Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30086 discussions

Setup & Configuration Error
by Hossein Shooli 01 Apr '20

01 Apr '20

External Email - Use Caution Hello FreeSurfer Development Team, I have just install the FreeSurfer (freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c) on my mac Catalina OS (10.15.2). The installation path was set as default (/Application/freesurfer). Then, in the Setup & Configuration step I have faced some troubles that I'm in need to fix it. In this step the first line " $> export FREESURFER_HOME=/Applications/freesurfer" works properly. But when I typed the " $> source $FREESURFER_HOME/SetUpFreeSurfer.sh ". an error occurred as below: Hosseins-MacBook-Pro:~ dhs$ > export FREESURFER_HOME=/Applications/freesurfer Hosseins-MacBook-Pro:~ dhs$ > source $FREESURFER_HOME/SetUpFreeSurfer.sh /Applications/freesurfer/SetUpFreeSurfer.sh: line 14: return: can only `return' from a function or sourced script /Applications/freesurfer/SetUpFreeSurfer.sh: line 42: /FreeSurferEnv.sh: No such file or directory Hosseins-MacBook-Pro:~ dhs$ I have done this steps using bash shell but the results was the same as following: bash-3.2$ chsh -s /bin/sh Changing shell for dhs. Password for dhs: bash-3.2$ > export FREESURFER_HOME=/Applications/freesurfer/ bash-3.2$ > source $FREESURFER_HOME/SetUpFreeSurfer.sh /Applications/freesurfer//SetUpFreeSurfer.sh: line 14: return: can only `return' from a function or sourced script /Applications/freesurfer//SetUpFreeSurfer.sh: line 42: /FreeSurferEnv.sh: No such file or directory bash-3.2$ I have checked the mail archives but there no answer to my problem. Please help me to solve the issue and setup freesurfer successfully. Bests regard Hossein [image: Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=sig…> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=sig…> 04/01/20, 12:44:24 PM

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Recon-all exited with errors
by Wang, Lily 01 Apr '20

01 Apr '20

Hi All, I have a subject whose T1 quality is quite good but reconstruction exited with errors so I am not sure what the issue could be. Attached is the recon-all.log. Could it be that the subject is very old and has a lot of degeneration? Thank you, Lily

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Color map - color bar
by Adam Rytina 01 Apr '20

01 Apr '20

External Email - Use Caution Hello all, I did the post-processing on brain images in Freesurfer. I changed the color coding to display where MR signals values are higher or lower. I need to add the color bar onto the image in order to easily identify what "blue" or "red" color means. Please, in which program is it possible to change the color map and to add the color bar as well? I tried to implement it in ITK-SNAP but the option of adding the color bar is not implemented there. Thanks a lot Regards Adam

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Re: [Freesurfer] Setup & Configuration Error (Mac OS Catalina)
by fsbuild 01 Apr '20

01 Apr '20

External Email - Use Caution Hello Hossein, Not sure what you have set for your shell in terminal, but the default shell in Mac OS 10.15 is no longer bash but zsh instead. So first try running the bash shell, $ bash … then try again to do … $ export FREESURFER_HOME=/Applications/freesurfer$ source $FREESURFER_HOME/SetUpFreeSurfer.sh - R. On Apr 1, 2020, at 02:35, Hossein Shooli <h.shooly(a)gmail.com> wrote:return: can only `return' from a function or sourced script

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Setup & Configuration Error
by Hossein Shooli 01 Apr '20

01 Apr '20

External Email - Use Caution Hello FreeSurfer Development Team, I have just install the FreeSurfer (freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c) on my mac Catalina OS (10.15.2). The installation path was set as default (/Application/freesurfer). Then, in the Setup & Configuration step I have faced some troubles that I'm in need to fix it. In this step the first line " $> export FREESURFER_HOME=/Applications/freesurfer" works properly. But when I typed the " $> source $FREESURFER_HOME/SetUpFreeSurfer.sh ". an error occurred as below: Hosseins-MacBook-Pro:~ dhs$ > export FREESURFER_HOME=/Applications/freesurfer Hosseins-MacBook-Pro:~ dhs$ > source $FREESURFER_HOME/SetUpFreeSurfer.sh /Applications/freesurfer/SetUpFreeSurfer.sh: line 14: return: can only `return' from a function or sourced script /Applications/freesurfer/SetUpFreeSurfer.sh: line 42: /FreeSurferEnv.sh: No such file or directory Hosseins-MacBook-Pro:~ dhs$ I have checked the mail archives but there no answer to my problem. Please help me solve the issue and setup freesurfer successfully. Bests regard Hossein [image: Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=sig…> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=sig…> 04/01/20, 11:04:28 AM

