Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

Re: [Freesurfer] on Ubuntu (was FreeSurfer V 7.0 on Centos 8) {Disarmed}
by fsbuild 14 May '20

14 May '20

External Email - Use Caution Hello Tristan, I can send you an email directly later today with some tests you can try for freeview and some other commands  If the test succeeds, then at least it would mean your environment is good. The original bug report on the Arch Linus page - while listing  a signal 11 - did not look to me like it was not from the same cause as what you subsequently posted.  That error was detecting a divide by zero (before it happened) in the hardware from some calculation which I take to mean the loader had previously found everything it needed to load the binaries into memory and run them. BTW - the 7.1.0 binaries on the download page should work on CentOS8 if you have that OS to try. - R. On May 13, 2020, at 18:09, TRISTAN J PAUTSCH <tpautsch(a)wisc.edu> wrote:        External Email - Use Caution        Just following up to confirm that this issue persists in 7.1..0 in case anyone has any ideas; I've tried everything I can think of at this point.:(From: TRISTAN J PAUTSCH <tpautsch@wisc.edu>Sent: Friday, April 17, 2020 12:21 PMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Cc: ts+ml@rcmd.org <ts+ml@rcmd.org>Subject: Re: [Freesurfer] on Ubuntu (was FreeSurfer V 7.0 on Centos 8) {Disarmed} Just a quick follow up, I've now been able to find my issue in the wild as well (not just on my own machines). I use Arch Linux personally and on a small handful of workstations professionally, and when investigating using FS on Arch, I stumbled upon an AUR build someone had done. While I didn't intend to use this buildfile (still version 6.x), the top comment on the below link alludes to the same PETSC error message with FS as I'm experiencing on my Ubuntu machines:https://aur.archlinux.org/packages/freesurfer-bin/TFrom: TRIS… J PAUTSCH <tpautsch@wisc.edu>Sent: Monday, April 6, 2020 1:32 PMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Cc: ts+ml@rcmd.org <ts+ml@rcmd.org>Subject: Re: [Freesurfer] on Ubuntu (was FreeSurfer V 7.0 on Centos 8) {Disarmed} Apologies for the late reply, hectic times. Please find the requested files here:https://uwmadison.box.com/s/vod1t4vlycd9baom42qqqwkc6unj9auiLet me know how else I can help!TFrom: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard..edu> on behalf of fsbuild(a)contbay.com <fsbuild@contbay.com>Sent: Tuesday, March 31, 2020 6:20 PMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Cc: ts+ml@rcmd.org <ts+ml@rcmd.org>Subject: Re: [Freesurfer] on Ubuntu (was FreeSurfer V 7.0 on Centos 8) {Disarmed}         External Email - Use Caution        Hello Tristan,Going back to that thread, I’d like to try the command you uploaded data for as freesurfer_data.tar.gz on a couple of Ubuntu systems, but either I’m looking in the wrong place or it’s not there anymore.  Is there a shared google drive link or something you point me to for a download link? > freeview -v brainmask.mgz T1.mgz -f lh.white:edgecolor=yellow > lh.pial:edgecolor=magenta rh.white:edgecolor=yellow rh.pial:edgecolor=magenta > > We can also replicate the error by opening freeview and opening all the above > files sequentially through the GUI.- R.On Mar 31, 2020, at 13:41, TRISTAN J PAUTSCH <tpautsch(a)wisc.edu> wrote:        External Email - Use Caution        Thanks for the reply, all.The issues I'm having are the same as they were in my prior thread, found here:MailScanner has detected a possible fraud attempt from "www..mail-archive.com" claiming to be https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg6345… tried everything up to and including compiling everything from scratch (including FS itself, missing libs, PETSC, etc.). The main takeaway is that I pretty convincingly narrowed the issue down to PETSC+Ubuntu 18.04, the most pertinent details for that being in the following post:https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg63702.h… when I was active in that thread, I emailed the PETSC mailing list and got no response, and at the time I was pretty busy with other projects so I had to let it go for the time being; I maintained my old RHEL6 server so people could continue to use FS. Now with everyone in quarantine (and RHEL6 entering ELS this November), it's a decent