Freesurfer September 2023

freesurfer@nmr.mgh.harvard.edu

71 participants
88 discussions

FreeSurfer hippo-amygala module
by Dr. Anton Jakovcic 06 Sep '23

06 Sep '23

External Email - Use Caution Dear all, here is Anton - a PhD candidate from Max Planck Institute for Human Cognitive and Brain Research in Leipzig, Germany. Using FreeSurfer module segment_subregions, I successfully segmented amygdala for individual HCP subjects. Thanks a lot for developing it! Currently, I am trying to get a group-level or a MNI-level segmentation to build a representative figure. Do you think, is it possible to segment amygdala in MNI-registration template? Any help/suggestion is appreciated. Kind regards Anton Jakovcic

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Re: [Freesurfer] converting preprocessed surface functional data to volume
by wangzhiwei3233 06 Sep '23

06 Sep '23

External Email - Use Caution Dear Doug, Thank you for your replying. I collected the data by myself using a SIEMENS machine. Sorry, what do you mean by mapping the time course. I guess I am not trying to do that. I would like to do beta series analysis. I used the command in its old way, and I mapped it to 2mm template. It is OK now. The time and space are both acceptable. The code is as follows, I will really appricate it if you can help me to check the code. mri_surf2vol --hemi ${hemi} --o ${ROOTDIR}/$isub/bold/${irun}/spmRibbon${hemi}/${iVolume} --projfrac 0 --fillribbon --template ${SUBJECTS_DIR}/fsaverage/mri.2mm/brain.mgz \ --reg ${SUBJECTS_DIR}/fsaverage/mri.2mm/reg.2mm.dat --surfval ${ROOTDIR}/$isub/bold/${irun}/spm${hemi}/${iVolume} Best, Zhiwei >Message: 5 >Date: Sun, 20 Aug 2023 17:23:52 -0400 >From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> >Subject: Re: [Freesurfer] converting preprocessed surface functional > data to volume >To: freesurfer(a)nmr.mgh.harvard.edu >Message-ID: <c31ec38b-fcd6-c47a-8b29-f32857181a0f(a)mgh.harvard.edu> >Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > >where did the functional data come from? Are you trying to map the time >courses? That usually does not work that well as your resulting image >will be huge. One thing to do is to map it to a cropped volume (most of >the 256^3 is outside the brain) and or also map it to 2mm instead of 1mm. > >On 8/13/2023 11:02 PM, wangzhiwei3233 wrote: >> >> ????????External Email - Use Caution >> >> Dear Freesurfer experts, >> I am going to convert the preprocessed surface functional data to >> volume in fsaverage space so that I can used the processed data in SPM >> for further analysis, for example, beta series analysis. I tried >> mri_surf2vol, it worked. But it is time consuming. It takes around 5 >> minutes per 10 volumes. In addition, the result volume is too big >> (67MB/ volume for 256*256*256 matrix, 1mm resolution). My data >> contains about??70800 brain volumes, so the needed time is about >> 40days and the storage space is about 7TB , which is unacceptable. The >> code is? as follows: >> >> /mri_surf2vol --o >> ${Dir_Subj_fMRI}/$isub/bold/${irun}/Ribbon/${iVolume} --subject >> fsaverage --so ${SUBJECTS_DIR}/fsaverage/surf/lh.white >> ${Dir_Subj_fMRI}/$isub/bold/${irun}/LH/${iVolume} --so >> ${SUBJECTS_DIR}/fsaverage/surf/rh.white >> ${Dir_Subj_fMRI}/$isub/bold/${irun}/RH/${iVolume} / >> / >> / >> Are there methods with faster speed and outputing volumes with lower >> resolution? >> >> Best, >> Zhiwei

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registration error (reCAPTCHA not checked)
by lizhao_du＠sjtu.edu.cn 06 Sep '23

06 Sep '23

External Email - Use Caution Hi there, I am Oscar. Recently I am using FreeSurfer for fMRI data analysis. A license is required yet I could not get the license.txt from my e-mail. After filling the form from https://secure-web.cisco.com/174jctt4T-x9hrxRO4K0cJXM-oWXh3mvxRN7Dqptum9XXF…, a registration error occured (see below). Is there something wrong for my internet? Or what could I do to get the license? A few words from you may help me a lot. Thanks in advance. Best! Lizhao Du School of Biomedical Engineering, Shanghai Jiao Tong University Lizhao_Du(a)sjtu.edu.cn

