Freesurfer

freesurfer@nmr.mgh.harvard.edu

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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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Help
by Nilab Nasrullah 18 Nov '21

18 Nov '21

External Email - Use Caution Hi, I am editing about 120 subjects for a research project. In some reconstructions, the grey matter boundary is not recognised, thus Freesurfer classifies it as white matter. I have tried to remove additional pial surface in the area and it gets a bit better. I have also tried to erase the wm that is classified as gm but the results don't change. Using control points is useless since the white matter is classified correct. Is there any way I can edit the subject to get better boundaries for the grey matter? Thank you for your help in advance. //Nilab Nasrullah När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://secure-web.cisco.com/15j2MT98v_oiKQhHBGfuJhMcwjnzZPBW7DMojlJbPAlvTd…>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI's processing of personal data here<https://secure-web.cisco.com/1DlyxTNQzYpSS-fXeLORGmWPkKUEgUdunIz5JVvQmQ8_9o…>.

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Re: [Freesurfer] freeview error after installation: Segmentation fault(core dumped) / free( ): invalid pointer, Aborted(core dumped)
by fsbuild 17 Nov '21

17 Nov '21

External Email - Use Caution Hello, Xuxiao, You need to go to this URL, https://secure-web.cisco.com/1crNBAUgLZ3m6E0Fhbayk9W3IGxcTGzIN3PT…, 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/1H_CTeKTz6NdVgYALgwJR96KSB3QipiR_myHy5… 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/1ZL6MYJBHRf57DH2b32bhIZVsh9Do26VHKbPCwa6qZJKfj… 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

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Fwd: OpenNeuroPET hackathon at MGH -- Dec 6th and 7th
by Douglas N. Greve 17 Nov '21

17 Nov '21

For those interested in PET and BIDS, this should be pretty useful. -------- Forwarded Message -------- Subject: OpenNeuroPET hackathon at MGH -- Dec 6th and 7th Date: Wed, 17 Nov 2021 19:31:48 -0500 From: Wighton, Paul <PWIGHTON(a)mgh.harvard.edu> To: Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu> Hi Doug, I was hoping you could forward this to anyone you think may be interested. Thanks. We are hosting a hackathon on Dec 6th and 7th in close collabration with the OpenNeuroPET group (openneuropet.github.io). The goal of the Hackathon is to educate researchers about the new BIDS-PET standard, to help researchers curate BIDS-PET datasets and to discuss how to build and execute pipelines that can operate on BIDS datasets. We are also super interested in multi-modal imaging more generally. Details can be found here: https://github.com/openneuropet/outreach/tree/main/Brainhack-MGH2021. Please reach out to Paul Wighton (pwighton(a)mgh.harvard.edu) if you have any questions or would like to give a talk or have a project you would like to propose. If you'd like to attend some or all of the talks either virtually, or in person (for MGH employees only due to COVID) but don't have the bandwidth to give a talk or work on a project, that's ok too! -Paul

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Using Mri_vol2surf
by m-maiworm＠web.de 17 Nov '21

17 Nov '21

2 3

hippocampal subfield segmentation with DCM
by Wei Shao 17 Nov '21

17 Nov '21

External Email - Use Caution Hi, FreeSurfer experts I'm wondering if there is a way to do hippocampal subfield segmentation with T2 DCM images, instead of NifTi. like this ADNI_002_S_0295_MR_Axial_T2-Star__br_raw_20110602125226394_36_S110471_I238619.dcm Best, Wei

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[recon-all error] Excessive topologic defect encountered
by Alec Süwolto 17 Nov '21

17 Nov '21

2 1

FREESURFER - Re-con all problems
by Alison McDonnell 17 Nov '21

17 Nov '21

External Email - Use Caution when i run recon all it creates all the subfolders but they're empty. the only thing that is actually generated is orig.mgz and rawavg.mgz in the mri subfolder. i didn't get any errors when running recon all so was hoping someone could shed some light on this. Many thanks

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