time to look back into this issue. I wouldn't have reached back out to the FS list, however when I saw that a focus was being placed on Ubuntu (and that there was a working Ubuntu VM), I became hopeful that maybe this issue was resolved?TFrom: fsbuild@contbay.com <fsbuild@contbay.com>Sent: Tuesday, March 31, 2020 3:57 AMTo: freesurfer@nmr.mgh..harvard.edu <freesurfer@nmr.mgh.harvard.edu>Cc: ts+ml@rcmd.org <ts+ml@rcmd.org>; TRISTAN J PAUTSCH <tpautsch@wisc..edu>Subject: Re: [Freesurfer] on Ubuntu (was FreeSurfer V 7.0 on Centos 8) We would also like to know about any issues you are seeing on Ubuntu.I think Ubuntu eliminated some jpeg/png packages from their repos.  Those can be downloaded and installed manually,e.g., libpng12-0_1.2.54-1ubuntu1.1_amd64.deb, libjpeg62_6b2-3_amd64.deb.  That is part of the reason we made an Ubuntu 18 VM available with everything pre-installed. The VM is essentially what has been used for the freesurfer course which runs mostly freeview commands with some mri* commands (though I believe a recon-all also works).  The VM is running binaries built on CentOS7 - as the reference platforms for freesurfer dev are currently CentOS and MacOS.  We are looking at making a .deb installer for freesurfer on Ubuntu though.There is some info on the wiki about packages required to compile the source on Ubuntu - but you don’t need all of these to run (even the CentOS) binaries.MailScanner has detected a possible fraud attempt from "surfer..nmr.mgh.harvard..edu" claiming to behttps://surfer.nmr.mgh.harvard.edu/fswiki/BuildRequirements- R.On Mar 31, 2020, at 02:50, Tim Schäfer <ts+ml(a)rcmd.org> wrote:       External Email - Use Caution        Hi Tristan,I'm about to setup a FreeSurfer installation on an Ubuntu system, and I wondered whether you could elaborate on the kind of issues you are experiencing.Best,Tim--Dr. Tim SchäferPostdoc Computational NeuroimagingDepartment of Child and Adolescent Psychiatry, Psychosomatics and PsychotherapyUniversity Hospital Frankfurt, Goethe University Frankfurt am Main, GermanyOn March 30, 2020 at 11:01 PM TRISTAN J PAUTSCH <tpautsch(a)wisc.edu> wrote:       External Email - Use Caution        Is there going to be an "official" Ubuntu build this time around (as in, built and tested in Ubuntu) that isn't the VM? Both the current CentOS and the dev builds continue to have issues (even when compiled from scratch) on my Ubuntu 18.04 servers.Thanks!T________________________________From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of fsbuild(a)contbay.com <fsbuild(a)contbay.com>Sent: Monday, March 30, 2020 9:40 AMTo: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu>Cc: dr.minafakhry(a)live.com <dr.minafakhry(a)live.com>Subject: Re: [Freesurfer] FreeSurfer V 7.0 on Centos 8       External Email - Use CautionHello Mina,I see from https://www.centosblog.com/centos-eol-dates/ that CentOS 6 will no longer be updated as of 11/2020, and similarly for CentOS 7 in 6/2024.  It looks like CentOS 8 was released around September of 2019.While we do not currently build/test on CentOS8, I am sure it will eventually be supported.   Given some users will continue to use CentOS 6 even after 11/2020 and that many people have been running the freesurfer 6 release on CentOS6, then even the upcoming freesurfer 7 release is targeting CentOS6, CentOS7 and Ubuntu linux (as well as Mac OS).There is also currently an Ubuntu 18 VM with freesurfer 6 and the beta release of freesurfer 7 pre-installed which you can find here, https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67- R.On Mar 30, 2020, at 08:52, Mina Rizkallah <dr.minafakhry(a)live.com> wrote:       External Email - Use CautionGreetings FreeSurfer team,I recently upgraded by workstation from Centos 7 to 8.1 as the support for centos  7 will be over soon.I tried installing freesurfer version 7.0 beta 1 but failed due to some unresolved dependencies (tried on a  virtual centos 7 and worked fine) !!so, when will there be support for centos 8, thank youBest regardsMina_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________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_______________________________________________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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Recon-all Talairach failed error
by Peng Liu 14 May '20