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Re: [Freesurfer] Voxel co-ordinates under pial surface patch
by Alastair Snell 05 Sep '23

05 Sep '23

External Email - Use Caution Hi Yujing, Thanks for the reply. That's correct, I received an annotation file from running 'mris_find_flat_regions -t 0.99 -s 20 <input file> <output file>'. If I'm not mistaken, it seems that mri_annotations2label would output labels which correspond to the same surface as the annotation; I would like to achieve a label file pertaining to the volume of cortex immediately underneath the flat patch of pial surface for which I have an annotation file. I hope this makes sense and any help from anyone is really appreciated. Thanks, Alastair

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Re: [Freesurfer] MATLAB autorecon3 glibc error
by fsbuild 05 Sep '23

05 Sep '23

External Email - Use Caution  If you have not already done so, I would try installing and running a version of the Matlab runtime environment (which is not a full blown Matlab installation) that freesurfer was tested with.  For the 7.4.1 freesurfer release, that should be R2019b.  (Prior to that, it was R2014b - which you could try as well - but that would likely contain an even older version of glibc). Assuming that you can write to your own installed version of freesurfer, then once you have set FREESURFER_HOME, you can try running the fs_install_mcr script included with the freesurfer distribution.  See bash shell commands below. - R. $ export FREESURFER_HOME=<your install path> $ cd $FREESURFER_HOME/bin $ sudo FREESURFER_HOME=$FREESURFER_HOME  ./fs_install_mcr  R2019b … answer y to any installer questions ... Then I think it should work to find the Matlab libraries by at least start off with setting, $ export LD_LIBRARY_PATH=$FREESURFER_HOME/MCRv97/bin/glnxa64 Please make sure you have otherwise removed any references to your previous matlab 2020a environment from PATH, LD_LIBRARY_PATH, etc.  - R.

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MATLAB autorecon3 glibc error
by Paulk, Angelique C.,PhD 05 Sep '23

05 Sep '23

External Email - Use Caution Hello FreeSurfer Developers, I am attempting to run recon-all, whether the full recon or a part of the process (e.g. recon-all -autorecon3 -s $SUBJECT -localGI) and am finding there would be what seems to be a glibc error (e.g. https://secure-web.cisco.com/1aJXVSDwcefv7rhlrTYwyBgTiVEvYt2dSphBaETv3j1Zle…) that occurs during any one of the MATLAB steps of the recon-all process. Certain versions of MATLAB appear to be missing the correct installations for glibc so I did follow the steps to install it (e.g. https://secure-web.cisco.com/1Zt0UN3L2lns-RzoRlpw4wwob_uSJBgC8w5Pk-IdqY6Mvb… ), but this error has been wildly inconsistent. For instance, the challenging issue is that this Freesurfer installation appears to work perfectly fine for some cases but would error out (one example set of errors below) causing me to think it is the glibc issue. Further, it is not consistent which MATLAB-based step causes the error (it could error out in one of the many MATLAB steps for one brain scan but it would be a different MATLAB step for another brain scan). Therefore, I have multiple error-ed out recon-all files across 15 scans (different participants) which all appear to stop at different stages of the process. Error example: MATLAB is selecting SOFTWARE OPENGL rendering. Inconsistency detected by ld.so: ../elf/dl-tls.c: 481: _dl_allocate_tls_init: Assertion `listp->slotinfo[cnt].gen <= GL(dl_tls_generation)' failed! ERROR: find_corresponding_center_FSformat did not complete successfully! Command exited with non-zero status 1 @#@FSTIME 2023:09:04:18:17:29 mris_compute_lgi N 2 e 17.45 S 4.32 U 44.58 P 280% M 2246188 F 0 R 1909235 W 0 c 909 w 36844 I 0 O 39440 L 1.01 1.06 1.07 @#@FSLOADPOST 2023:09:04:18:17:47 mris_compute_lgi N 2 1.74 1.22 1.13 Linux ebonyandrgb 5.4.0-137-generic #154~18.04.1-Ubuntu SMP Tue Jan 10 16:58:20 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux recon-all -s XXXXXX_SurferOutput exited with ERRORS at Mon Sep 4 18:17:47 EDT 2023 I've searched the list and no similar errors have been reported for recent MATLAB installations. Does anyone have any thoughts on how to trouble-shoot this one? I can send the recon-all log as well if need be though there are a number of them. 1) FreeSurfer version: freesurfer-linux-ubuntu18_amd64-7.4.1 2) Platform: Ubuntu 18 3) uname -a: Linux ebonyandrgb 5.4.0-137-generic #154~18.04.1-Ubuntu SMP Tue Jan 10 16:58:20 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: Can send following deidentification if need be but there are multiple examples of recon-all.log errors 5) MATLAB 2020a

