Freesurfer November 2021

freesurfer@nmr.mgh.harvard.edu

77 participants
118 discussions

recon-all reconbatchjobs Segmentation fault
by Peled, Noam 19 Nov '21

19 Nov '21

Dear Freesurfer group, I was running recon-all (Freesurfer 7.2 on Ubuntu) and received the following error: " mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 UC07 rh Waiting for PID 6337 of (6337 6340) to complete... Waiting for PID 6340 of (6337 6340) to complete... /home/basuia/Documents/mmvt_root/freesurfer/bin/reconbatchjobs: line 77: 6340 Segmentation fault (core dumped) exec $JOB >> $LOG 2>&1 PIDs (6337 6340) completed and logs appended. " Please find the log file attached. Any idea what is the problem? Thanks, Noam

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recon-all error with T1 dcm images
by Wei Shao 19 Nov '21

19 Nov '21

External Email - Use Caution Hi, Dear Freesurfer experts I'm have met a recon-all errors with data collected recently like this ADNI_002_S_6652_MR_Accelerated_Sagittal_MPRAGE__br_raw_20190122095958285_147_S786989_I1118713.dcm The attachments are the recon-all script and the output log. Can you help me with this? Thanks Best, Wei

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"Vertex Talairach" in tksurfer?...
by Gonzalo Rojas Costa 19 Nov '21

19 Nov '21

External Email - Use Caution Hi: "Vertex Talairach" in tksurfer: how does it relate to MNI coordinates? Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 https://secure-web.cisco.com/1jo94BTSUPIktp_eQAT5GZbTfpsA5KIpUTdHrT-g0xQG4-… https://secure-web.cisco.com/13i-ZsZNcbWZqtgw0IQqpdq0G6AvtrIwdfNJ8UTQmrf8Eh… https://secure-web.cisco.com/1nQ-nK1zgqFE9FeklGRmkE8GyAOu5VBkwnRcdrdjH0AT19… http://secure-web.cisco.com/16_Ws70db2hTLXeCVLoJofARkDDcVXKV7r9SqYHL1F22JaH… https://secure-web.cisco.com/1Q9jZG4ZNnNMXhDtADVtnz_v3JI4jUseEVnhR7Yv-c6tC1…

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MNI coordinates to vertex...
by Gonzalo Rojas Costa 19 Nov '21

19 Nov '21

External Email - Use Caution Hi: I have MNI 152 coordinates equivalent to 10-10 and 10-20 EEG electrodes (see Supplementary Tables 1 and 2 in paper https://secure-web.cisco.com/1h63DivIA2LKRlpONd2jZm_aVQOA0BCPi_yLJr4IOlwxEn… How to convert that MNI coordinates to vertex in the pial surface ? Sincerely Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 http://secure-web.cisco.com/15G7UB7H3xj-A5kT53KhLNPISazwoqZ-keP4CKddUdONSza… https://secure-web.cisco.com/12viTch2L-4x6NKy94c7WpcDwZ3HTM2I3oGRkhAsSGTmNz… https://secure-web.cisco.com/1j6d3d9sra7KYe340OH3hwmLgVbtcqgErcrjhSz4FftpTg… https://secure-web.cisco.com/1U5osbupkYDzRTSQetIvNibKkd020KxYF82vGNYJMRCBn6… http://secure-web.cisco.com/14Rn0C97f3SuE-gY9gJeCiBXYhQ9pvBuNH5M-itIL_uLqiI… https://secure-web.cisco.com/1DJcTJuO0lQGWBymluz9_ARIefxo929bzOP041a22SpnJK…

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V5 / v7
by Brusaferri, Ludovica 19 Nov '21

19 Nov '21

Hi! I am using a pipeline that was implemented and validated using fs 5.3 , which does the following: * compute transformation matrix for linear registration of SUV with T1-2mm, with spm * use tkergister to transform the matrix into .mat, and then invert the matrix * use flirt to move T1 images into PET space The last step gives me different results if I enable FS vs 7, and the registration seems to be off. Do you know why this would be the case? Thank you! Ludovica