14 May '20

External Email - Use Caution Dear Freesurfer experts, I am trying to run recon-all for a new subject, however I came across with this error 'Talairach failed'. The error log is as following: *talairach done\n cp transforms/talairach.auto.xfm transforms/talairach.xfm \n#--------------------------------------------#@# Talairach Failure Detection Thu May 14 15:11:47 CEST 2020/Users/pliu/Documents/DataAnalysis0512/subjects/Pilot03/mri\n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \nERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0153, pval=0.0000 < threshold=0.0050)\nManual Talairach alignment may be necessary, orinclude the -notal-check flag to skip this test,making sure the -notal-check flag follows -allor -autorecon1 in the command string.See:\nhttp://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach <http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach>\nERROR: Talairach failed!\n* I have read online that I might need to perform a rough coregistration for the input image before running recon-all. But I am a bit lost by which image should it be registered to... Would 'mni305.cor.mgz' be okay as reference image? Any help would be much appreciated. Kindly Regards Peng Liu -------------------------------------------- [image: Otto-von-Guericke University Magdeburg] Peng Liu, PhD Candidate Institut für Kognitive Neurologie und Demenzforschung (IKND) Otto-von-Guericke Universität Magdeburg Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE) Leipziger Str. 44| Haus 64| Raum 217 39120 Magdeburg, Deutschland Email: peng.liu@med.ovgu.de/Peng.Liu@dzne.de Phone: +49 391 67 25074

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trac-all prep error
by Zeng, Qi 13 May '20

13 May '20

External Email - Use Caution Hi, I have an error message when processing trac-all prep. attached the log file. error: "terminate called after throwing an instance of 'std::logic_error' what(): Mat::operator(): index out of bounds" Recon-all was finished without error. However, my raw DTI DCM file is 120 compared to others with over 2000 slices. Would that be a problem? Best, Qi -- Ph.D. candidate Icahn School of Medicine at Mount Sinai

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Re: [Freesurfer] on Ubuntu (was FreeSurfer V 7.0 on Centos 8) {Disarmed}
by fsbuild 13 May '20

