Freesurfer

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30076 discussions

2x2 ANOVA tp2-tp1 is not an option to be done
by stdp82＠virgilio.it 02 Jan '22

02 Jan '22

External Email - Use Caution Hi list, I have two groups undergoing two different treatments: one's placebo , one's drug. Two timepoints, at baseline (T1, no treatment) and at treatment (T2). 2x2 ANOVA, repeted measures has been applied by following the guidlines and mailing list. IMPORTANTLY, to compute tp2-tp1, as reported in the fsgd example, is not an option to be done because we aiming to assess the interaction between time and treatment. Please chech the design matrix, the command line produces an error. GroupDescriptorFile 1 Title 2x2_repeted_measures Class Subject1 Class Subject2 Class Subject3 Class Subject4 Class Subject5 Class Subject6 Class Subject7 Class Subject8 Class Subject9 Class Subject10 Class Subject11 Class Subject12 Class Subject13 Class Subject14 Class Subject15 Class Subject16 Class Subject17 Class Subject18 Class Subject19 Class Subject20 Class Subject21 Class Subject22 Class Subject23 Class Subject24 Variables tp1-vs-tp2.drug tp1-vs-tp2.plb Input CODE01_tp1 Subject1 1 0 Input CODE02_tp1 Subject2 1 0 Input CODE03_tp1 Subject3 1 0 Input CODE05_tp1 Subject4 1 0 Input CODE06_tp1 Subject5 0 1 Input CODE07_tp1 Subject6 0 1 Input CODE09_tp1 Subject7 0 1 Input CODE10_tp1 Subject8 1 0 Input CODE11_tp1 Subject9 1 0 Input CODE12_tp1 Subject10 0 1 Input CODE13_tp1 Subject11 0 1 Input CODE14_tp1 Subject12 1 0 Input CODE15_tp1 Subject13 1 0 Input CODE16_tp1 Subject14 1 0 Input CODE17_tp1 Subject15 0 1 Input CODE18_tp1 Subject16 1 0 Input CODE19_tp1 Subject17 0 1 Input CODE20_tp1 Subject18 0 1 Input CODE21_tp1 Subject19 0 1 Input CODE22_tp1 Subject20 1 0 Input CODE23_tp1 Subject21 0 1 Input CODE24_tp1 Subject22 0 1 Input CODE25_tp1 Subject23 1 0 Input CODE26_tp1 Subject24 0 1 Input CODE01_tp2 Subject1 -1 0 Input CODE02_tp2 Subject2 -1 0 Input CODE03_tp2 Subject3 -1 0 Input CODE05_tp2 Subject4 -1 0 Input CODE06_tp2 Subject5 0 -1 Input CODE07_tp2 Subject6 0 -1 Input CODE09_tp2 Subject7 0 -1 Input CODE10_tp2 Subject8 -1 0 Input CODE11_tp2 Subject9 -1 0 Input CODE12_tp2 Subject10 0 -1 Input CODE13_tp2 Subject11 0 -1 Input CODE14_tp2 Subject12 -1 0 Input CODE15_tp2 Subject13 -1 0 Input CODE16_tp2 Subject14 -1 0 Input CODE17_tp2 Subject15 0 -1 Input CODE18_tp2 Subject16 -1 0 Input CODE19_tp2 Subject17 0 -1 Input CODE20_tp2 Subject18 0 -1 Input CODE21_tp2 Subject19 0 -1 Input CODE22_tp2 Subject20 -1 0 Input CODE23_tp2 Subject21 0 -1 Input CODE24_tp2 Subject22 0 -1 Input CODE25_tp2 Subject23 -1 0 Input CODE26_tp2 Subject24 0 -1 a) groupxtime.mtx 0 0 1 -1 b) tp1-vs-tp2.Mod.mtx 0 0 1 0 c) tp1-vs-tp2.Plb.mtx 0 0 0 -1 mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage rh --glmdir repeted_measures.wls --nii.gz --fsgd Repeted_measure.fsgd --C Tp1-vs-Tp2.Mod.mtx --C Tp1-vs-Tp2.Plb.mtx --C groupxtime.mtx ERROR: dimension mismatch between X and contrast Tp1-vs-Tp2.Mod.mtx X has 72 cols, C has 4 cols

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Re: [Freesurfer] Trac-all -Prep -C Error
by fsbuild 31 Dec '21