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permutation simulation errror
by Brown, Alexander 19 Nov '21

19 Nov '21

External Email - Use Caution Hello, I am attempting to run a permutation simulation to correct for multiple comparisons and am getting the following error: < mri_glmfit-sim --glmdir /home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled --perm 1000 1.3 neg --perm-resid ERROR: cannot find residual /home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled/eres needed with --perm-resid when running mri_glmfit, make sure to include --eres-save > Attached is the mri glmfit log. I ran the command with the --eres-save flag, and the eres.mgh file is generated in the glm directory. I have downloaded the patch and have run this style of analysis multiple times without issue until today. I appreciate any help! Please let me know if you need any additional information. Thanks, Alex Alex Brown CNS Core Facility Department of Psychological Sciences 115 Melvin H. Marx Building 1416 Carrie Francke Drive Columbia, MO 65211 Contact: 573-884-8779

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Hippocampal Subfield segmentation problem - Matlab exits due to fatal error
by Georgia Kapizioni 19 Nov '21

19 Nov '21

External Email - Use Caution Dear Freesurfer experts, I am trying to run hippocampal subfields segmentation, using the command: segmentHA_T1.sh subject The analysis is running for approximately 20 mins and then the following error appears: f this problem is reproducible, please submit a Service Request via: http://secure-web.cisco.com/1BR3I-eWJj4WoMclKofhZEhxAL0gJoDY1byinZeM2eZlrhY… A technical support engineer might contact you with further information. Thank you for your help.** This crash report has been saved to disk as /Users/theodore/matlab_crash_dump.4118-1 ** MATLAB is exiting because of fatal error /Applications/freesurfer/7.1.1/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 33: 4118 Killed: 9 /Applications/freesurfer/7.1.1/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML 6529 /Users/xxx/Downloads/xxx/qcache 0.333333333333333333333333333333333333 /Applications/freesurfer/7.1.1/average/HippoSF/atlas/AtlasMesh.gz /Applications/freesurfer/7.1.1/average/HippoSF/atlas/AtlasDump.mgz /Applications/freesurfer/7.1.1/average/HippoSF/atlas/compressionLookupTable.txt 0.05 left L-BFGS v21 '/Applications/freesurfer/7.1.1/bin/fs_run_from_mcr /Applications/freesurfer/7.1.1/bin/' 0 Darwin MacBook-Pro-Theodore.local 20.3.0 Darwin Kernel Version 20.3.0: Thu Jan 21 00:07:06 PST 2021; root:xnu-7195.81.3~1/RELEASE_X86_64 x86_64 T1 hippocampal subfields exited with ERRORS at Πεμ 18 Νοε 2021 15:34:58 EET Attached please also find the script output. I am using the 7. 1. version of FS. Could you please help me resolve this issue? Thank you in advance, Georgia

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Re: [Freesurfer] freeview error after installation: Segmentation fault(core dumped) / free( ): invalid pointer, Aborted(core dumped)
by fsbuild 19 Nov '21