13 May '20

External Email - Use Caution Hello Tristan, Going back to that thread, I’d like to try the command you uploaded data for as freesurfer_data.tar.gz on a couple of Ubuntu systems, but either I’m looking in the wrong place or it’s not there anymore.  Is there a shared google drive link or something you point me to for a download link?  > freeview -v brainmask.mgz T1.mgz -f lh.white:edgecolor=yellow > lh.pial:edgecolor=magenta rh.white:edgecolor=yellow rh.pial:edgecolor=magenta > > We can also replicate the error by opening freeview and opening all the above > files sequentially through the GUI. - R. On Mar 31, 2020, at 13:41, TRISTAN J PAUTSCH <tpautsch(a)wisc.edu> wrote:        External Email - Use Caution        Thanks for the reply, all.The issues I'm having are the same as they were in my prior thread, found here:https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg63458.h… tried everything up to and including compiling everything from scratch (including FS itself, missing libs, PETSC, etc.). The main takeaway is that I pretty convincingly narrowed the issue down to PETSC+Ubuntu 18.04, the most pertinent details for that being in the following post:https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg63702.h… when I was active in that thread, I emailed the PETSC mailing list and got no response, and at the time I was pretty busy with other projects so I had to let it go for the time being; I maintained my old RHEL6 server so people could continue to use FS. Now with everyone in quarantine (and RHEL6 entering ELS this November), it's a decent time to look back into this issue. I wouldn't have reached back out to the FS list, however when I saw that a focus was being placed on Ubuntu (and that there was a working Ubuntu VM), I became hopeful that maybe this issue was resolved?TFrom: fsbuild@contbay.com <fsbuild@contbay.com>Sent: Tuesday, March 31, 2020 3:57 AMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Cc: ts+ml@rcmd.org <ts+ml@rcmd.org>; TRISTAN J PAUTSCH <tpautsch@wisc.edu>Subject: Re: [Freesurfer] on Ubuntu (was FreeSurfer V 7.0 on Centos 8) We would also like to know about any issues you are seeing on Ubuntu.I think Ubuntu eliminated some jpeg/png packages from their repos.  Those can be downloaded and installed manually,e.g., libpng12-0_1.2.54-1ubuntu1.1_amd64.deb, libjpeg62_6b2-3_amd64.deb.  That is part of the reason we made an Ubuntu 18 VM available with everything pre-installed.. The VM is essentially what has been used for the freesurfer course which runs mostly freeview commands with some mri* commands (though I believe a recon-all also works).  The VM is running binaries built on CentOS7 - as the reference platforms for freesurfer dev are currently CentOS and MacOS.  We are looking at making a .deb installer for freesurfer on Ubuntu though.There is some info on the wiki about packages required to compile the source on Ubuntu - but you don’t need all of these to run (even the CentOS) binaries.MailScanner has detected a possible fraud attempt from "surfer..nmr.mgh.harvard.edu" claiming to behttps://surfer.nmr.mgh.harvard.edu/fswiki/BuildRequirements- R.On Mar 31, 2020, at 02:50, Tim Schäfer <ts+ml(a)rcmd.org> wrote:       External Email - Use Caution        Hi Tristan,I'm about to setup a FreeSurfer installation on an Ubuntu system, and I wondered whether you could elaborate on the kind of issues you are experiencing.Best,Tim--Dr. Tim SchäferPostdoc Computational NeuroimagingDepartment of Child and Adolescent Psychiatry, Psychosomatics and PsychotherapyUniversity Hospital Frankfurt, Goethe University Frankfurt am Main, GermanyOn March 30, 2020 at 11:01 PM TRISTAN J PAUTSCH <tpautsch(a)wisc.edu> wrote:       External Email - Use Caution        Is there going to be an "official" Ubuntu build this time around (as in, built and tested in Ubuntu) that isn't the VM? Both the current CentOS and the dev builds continue to have issues (even when compiled from scratch) on my Ubuntu 18.04 servers.Thanks!T________________________________From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of fsbuild(a)contbay.com <fsbuild(a)contbay.com>Sent: Monday, March 30, 2020 9:40 AMTo: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu>Cc: dr.minafakhry(a)live.com <dr.minafakhry(a)live.com>Subject: Re: [Freesurfer] FreeSurfer V 7.0 on Centos 8       External Email - Use CautionHello Mina,I see from https://www.centosblog.com/centos-eol-dates/ that CentOS 6 will no longer be updated as of 11/2020, and similarly for CentOS 7 in 6/2024.  It looks like CentOS 8 was released around September of 2019.While we do not currently build/test on CentOS8, I am sure it will eventually be supported.   Given some users will continue to use CentOS 6 even after 11/2020 and that many people have been running the freesurfer 6 release on CentOS6, then even the upcoming freesurfer 7 release is targeting CentOS6, CentOS7 and Ubuntu linux (as well as Mac OS).There is also currently an Ubuntu 18 VM with freesurfer 6 and the beta release of freesurfer 7 pre-installed which you can find here, https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67- R.On Mar 30, 2020, at 08:52, Mina Rizkallah <dr.minafakhry(a)live.com> wrote:       External Email - Use CautionGreetings FreeSurfer team,I recently upgraded by workstation from Centos 7 to 8.1 as the support for centos  7 will be over soon.I tried installing freesurfer version 7.0 beta 1 but failed due to some unresolved dependencies (tried on a  virtual centos 7 and worked fine) !!so, when will there be support for centos 8, thank youBest regardsMina_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________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_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] mri_glmfit ERROR: matrix is ill-conditioned or badly scaled -
by Marina Fernández 13 May '20

13 May '20

External Email - Use Caution Thank you, Doug. That makes sense. Do you think in this case it is a good option to add the flag --illcond to run this analysis without getting an error? or is it better not to use the variable apoe in these statistical analyzes? What do you recommend us? Best wishes, Marina.

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Re: [Freesurfer] Compare individual to a group
by Xiaojiang Yang 13 May '20