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kill recon-all programatically/remotely
by Octavian Lie 31 Mar '20

31 Mar '20

External Email - Use Caution Dear All, Is there a way to kill a recon-all run on linux via ssh/putty. Ctrl+C is not working, obviously, and it is not easy to figure out which process encodes the recon-all runs with commands such as ps aux, top etc. One gross way may be removing the subject directory all together midway, but not sure how this affects FS, subsequent runs Thank you, Octavian

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Reducing FreeSurfer recon-all time
by Xiaojiang Yang 31 Mar '20

31 Mar '20

External Email - Use Caution Freesurfer experts: I know in my powerful Linux machine, recon-all needs about 10 hours to finish all computation. What is the possible way I can use to greatly reduce this computation time from 10 hours to, say 1-3 hours? Is Sun Grid Engine (SGE), or GPU/CUDA, or any other technique, helpful? Thank you! Xiaojiang

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Problem with version of mri_surfcluster provided with fspalm
by Syam Gadde 31 Mar '20

31 Mar '20

External Email - Use Caution Hi, We have a user trying to use fspalm. I followed all the directions to install, but are getting an error with the new mri_surfcluster that we were asked to download with fspalm. Here is the dummy command I ran to replicate the error: mri_surfcluster --thmin 0 --subject fsaverage --hemi lh --in /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/lh.white and the end of its output: <...> subjectsdir = /usr/local/packages/freesurfer_v6.0.0/subjects FixMNI = 1 ------------- XFM matrix (RAS2RAS) --------------- /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/mri/transforms/talairach.xfm 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; ---------------------------------------------------- Reading source surface /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/lh.white MRISread(x�<m�): could not open file No such file or directory mri_surfcluster: could not read surface /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/lh.white No such file or directory ----- It is the same error reported in these emails: https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=su… but the error message is misleading. The problem is not in reading the surface file, but in trying to read a file name made up of non-ascii (or presumably unicode) characters. As shown by strace: ... read(3, "", 8192) = 0 open("/proc/sys/crypto/fips_enabled", O_RDONLY) = 4 read(4, "0\n", 31) = 2 close(4) = 0 close(3) = 0 munmap(0x7f8413571000, 8192) = 0 open("\310\215\26\f\376\177", O_RDONLY) = -1 ENOENT (No such file or directory) write(2, "MRISread(\310\215\26\f\376\177): could not open"..., 37MRISread(ȍ^V^L<FE>^?): c ould not open file) = 37 ... Any thoughts on how to proceed? Thanks, -syam

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Re: [Freesurfer] on Ubuntu (was FreeSurfer V 7.0 on Centos 8) {Disarmed}
by fsbuild 31 Mar '20

31 Mar '20

External Email - Use Caution 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. https://surfer.nmr.mgh.harvard.edu/fswiki/BuildRequirements - R. On Mar 31, 2020, at 02:50, Tim Schäfer <ts+ml@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

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Re: [Freesurfer] Using freeview to view (and edit?) talairach registrations
by Ruopeng Wang 31 Mar '20

31 Mar '20

You can go to menu Tools -> Transform Volume to adjust the registration and save it as a lta registration file. Then run lta_convert to convert it to xfm: lta_convert --inlta foo.lta --outmni foo.xfm > On Mar 31, 2020, at 1:06 PM, Rachel Hoel <hoel2(a)wisc.edu <mailto:hoel2@wisc.edu>> wrote: > > External Email - Use Caution > > > Hi Ruopeng, > > I entered the full path for the transformation file, and this is what I’m seeing in freeview (screenshot attached). Is it possible to edit the talairach registrations in freeview similar to how they could be edited in tkmedit, or can freeview only be used for looking at talairach registrations? > > Thanks again, > Rachel > > <Screen Shot 2020-03-31 at 12.02.47 PM.png> > > >

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Freesurfer