19 Nov '21

External Email - Use Caution In your terminal window after you’ve sourced the freesurfer setup script you should be able to do,$ which freeview … and it will show something like … /usr/local/freesurfer/bin/freeview So using whatever that absolute path is to freeview on your system, then do, $ ldd  /usr/local/freesurfer/bin/freeview | grep not If you see output that says a library was not found, then something is not right with your system - which could explain the segfault.  In that case I would try to find a way to download and install the freesurfer 7.2.0 Debian package installer as that should install any missing libraries.https://secure-web.cisco.com/17qbBdi-wXIfcvgJHoFSyqwZNNfccEzYQiqa… If no libraries are reported as missing for freeview, then if you have not already tried the variations on setting DISPLAY listed at the end of this page, then I would do so, https://secure-web.cisco.com/1ZTeXQ90uTtWNjlyitGyKt3hbJVwUsSL_sYysu7DQgUWeV…   You may have to use your IP address and append :0 or :1 to it. If that does not work, then send back your default setting for DISPLAY and I will check with other people who use the WSL setup. - R. On Nov 17, 2021, at 21:02, 许霄 <xuxiao(a)xii.ac.cn> wrote:        External Email - Use Caution        I downloaded a license file, and copied the content in it to a new file created in $HOME path, named the new file 'license.txt'. After that,  reset the environment variables:$ echo "export XDG_RUNTIME_DIR=$HOME/.xdg" >> $HOME/.bashrc$ echo "export DISPLAY=:0" >> $HOME/.bashrc$ echo "export FREESURFER_HOME=/usr/local/freesurfer/7-dev" >> $HOME/.bashrc$ echo "export FS_LICENSE=$HOME/license.txt" >> $HOME/.bashrc$ echo "source /usr/local/freesurfer/7-dev/SetUpFreeSurfer.sh" >> $HOME/.bashrcMeanwhile, to test if Xming was running, I executed xeyes, and it worked. But the same error "Segmentation fault (core dumped)" still appeared. I found that there was no .xdg file under $HOME path, mentioned in the command"export XDG_RUNTIME_DIR=$HOME/.xdg" >> $HOME/.bashrc". Please see the details in the attachment. What should I do to fix it?Best Xiao-----原始邮件-----发件人:fsbuild <fsbuild@contbay.com>发送时间:2021-11-18 03:05:29 (星期四)收件人: freesurfer@nmr.mgh.harvard.edu抄送: xuxiao@xii.ac.cn主题: Re: [Freesurfer] freeview error after installation: Segmentation fault(core dumped) / free( ): invalid pointer, Aborted(core dumped)        External Email - Use Caution        Hello, Xuxiao,You need to go to this URL, MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1-AZrSjO8Cl_Hc1uoojvBIGTFics6sBFWG99iZ…, fill out the form and agree to the terms of the freesurfer license.  Then you will be able to download a license file.- R.On Nov 17, 2021, at 06:10, 许霄 <xuxiao(a)xii.ac.cn> wrote:        External Email - Use Caution        Hello FreeSurfer Developers, According to your reply, I found that xeyes worked, but there was no license file. I thought the license file would be created automatically after installation of freesurfer, or by the command "echo "export FS_LICENSE=$HOME/license.txt" >> $HOME/.bashrc". Do I need to create a license file manually?-----原始邮件-----发件人:fsbuild <fsbuild@contbay.com>发送时间:2021-11-17 10:16:00 (星期三)收件人: freesurfer@nmr.mgh.harvard.edu抄送: xuxiao@xii.ac.cn主题: Re: [Freesurfer] freeview error after installation: Segmentation fault(core dumped) / free( ): invalid pointer, Aborted(core dumped)        External Email - Use Caution        Hello Xuxiao, In a terminal window in Ubuntu running under WSL, please try just running a simple X windows program like xeyes to test that your X-server is running on Windows, $ xeyes(see attachment for what it should look like)Keep an eye out for a flashing X server icon at the bottom of your Windows desktop.  You may have to click on that flashing icon for the xeyes X window to open.  But if you can’t display something simple like xeyes with the X server on Windows 10, then freeview is not going to work.If you installed the Xming X-server on Windows, then you should see an X icon on your desktop that you can click on to start the X-server.  And you can check you see the X icon in the “hidden” area at the bottom of the screen which shows the X server is running on Windows.  See the bottom of this page for how to see Xming is running and then scroll up to see the X windows desktop icon, MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1TBZgGoCMRxatsJxkiVLCRpMVWvUvFkTaOzcvQ… xeyes works, then check your freesurfer license file can be found.  One way to do that is to set the environment variable FS_LICENSE to the absolute path to your license file.  So you could for example call your license file “license.txt” and copy it into your home directory (denoted by the environment variable $HOME).  You can also set FS_LICENSE in your shell init file.$ cd $HOME$ pwd<output deleted>$ ls license.txtlicense.txt$ export FS_LICENSE=$HOME/license.txt… check it can be read …$ cat $FS_LICENSE<output deleted>Now set FREESURFER_HOME, source the setup environment script as you did in the screenshot you sent below, and try running freeview with no arguments to see if a blank window opens.$ freeviewAnother thing to consider is to try and install the latest version of freesurfer (7.2.0) using the Ubuntu .deb package installer from https://secure-web.cisco.com/1bD8OkPccvOAmV7HP2pmcm7yP9Bsy6_MyEW01eJ2F-rwfj… and install it with,$ sudo apt-get install ./freesurfer_7.2.0_amd64.debThen you should see 7.2.0 installed as something like /usr/local/freesurfer/7.2.0 which you would use for FREESURFER_HOME- R.On Nov 16, 2021, at 07:26, 许霄 <xuxiao(a)xii.ac.cn> wrote:        External Email - Use Caution        Hello FreeSurfer Developers,I can't access the website of archives, so I have to ask questions in this way. I installed freesurfer7-dev in Ubuntu18 in wsl according to the tutorials  FS7_wsl - Free Surfer Wiki (harvard.edu) and FS7_wsl_ubuntu - Free Surfer Wiki (harvard.edu) After adding the license, when I tried to run the 'freeview' command to test if everything works well, an error popped out: Segmentation fault(core dumped). more information about my freesurfer environment is shown as attached. Could anyone help me figure it out? Thanks in advance.<freeview-Segmentation fault.png>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard..edu/mailman/listinfo/freesurfer<bug.png>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] V5 / v7
by fsbuild 18 Nov '21