13 May '20

External Email - Use Caution Hi Douglas, I have tried to follow your suggestion to use the transformed thickness file like this: mris_preproc --fsgd xxx.fsgd \ --meas $meas.fwhm$smoothing.xformed.mgz \ --target fsaverage \ --hemi $hemi \ --out $hemi.$meas.$smoothing.mgh But it says $meas.fwhm$smoothing.xformed.mgz does not match surface (163842,166904). My files $meas.fwhm$smoothing.xformed.mgz come from $meas.fwhm$smoothing.fsaverage (just by multiplying it with a weight). If I use "--cache-in" in the mris_preproc like below: mris_preproc --fsgd xxx.fsgd \ --cache-in $meas.fwhm$smoothing.fsaverage \ --target fsaverage \ --hemi $hemi \ --out $hemi.$meas.$smoothing.mgh The above command line runs fine. I know the problem in the first command line might be that the files $meas.fwhm$smoothing.xformed.mgz are already on the fsaverage surface, not the subject surface. But mris_preproc is still trying to use mri_surf2surf to resample those mgh file from the subject surface to fsaverage surface, which leads to the "does not match surface" error. My question is: How can I tell mris_preproc to regard those transformed files to be on the fsaverage surface already (instead of subject's surface), just like the second command line where the "-cache-in" option is used? You know, my transformed files are Just derived from cached files $hemi.$meas.fwhm$smoothing.fsaverage.mgh in the $subject/surf directories. I do not want to use mri_surf2surf to transform them to the subject surface first, and then let mris_preproc transform them back to fsaverage surface again. Thanks! Xiao <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from :%22Douglas+N.+Greve%22> Douglas N. Greve <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date :20200511> Mon, 11 May 2020 14:14:42 -0700 Just call your thickness file some other name, eg, lh.xformed.thickness.mgz, the just specify --meas xformed.thickness.mgz On 5/11/2020 3:52 PM, Xiaojiang Yang wrote: External Email - Use Caution Thank you Douglas! If I apply my transform to both the healthy controls and the patient, I guess I would lose the convenience of using mri_glmfit, which eventually loses the convenience of using mri-glmfit-sim (I don't care not using mri_glmfit, but I want to use mri_glmfit-sim to do multiple comparisons correction). That is because mri_glmfit uses the prepared output from mris_preproc, which I have no control over to use the transformed subject. The only way I can circumvent this is to use my transformed thickness file to overwrite the FS calculated thickness file, but that is what I am hesitant to do. If you have good suggestions regarding this, please let me know. Thanks! Xiao On Mon, May 11, 2020 at 12:25 PM Douglas N. Greve <dgr...(a)mgh.harvard.edu < <mailto:dgr...@mgh.harvard.edu> mailto:dgr...@mgh.harvard.edu>> wrote: I guess you could apply your transform to both the healthy controls and to your patient, can then create an FSGD file with two classes as before but no continuous variable. Then just have a contrast that computes the diff between the patient and the mean of the controls.

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Re: [Freesurfer] mri_glmfit ERROR: matrix is ill-conditioned or badly scaled -
by Marina Fernández 13 May '20

13 May '20

External Email - Use Caution Hi Douglas, I email you the fsgd file and I have also sent it through FTP. Thank you for your attention. Best regards, Marina.

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Which subject does recon-all register surfaces to?
by Ian 13 May '20

13 May '20

External Email - Use Caution Hi guys. After recon-all, the /surf/?h.sphere.reg file implies a registration has been performed to an "average" subject on a sphere. Can you please tell me which subject this is? Is it SUBJECTS_DIR/fsaverage? If so, what is SUBJECTS_DIR/fsaverage/lh.sphere.reg a registration to? If not, where can I find the subject that recon-all registers to? Thanks, Ian -- *Ian Hardingham*

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Issue of freesurfer ubuntu 18 VM setup on windows 10
by Yue Liu 13 May '20

13 May '20

External Email - Use Caution Hello FreeSurfer Developers. I installed and setup freesurfer ubuntu 18VM following steps in the website https://surfer.nmr.mgh.harvard.edu/fswiki//VM_67_win. However, when I clicked green start button to run VM at the last step, it did not go directly to an empty desktop. A login interface appeared instead with the account name as "Developer" (Please see attached screeshot). I tried some passwords or using other account names, while none did work. Do you have any idea what is the problem? Thank you, Yue Liu

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FreeSurfer v6.0 minimal Docker image
by Ерохин Александр 13 May '20

13 May '20

External Email - Use Caution Hello together! I’d like to share my attempt on providing minimal Docker image of the FreeSurfer that is fully operational in terms of recon-all functionality. Please see: https://hub.docker.com/r/alerokhin/freesurfer6 Compressed size is 732.6 MB Size of pulled image is 1.92GB Please follow simple instructions from Docker hub repository in order to get it running. In case of any issues or suggestions please contact me by email specified in the description of the repository. Really hope that it would be helpful for someone. Best regards, Aleksandr Erokhin.

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