTpiCikQDZWiFccCRyhtW_q_C3nlwIEgjD_S4xBcegNL4wFTlj9DY7PSanZGnfTTMPaigtNE89HaUY3bMazDc2VUtm0-zzcnx5xUYw-BSmO7AIPjOd97McD1sMCWlCXNeqalX98VmbZdCqT1VBdwtam8sY3ZCnp8h4GgZ8CQPmYdAFWhnW8ErSl3nRNKIVT6oflvJ79MigCrt8VcFVJonMLnKXigZ5_wNg_TuteqpSrwrStpy4THTu7x47gf70NU9uz3/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > > <smime.p7s> External Email - Use Caution > External Email - Use Caution > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto: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/19u5yrx1hEBh57aEQRnpFtUiQK-dS5rJ76xYC65HhTa_BvN0TGk9Vfi2AeR1OU6jHQ3n-0iZiJTAqEvRy3TEq-i-2b6QbNPEsnT_BcKYzT7qpyOdJJQoDA3rt2sLfg5opm0kQcz53NiimjtO57eoQIuNz8AmCQZ8YhctP2rj1FI5wQuEsFJqGYSLNvd4QO2RphNpOhZktdJI9Qv0nAS6qIAU3Jmf8cHu6icA1Jr86jXgn1FakAP8-K3JBixOxnS44Xy0a1yEoL_aCa3t6DeqGPAZ7iTA901eH9fQjIaZ7GVm1gFI69_KYWTo9Aw-zE3SQb4rmGNK-YO1WfY1Fyd3aiw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/1hhsmBghDvdXvV8bIdu3XWLPammaCaGvm3GPUp7fLDRWRr4KujzWNQGEvUK5rd3G-_cXl3PAwnjaYULHKTQELBUcOawcDOJWApoD_fsATRk1tAKcadLeQRW8dJA0AVpl9zdtRMa5ztZ3MPx0CEAmdH40EwZ99OrNoCN-HA6lm1RZUyHRP6CdesneUhhCm1mhGEoyFJQXD6dlMRUa6UuRNu8fVar0zTwISqwEqNg6p2l0LOAbfK1esjbup4bhWhL0SaRrTlUzv322_mgMpzD8C8zJIQB6a2VPSd2F6ZOFW_5RI1izWLJNEjvWTPra_z4RW/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. 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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. > > External Email - Use Caution > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto: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/19u5yrx1hEBh57aEQRnpFtUiQK-dS5rJ76xYC65HhTa_BvN0TGk9Vfi2AeR1OU6jHQ3n-0iZiJTAqEvRy3TEq-i-2b6QbNPEsnT_BcKYzT7qpyOdJJQoDA3rt2sLfg5opm0kQcz53NiimjtO57eoQIuNz8AmCQZ8YhctP2rj1FI5wQuEsFJqGYSLNvd4QO2RphNpOhZktdJI9Qv0nAS6qIAU3Jmf8cHu6icA1Jr86jXgn1FakAP8-K3JBixOxnS44Xy0a1yEoL_aCa3t6DeqGPAZ7iTA901eH9fQjIaZ7GVm1gFI69_KYWTo9Aw-zE3SQb4rmGNK-YO1WfY1Fyd3aiw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/1hhsmBghDvdXvV8bIdu3XWLPammaCaGvm3GPUp7fLDRWRr4KujzWNQGEvUK5rd3G-_cXl3PAwnjaYULHKTQELBUcOawcDOJWApoD_fsATRk1tAKcadLeQRW8dJA0AVpl9zdtRMa5ztZ3MPx0CEAmdH40EwZ99OrNoCN-HA6lm1RZUyHRP6CdesneUhhCm1mhGEoyFJQXD6dlMRUa6UuRNu8fVar0zTwISqwEqNg6p2l0LOAbfK1esjbup4bhWhL0SaRrTlUzv322_mgMpzD8C8zJIQB6a2VPSd2F6ZOFW_5RI1izWLJNEjvWTPra_z4RW/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://secure-web.cisco.com/19u5yrx1hEBh57aEQRnpFtUiQK-dS5rJ76xYC65HhTa_BvN0TGk9Vfi2AeR1OU6jHQ3n-0iZiJTAqEvRy3TEq-i-2b6QbNPEsnT_BcKYzT7qpyOdJJQoDA3rt2sLfg5opm0kQcz53NiimjtO57eoQIuNz8AmCQZ8YhctP2rj1FI5wQuEsFJqGYSLNvd4QO2RphNpOhZktdJI9Qv0nAS6qIAU3Jmf8cHu6icA1Jr86jXgn1FakAP8-K3JBixOxnS44Xy0a1yEoL_aCa3t6DeqGPAZ7iTA901eH9fQjIaZ7GVm1gFI69_KYWTo9Aw-zE3SQb4rmGNK-YO1WfY1Fyd3aiw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/19u5yrx1hEBh57aEQRnpFtUiQK-dS5rJ76xYC65HhTa_BvN0TGk9Vfi2AeR1OU6jHQ3n-0iZiJTAqEvRy3TEq-i-2b6QbNPEsnT_BcKYzT7qpyOdJJQoDA3rt2sLfg5opm0kQcz53NiimjtO57eoQIuNz8AmCQZ8YhctP2rj1FI5wQuEsFJqGYSLNvd4QO2RphNpOhZktdJI9Qv0nAS6qIAU3Jmf8cHu6icA1Jr86jXgn1FakAP8-K3JBixOxnS44Xy0a1yEoL_aCa3t6DeqGPAZ7iTA901eH9fQjIaZ7GVm1gFI69_KYWTo9Aw-zE3SQb4rmGNK-YO1WfY1Fyd3aiw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