18 Nov '21

External Email - Use Caution Hello Ludovica, When binaries (libraries and commands) are built with different (newer) compilers and/or run on different (newer) versions of an operating system, then the numerical results aren’t guaranteed to be the same between between releases.  See the IMPORTANT NOTE at the bottom of the downloads page, https://secure-web.cisco.com/1Of-G3pv8_jYIju10j21uSajW2HRrYUJxk9… Apart from being built with newer compilers and operating systems, how specific commands perform computations may also have changed in version 7 compared to version 5.  See the release notes for versions 6 and 7 on this page, https://secure-web.cisco.com/1NuFoGxg65bB9oU3RVYIhCjgc245S9FNl9W… If you are interested in the development history of an individual command, then you could look at the source on GitHub and read the log of changes.  For example, to look at the development history for mri_glmfit, you could route to https://secure-web.cisco.com/1qq01hy_US_gpsCh6hj0XMtzJwWQV_PcnJdrYJJllMgKQg…  and then click on the text for “History” near the top of the page on the left hand side. - R. On Nov 18, 2021, at 14:03, Brusaferri, Ludovica <LBRUSAFERRI(a)mgh.harvard.edu> wrote:Hi!I am using a pipeline that was implemented and validated using fs 5.3 , which does the following:* compute transformation matrix for linear registration of SUV with T1-2mm, with spm* use tkergister to transform the matrix into .mat, and then invert the matrix* use flirt to move T1 images into PET spaceThe last step gives me different results if I enable FS vs 7, and the registration seems to be off. Do you know why this would be the case?Thank you!Ludovica_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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longitudinal analysis – Is correcting the Base enough?
by Eszter Boros 18 Nov '21

18 Nov '21

External Email - Use Caution Dear FreeSurfer Team, I am working with a longitudinal design (before and after treatment), and based on the website's recommendation ( https://secure-web.cisco.com/1zrVKA2yLWZKJu8t_xqtLsDY49D7WzDkL9DDKJIkf-aD-t…) editing the Base could be enough for this. If I understand this right, I should generate the Base image (without editing the two Cross images) and then edit the Base only. After that, I could create the two longitudinal runs (Long) without editing them as well. Did I get this right? This could save a huge amount of time since I should edit one image (Base) instead of two (Cross images). I am using Freesurefer 7.1.1. Thank you for your answer! I greatly appreciate it. All the best, Eszter Boros

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Freesurfer November 2021