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Voxel co-ordinates under pial surface patch
by Alastair Snell 05 Sep '23

05 Sep '23

External Email - Use Caution Dear Freesurfer experts, After using mris_find_flat_regions to locate a flat patch on the pial surface, I now wish to extract the voxel co-ordinates of the volume within the cortex just below this flat region. Any ideas on how I can do this? As always, any help is much appreciated. Thanks, Alastair

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FS license for VM image
by Anna-Liisa Iive Sepp 05 Sep '23

05 Sep '23

External Email - Use Caution Hi Freesurfer experts, I am running the Ubuntu VirtualBox image with the pre downloaded 7.2.0 Freesurfer. However, it claims that it doesn't have a Freesurfer license. The online Google drive tutorial document provides a link to a form, but the link does not work. How can I obtain the license? Thanks, Anna -- PhD Candidate Microscale Biocomplexity Laboratory Dept. Biomedical Engineering at Columbia University

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Re: [Freesurfer] [COPY] Fwd: Installation Support for Windows (WSL Linux)
by fsbuild 05 Sep '23

05 Sep '23

External Email - Use Caution  The Freesurfer WSL wiki page has been updated to show the download, install and setup of the freesurfer 7.4.1 Ubuntu 22 package (latest release).. - R. On Sep 4, 2023, at 19:51, Michael Mc Laughlin <michael(a)thecurate.com> wrote:        External Email - Use Caution        Cool! Thanks for the update! On Mon, Sep 4, 2023 at 6:17 PM Sabrena Tuy <stuy2746(a)sdsu.edu> wrote:Hello!After wiping out WSL and Ubuntu, I restarted the process with some different instructions guides by an outdated page from the website and I believe someone linked it in a response of supporting me as well. Fortunately, I was able to figure it out!! Thanks for all of your help!Sincerely,Sabrena TuyOn Mon, Sep 4, 2023 at 1:22 AM Michael Mc Laughlin <michael(a)thecurate.com> wrote:Hi Sabrena,Once you get it working the WSL option works flawlessly but it can be tricky to get over the first hurdle. The help instructions are written assuming that you are fluent in Linux.Check which version of Ubuntu you have. When you start WSL it will give you a message like:Welcome to Ubuntu 22.04.2and download the corresponding release of Freesurfer 7.4.1The help doesn't tell you how to download or install the package and I'm afraid I have forgotten the commands. Maybe someone else can chime in here?I use VcXsrv for my X-server graphics interface.MichaelOn Sun, Sep 3, 2023 at 7:23 AM fsbuild <fsbuild(a)contbay.com> wrote:        External Email - Use Caution        Hello Sabrena,We have some notes posted about setting up WSL on the wiki page under, MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1BBLvc8hOj6S4O_4mbyaaPyyXKlrB_xFdTx9Ja… are probably running some version of WSL version 2 (WSL2), but since WSL can change w/o notice, we can’t guarantee our notes work for every Windows 11 (or Windows 10) setup.  See the section there "Setup and Install WSL version 2” including the link to the MS documentation.   If you can get WSL working and login to its Ubuntu Linux terminal window, then we can direct you how to install the freesurfer 7.4.1 release.If you want to run freeview to view brain images with WSL, you will also need to install a 3rd party X-server like XMing to MobaXterm as well on your Windows system.  Some users have not been able to get freeview to work on their system after consulting our wiki page notes.An alternative to using WSL is to use a different virtualization application like VirtualBox.  Some users find VirtualBox easier to setup and manage especially compared to getting WSL to work with freeview and viewing images.  You would download and install the VirtualBox application on your Windows machine, and then download and install our Ubuntu 18 Linux OS image with Freesurfer pre-installed.   The notes for that are under,MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1OyYdKcf5JD9g74UZ0Jn9zcZYssuDtbBCfIeyk… can send you the codes to unlock the VirtualBox image and login.  With the VirtualBox setup, there is no additional 3rd party X-server setup needed in order to view images with freeview.- R.Begin forwarded message:From: Sabrena Tuy <stuy2746@sdsu.edu>Subject: [Freesurfer] Installation Support for Windows (WSL Linux)Date: September 2, 2023 at 20:18:48 EDTTo: freesurfer@nmr.mgh.harvard.eduReply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>        External Email - Use Caution        Hello,I am a student in an MRI lab at SDSU that uses Freesurfer religiously, and unfortunately, I am a Windows (11) user. I have scrolled mindlessly and have made some progress on beginning the installation for Freesurfer, but I have come to a complete standstill.. Is there any way you can help me install the program onto my PC since I will need to use it for my lab work?Sincerely,Sabrena TuySincerely,Sabrena Tuy_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh..harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/15gClFtc6FO3hbdmG0SDPPXtdWvcmG_RhlHC2D… is a copy of a message which has been originally sent to: "To" field: freesurfer@nmr..mgh.harvard.edu"Copy" field: stuy2746@sdsu.eduThe message has been sent by MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1-c76h5r4lhOo3vFU9RHn3RmQ-1qgGrL6tuwUj… the used account name was: SSL  _______________________________________________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/178XO9Va1WJYxViVk8o3JRpEGX5kYSqPMdY-8o… note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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[COPY] Fwd: Installation Support for Windows (WSL Linux)
by fsbuild 04 Sep '23