31 Dec '21

External Email - Use Caution Hello Elizabeth, To use the latest development build you can set freesurfer home to, /autofs/vast/freesurfer/centos7_x86_64/dev  or /usr/local/freesurfer/dev - R. On Dec 31, 2021, at 16:11, Kaplan, Elizabeth <elizabeth_kaplan(a)brown.edu> wrote:        External Email - Use Caution        Thanks for your prompt response, Anastasia. How do I switch to the dev version? Would I set my FREESURFER_HOME variable to a different pathway? The one I currently use is /autofs/vast/freesurfer/centos7_x86_64/7.2.0Thank you, again! Happy New Year! On Fri, Dec 31, 2021 at 4:01 PM Yendiki, Anastasia <AYENDIKI(a)mgh.harvard.edu> wrote:Hi Elizabeth - If you're using launchpad, just switch to the dev version. It has the latest bug fixes.Happy new year! Anastasia. From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Kaplan, Elizabeth <elizabeth_kaplan@brown.edu>Sent: Friday, December 31, 2021 1:56 PMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: [Freesurfer] Trac-all -Prep -C Error         External Email - Use Caution        Hi All, I am working to process DWI images using Tracula, however I am running into an error when attempting to run the "trac-all -prep -c" command line. The error reads: "Error when attempting to read --index file". I have searched through the archives for guidance and found a similar error resolved here: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1ltIzM0k-Zs8u6rwdCkwRDCFBNNQGMl7Bl2tUZ… attempted to save the bug fix file to my $FREESURFER_HOME/bin/ directory, however because I am working remotely on Launchpad, I am unable to edit files within this directory. Any suggestions on how to navigate this issue would be greatly appreciated! Best, Liz _______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1DRzzjTq57GTrHTYtmc_7CQDJshuZP8JQjS4cK… Kaplan '22She / Her / HersSc.B. Candidate Cognitive Neuroscience B.A. Candidate Contemplative Studies 69 Brown St Mail #4391Providence, RI 02912_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Trac-all -Prep -C Error
by Kaplan, Elizabeth 31 Dec '21

31 Dec '21

External Email - Use Caution Hi All, I am working to process DWI images using Tracula, however I am running into an error when attempting to run the "trac-all -prep -c" command line. The error reads: "Error when attempting to read --index file". I have searched through the archives for guidance and found a similar error resolved here: https://secure-web.cisco.com/1KzdCREiIOVwQ0EaQYziYkN2ydk3Fbs-8eJWpb28ohBnEB… . I attempted to save the bug fix file to my $FREESURFER_HOME/bin/ directory, however because I am working remotely on Launchpad, I am unable to edit files within this directory. Any suggestions on how to navigate this issue would be greatly appreciated! Best, Liz

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QXcbConnection
by Carina Forster 30 Dec '21

30 Dec '21

External Email - Use Caution Dear Freesurfer community, I am using Windows 11 and Ubuntu on WSL2 to access freesurfer. I installed Xming. Unfortunately I get the following error msg when I try to open freeview: QXcbConnection: Could not connect to display 172.20.16.1 Could not connect to any X display. I added my IP adress to the HOST file as suggested but that doesn't help. I also played around with export DISPLAY (setting it to my IP adress, setting it to 0.0 etc). Nothing helped. This is the Xming log (I thought that might help). *Xming :0 -multiwindow -clipboard -acXdmcpRegisterConnection: newAddress 172.20.16.1winAdjustVideoModeShadowGDI - Using Windows display depth of 32 bits per pixelwinAllocateFBShadowGDI - Creating DIB with width: 1536 height: 864 depth: 32winInitVisualsShadowGDI - Masks 00ff0000 0000ff00 000000ff BPRGB 8 d 24 bpp 32glWinInitVisuals:1596: glWinInitVisualsglWinInitVisualConfigs:1503: glWinInitVisualConfigs glWinSetVisualConfigs:1581: glWinSetVisualConfigsinit_visuals:1055: init_visualsnull screen fn ReparentWindownull screen fn RestackWindowInitQueue - Calling pthread_mutex_initInitQueue - pthread_mutex_init returnedInitQueue - Calling pthread_cond_initInitQueue - pthread_cond_init returnedwinInitMultiWindowWM - HellowinInitMultiWindowWM - Calling pthread_mutex_lock ()winMultiWindowXMsgProc - HellowinMultiWindowXMsgProc - Calling pthread_mutex_lock ()glWinScreenProbe:1390: glWinScreenProbefixup_visuals:1303: fixup_visualsinit_screen_visuals:1336: init_screen_visuals(--) 5 mouse buttons found(--) Setting autorepeat to delay=500, rate=31(--) winConfigKeyboard - Layout: "00000407" (00000407)(--) Using preset keyboard for "German (Germany)" (407), type "4"Could not init font path element C:\Program Files (x86)\Xming/fonts/Type1/, removing from list!Could not init font path element C:\Program Files\Xming\fonts\dejavu, removing from list!Could not init font path element C:\Program Files\Xming\fonts\cyrillic, removing from list!Could not init font path element C:\WINDOWS\Fonts, removing from list!winInitMultiWindowWM - pthread_mutex_lock () returned.winInitMultiWindowWM - pthread_mutex_unlock () returned.winInitMultiWindowWM - DISPLAY=127.0.0.1:0.0winMultiWindowXMsgProc - pthread_mutex_lock () returned.winMultiWindowXMsgProc - pthread_mutex_unlock () returned.winMultiWindowXMsgProc - DISPLAY=127.0.0.1:0.0winProcEstablishConnection - HellowinInitClipboard ()winProcEstablishConnection - winInitClipboard returned.winClipboardProc - HelloDetectUnicodeSupport - Windows VistawinClipboardProc - DISPLAY=127.0.0.1:0.0winMultiWindowXMsgProc - XOpenDisplay () returned and successfully opened the display.winInitMultiWindowWM - XOpenDisplay () returned and successfully opened the display.winClipboardProc - XOpenDisplay () returned and successfully opened the display.* Anyone ideas on what could be the problem? Thank you so much. Best, Carina <https://secure-web.cisco.com/1ng5Zr4bbSkvs8cs0zHzZEKY6nqkvGCbjF81ZXgffmH7K1…> Virenfrei. http://secure-web.cisco.com/1m6lUHXphHkv8UYPf9uVnF4Ncx4_BrQJ-jK2FzNdqt0roB2… <https://secure-web.cisco.com/1ng5Zr4bbSkvs8cs0zHzZEKY6nqkvGCbjF81ZXgffmH7K1…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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GNU libc version
by Mohanad Arafe 29 Dec '21