://secure-web.cisco.com/1dImTfM1110TmABOg1tpNTClMvqe15liHmcN4ytOOQmIxF0mJeR7PLf_E0Yz1eZh5OcQJhuQNkr2ASURVRlqCMhJAMkfx-8yb7nk-uEIVmft5j7JhCPKk_cW9hcFZYx6DhZZgf3ATdg4fEJF9n12dCAz-wHkg96E3rMcMWXqYQkTXeJ4uJ6z31pJUsKEMpzhzsd0nRb4CiQedd_pvkEHg-jaCgYc-kz5POiFyeTDwFDiHAh08jJClbNosmnnDJGuStUpEQ1L5F6OljohJ86mUP44m5YnVw3a1AAB8vS18vuLQ97Sw3wrKvTkrR8nE4AZ-ce9VIPXl-szbcsuP9qf1ng/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20250104%2F6d603bfa%2Fattachment-0001.html > > > ------------------------------ > > Message: 5 > Date: Sat, 4 Jan 2025 18:00:40 +0530 > From: Ramesh Babu <mgrameshbabu2...@gmail.com> > Subject: [Freesurfer] registration error > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <CAHRhR0B+RuTGYSVPqiHVV=1sqtm4svemq-f3kbd5nqcnycr...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Hello, > > I want to register JHU-ICBM-tracts-maxprob-thr0-1mm.nii.gz with local > subject space. For this, I want to generate a registration.dat file which > will be used for registration with local subject image. But I am facing an > issue which I pasted below. > > echo $SUBJECTS_DIR > /usr/local/freesurfer/subjects > > bbregister --ss sample-001.mgz --mov > /usr/local/fsl/data/atlases/JHU/JHU-ICBM-tracts-maxprob-thr0-1mm.nii.gz > --reg registration_matrix.dat --init-fsl --dti > ERROR: Flag --ss unrecognized. > --ss sample-001.mgz --mov > /usr/local/fsl/data/atlases/JHU/JHU-ICBM-tracts-maxprob-thr0-1mm.nii.gz > --reg registration_matrix.dat --init-fsl --dti > > I tried with -s flag, but still the same error. Could you please provide me > a solution? > > Regards > Ramesh > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://secure-web.cisco.com/1mmkTwyq0M0UJNKle9iCremCgnVlcFu3_a-K8owoGt7yfMDqd78B6t-_bQ772-86omjeO5Xm-RLXXfE4rCAaoRfj8ralZuMTSOXK56P8r6_9f105GqouP2PS0qR69E1BTIqkcrZv04vlceiHcu7HmR32Y2gXZnbSbHDXs20mVW7gnsn-ERurNpSE2_gXgtuWP4etH5Y9xn77Rfxfg3UXqGAlRLwMWOCfKr1sxX0rxdPYb0uq5s61DMI6ImTyLd8m-_8WfHBzLbiIbvPePgJrq2717m2bd7UNdEXJ7L0UzZ-G205ObAEM6j7jmD2Wu0lghHNaAp690MwSnqmB9wUj11g/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20250104%2F93d68ed2%2Fattachment-0001.html > > > ------------------------------ > > Message: 6 > Date: Mon, 6 Jan 2025 09:12:16 -0500 > From: "Douglas N. Greve" <dgr...@mgh.harvard.edu> > Subject: Re: [Freesurfer] [External] Re: Assistance with mri_vol2surf: > Missing Surface Values in Output > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <1abf3024-8ba8-42b1-ab82-e1fb3f6a9...@mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > What kind of image is that? FS will only work on T1-weighted. I'm > surprised it did that good. > > > On 1/3/2025 2:12 PM, Pandey, Shraddha wrote: > > > > ????????External Email - Use Caution > > > > Hi, > > Thank you for your response. I suspect the gray regions might be > > problematic (incorrect) for the following reasons: > > > > 1. When I overlay |lh.white|?on the original volume, I notice some > > misregistration (see the figure below). > > 2. To address this, I applied the |transformationvolume.dat|?file > > generated from |bbregister|, which I used to create the surface > > with |mri_vol2surface|. > > > > However, the transformed |lh.white|?surface generated using the > > |transformationvolume.dat|?file appears to be incorrect?it seems to be > > rotated by 90 degrees (refer to the second figure below). > > I am unsure what I might be doing wrong. Could you please suggest what > > mistake I might be making? > > Thank you once again for your ?help. > > Shraddha > > > > ------------------------------------------------------------------------ > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce > > R.,PHD <bfis...@mgh.harvard.edu> > > *Sent:*?Friday, December 27, 2024 9:33 AM > > *To:*?Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > > *Subject:*?[External] Re: [Freesurfer] Assistance with mri_vol2surf: > > Missing Surface Values in Output > > > > Hi Shraddha > > > > Why do you think the gray regions are a problem? They are just surface > > locations where the values mapped from the volume are below threshold. > > You can change the threshold if you bring up the overlay configuration > > window > > > > cheers > > > > Bruce > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > > <freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Pandey, Shraddha > > *Sent:*?Thursday, December 26, 2024 7:25 PM > > *To:*?Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > > *Subject:*?[Freesurfer] Assistance with mri_vol2surf: Missing Surface > > Values in Output > > > > *????????External Email - Use Caution * > > > > Dear Free Surfer Experts, > > > > I am currently working on generating a surface from a volume using the > > |mri_vol2surf|?tool. The process I am following is as follows: > > > > 1. I first create the registration file using |bbregister|?with the > > following command: > > > > bash > > bbregister --s "${sub}xx${ses}" --mov "$input_mri" --reg > > "$output_reg_file" --o "$output_vol_file" --init-header --t1 > > > > 2. Here, the goal is to generate the |.dat|?registration file. > > 3. Next, I use this |.dat|?file in |mri_vol2surf|?to generate the > > surface with the following command: > > > > mri_vol2surf --mov "$input_volume" --reg "$output_reg_file" --hemi lh > > --projfrac 0.2 --o "$output_surface" > > > > The input MRI for the |bbregister|?command is flash data, and the > > input volume for |mri_vol2surf|?is a paramagnetic volume that has been > > registered with the Flash data. > > > > However, the surface output generated by |mri_vol2surf|?contains > > missing surface values (as shown in the figure below. For instance, > > the grey regions in the surface estimates). > > > > I would greatly appreciate any insights into why this might be > > occurring and how to resolve the issue. > > > > Thank you for your time and assistance! > > > > ??????Regards, > > > > ??????Shraddha > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://secure-web.cisco.com/19u5yrx1hEBh57aEQRnpFtUiQK-dS5rJ76xYC65HhTa_BvN0TGk9Vfi2AeR1OU6jHQ3n-0iZiJTAqEvRy3TEq-i-2b6QbNPEsnT_BcKYzT7qpyOdJJQoDA3rt2sLfg5opm0kQcz53NiimjtO57eoQIuNz8AmCQZ8YhctP2rj1FI5wQuEsFJqGYSLNvd4QO2RphNpOhZktdJI9Qv0nAS6qIAU3Jmf8cHu6icA1Jr86jXgn1FakAP8-K3JBixOxnS44Xy0a1yEoL_aCa3t6DeqGPAZ7iTA901eH9fQjIaZ7GVm1gFI69_KYWTo9Aw-zE3SQb4rmGNK-YO1WfY1Fyd3aiw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://secure-web.cisco.com/1yPzcT6F8Na9Hra08GzCw-BSW_XwT2VMlaIMFFqsIH9k4Tl8ixk3z_n3WUJhtiBmEmv_dMihCZj1IxFwqTAJW8Uqf4MrMjLduzuHzWmwLV3-GMUYtsOA4uMJ72IMw2AvncyFRN2_QPqiZkyaefMdnXzAT-gR1aawk0THEZKZqYGbsF1BA9wNMO0Km7oWaN4Oy7HE-AqCWE3iNClh9H9H_5Jbq8jq1mzDVG6-WDcxO2TS-vZVD3Bi-6P4rZUyFFO-5rO_ftaVLps5kM-5dCkAnduW23x14zzwsBoroedscIH-HAI51KEPZR77RbPia3s60H3IcOsImvb6Tv3Rvb2qIJA/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20250106%2F9531a741%2Fattachment.html > > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: image.png > Type: image/png > Size: 363426 bytes > Desc: not available > Url : > http://secure-web.cisco.com/1yJ-9ABU1xu6kx9yfA7ggsqTVlfGS8VZBT3oSByz1SxGvqjOeEyy-dTeZa-VcHmVoNMiKsSVe6U09_fE5BXds_oi1kKf4fZofb3YXktHIw22IzE9OxU9Vy1GZbpVYwXOsk7T1mTpJXnKnI6JTCjxJpkjaYS5ZmPcE4WFWhRfRdLlhXJBAHqbgWeYvYgxcpWnZ9Npw-apt94hOhyqPLVX6L6gLIq6jRGSHAjPVEZpC5JdKxq3NEx-kn8Knu-IqNl1Tyct90PT65ktXMR9RTXVqTAkLwGwAngvzCFbrR4UMmoTM5UUDvMjiLPuhsRPT81T7rh5aAGRlwCqEbSnzmxDGBg/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20250106%2F9531a741%2Fattachment.png > > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: image.png > Type: image/png > Size: 333261 bytes > Desc: not available > Url : > http://secure-web.cisco.com/1Aw5SjwboX9zstv06-4TfnHa-0z2Xf04VbEOrbL7FkPwm-we0K7vtX1xgr7V0KaHZKQo8P-BWfEJF14BfOiImHBuJ_fgGBrj5Ycow5KN4j_Xd7cp3D0LbkE5OEe-Fydz3AWIwX-x6MTNDOmgHMYya04Ck9fqVPwM7CnIZXO6yExMjl8STpkja7VMeAEiZFSRKqS8A8f7YmiJISimR705bY4p-Q-2a1rq4IbBZ8qmr4JzqJJxDBOMhRjnBGokPd95BLQokQHlRky4u8aIFiS3PlsPzt4sGuVzjCIC2fvO2rsCQRy6cly4l2MYsoi6FAie8eO2N6xb4mJabU1XurmkQVQ/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20250106%2F9531a741%2Fattachment-0001.png > > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: image001.png > Type: image/png > Size: 625632 bytes > Desc: not available > Url : > http://secure-web.cisco.com/1mLRXKP96org8U0P2c3pan7sUFzqM9jE6FUNpG9xx2Hd2t6_ZII7ExF9lIjUIV5uZnVJfbTohzM5pyiNavBRJyeB9I8YktCa0pYh1Z-StokPWWO6lcxqBecApYcqKYvYbPYTFUtivIQYDDQk4eQFBcDaNfX1tdhVA2cAjrhRXmDkB3LMzRXmHIHqec8Q04RO_jMW1lLW5dTHYXQ6N40Zin9WDER-jvRJaByZjUf-HO8xkFPWpERTEuyyLeKZlATPmRIqb2lcOMIZWAXDBLwGlPZOM-NyT_nXkQhs_zp9AOXfB1EvbVjTeosjRuZNUsWRvp7unup4uySKhrHYMXsXX2w/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20250106%2F9531a741%2Fattachment-0002.png > > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/19u5yrx1hEBh57aEQRnpFtUiQK-dS5rJ76xYC65HhTa_BvN0TGk9Vfi2AeR1OU6jHQ3n-0iZiJTAqEvRy3TEq-i-2b6QbNPEsnT_BcKYzT7qpyOdJJQoDA3rt2sLfg5opm0kQcz53NiimjtO57eoQIuNz8AmCQZ8YhctP2rj1FI5wQuEsFJqGYSLNvd4QO2RphNpOhZktdJI9Qv0nAS6qIAU3Jmf8cHu6icA1Jr86jXgn1FakAP8-K3JBixOxnS44Xy0a1yEoL_aCa3t6DeqGPAZ7iTA901eH9fQjIaZ7GVm1gFI69_KYWTo9Aw-zE3SQb4rmGNK-YO1WfY1Fyd3aiw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > End of Freesurfer Digest, Vol 251, Issue 6 > ****************************************** > The information in this e-mail is intended only for the person to whom it is > addressed. 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