04 Sep '23

External Email - Use Caution Hello Sabrena, We have some notes posted about setting up WSL on the wiki page under, https://secure-web.cisco.com/1c9KrekHizcdGhd-EUpY8z6zQtrZ7Hnb3D… You are probably running some version of WSL version 2 (WSL2), but since WSL can change w/o notice, we can’t guarantee our notes work for every Windows 11 (or Windows 10) setup.  See the section there "Setup and Install WSL version 2” including the link to the MS documentation.   If you can get WSL working and login to its Ubuntu Linux terminal window, then we can direct you how to install the freesurfer 7.4.1 release. If you want to run freeview to view brain images with WSL, you will also need to install a 3rd party X-server like XMing to MobaXterm as well on your Windows system.  Some users have not been able to get freeview to work on their system after consulting our wiki page notes. An alternative to using WSL is to use a different virtualization application like VirtualBox.  Some users find VirtualBox easier to setup and manage especially compared to getting WSL to work with freeview and viewing images.  You would download and install the VirtualBox application on your Windows machine, and then download and install our Ubuntu 18 Linux OS image with Freesurfer pre-installed.   The notes for that are under,https://secure-web.cisco.com/1P4pBW1lhSQIuXvY6PhRq81dp468Q3FTax8bdRBv… can send you the codes to unlock the VirtualBox image and login.  With the VirtualBox setup, there is no additional 3rd party X-server setup needed in order to view images with freeview. - R. Begin forwarded message:From: Sabrena Tuy <stuy2746(a)sdsu.edu> Subject: [Freesurfer] Installation Support for Windows (WSL Linux) Date: September 2, 2023 at 20:18:48 EDT To: freesurfer@nmr.mgh.harvard.edu Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu>         External Email - Use Caution        Hello,I am a student in an MRI lab at SDSU that uses Freesurfer religiously, and unfortunately, I am a Windows (11) user. I have scrolled mindlessly and have made some progress on beginning the installation for Freesurfer, but I have come to a complete standstill.. Is there any way you can help me install the program onto my PC since I will need to use it for my lab work?Sincerely,Sabrena TuySincerely,Sabrena Tuy_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- This is a copy of a message which has been originally sent to: "To" field: freesurfer@nmr..mgh.harvard.edu "Copy" field: stuy2746(a)sdsu.edu The message has been sent by https://secure-web.cisco.com/1q5buhaTDBn7kf7dqnltFmmqQFe0P3mcvBOkBwMIlZP0zw… and the used account name was: SSL  

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Freesurfer September 2023