29 Dec '21

External Email - Use Caution Hello, I am attempting to run recon-all on a simple NIFTI file in an HPC using FreeSurfer v6.0.0. I am running into the following problem: *GNU libc version: 2.17* *ERROR: Systems running GNU glibc version greater than 2.15* * require a newly formatted license file (it's free). Please* * download a new one from the following page:* I got a new license and I placed it in the FreeSurfer home directory but the issue remains. Thank you, Mohanad

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Re: [Freesurfer] Illegal Instruction Error
by fsbuild 27 Dec '21

27 Dec '21

External Email - Use Caution Hello Elizabeth, I don’t see anything wrong with how the 6.0..4/bin/bet2 binary is built. It would be interesting to see if the output is different with an older fsl version like 5.0.7. In a new/different terminal window you could setup your environment with 5.0.7 and then try again, $ setenv FSLDIR /usr/pubsw/packages/fsl/5.0.7$ setenv FSL_DIR "$FSLDIR" ..  .  . then source freesurfer setup or run .  .  . $ source $FSLDIR/etc/fslconf/fsl.csh - R. On Dec 27, 2021, at 15:34, Kaplan, Elizabeth <elizabeth_kaplan(a)brown.edu> wrote:        External Email - Use Caution        Hello All, I am running into an error when attempting to run the 'trac-all -prep -c" command. The error reads "/autofs/cluster/pubsw/2/pubsw/Linux2-2.3-x86_64/packages/fsl.64bit/6.0.4/bin/bet: line 399:  6625 Illegal instruction"I set my FSLDIR following the instructions on the FSL User guide and added these lines to my .bash_profile file. Any suggestions on how to navigate this issue? Thank you in advance!<trac-all.log><configuration.file.tutorial>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Developer password for Ubuntu log in
by fsbuild 27 Dec '21

27 Dec '21

External Email - Use Caution Sending the info to your email shortly ... - R. Sang-Han Choi (sanghanchoi(a)gmail.com) December 25, 2021 at 08:48         External Email - Use Caution        Dear FreeSurfer Manager I am currently setting up FreeSurfer using the Ubuntu VM by following (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1QGQZSIkEASZdRSKpPrM5N4xbfSHJd70xcSC-D-Mz_y96s…) But I can't log in because I don't have the developer password. Would it be possible to provide me with the password? Thank you! sincerely yours,  Sang-Han Choi _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1VfxXrSw7iLtZi9sYP-gRd5bC3fh4_lHDQYEoczrRjYYFW…

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Illegal Instruction Error
by Kaplan, Elizabeth 27 Dec '21

27 Dec '21

External Email - Use Caution Hello All, I am running into an error when attempting to run the 'trac-all -prep -c" command. The error reads "/autofs/cluster/pubsw/2/pubsw/Linux2-2.3-x86_64/packages/fsl.64bit/6.0.4/bin/bet: line 399: 6625 Illegal instruction" I set my FSLDIR following the instructions on the FSL User guide and added these lines to my .bash_profile file. Any suggestions on how to navigate this issue? Thank you in advance!

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Developer password for Ubuntu log in
by Sang-Han Choi 25 Dec '21

25 Dec '21

External Email - Use Caution Dear FreeSurfer Manager I am currently setting up FreeSurfer using the Ubuntu VM by following ( https://secure-web.cisco.com/146Qu5uXrq4DXeyoh_h2Rn9ul9DVRSvPNPQwb9piTjitro…) But I can't log in because I don't have the developer password. Would it be possible to provide me with the password? Thank you! sincerely yours, Sang-Han Choi

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Tracula error
by Nasiriavanaki, Zahra,M.D. 23 Dec '21

23 Dec '21

Hello, I’ve been running the trac-all -prep step and I faced this error: ConvertTransformFile 3 /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.mat /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.txt --hm --ras ConvertTransformFile: Command not found. Linux bee.nmr.mgh.harvard.edu<http://bee.nmr.mgh.harvard.edu> 3.10.0-1160.31.1.el7.x86_64 #1 SMP Thu Jun 10 13:32:12 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Fri Dec 3 14:29:56 EST 2021 Could you please let me know what the problem is? I’m running it in dev environment. Thanks, Mona Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry | MGH/HMS Department of Radiology | MGH/HMS 149 13th Street, 149-2615 Boston, MA, USA, 02129

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