Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

Re: [Freesurfer] FreeSurfer V 7.0 on Centos 8
by fsbuild 31 Mar '20

31 Mar '20

External Email - Use Caution Hello 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 Caution        Greetings 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.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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segmentThalamicNuclei.sh - Undefined symbol error, Invalid MEX file
by Chester Kang 30 Mar '20

30 Mar '20

External Email - Use Caution Hi, We are wanting to run the hippocampal subfields which is part of the developmental version of FreeSurfer ("freesurfer-darwin-macOS-dev.pkg"). The FreeSurfer v7.0.0 Dev and the Matlab2014b (Run Time Version) has also been installed. But are getting errors. E.g., "... Invalid MEX-file '/tmp/MCR_488630323/.mcrCache8.4/Segmen0/autofs/space/panamint_005/users/ig lesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64' ..." It looks like a similar problem existed in 2018 (though I cannot find a fix). https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg56815.html Any help would be greatly appreciated. Thanks in advance! Regards, Chester

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FreeSurfer V 7.0 on Centos 8
by Mina Rizkallah 30 Mar '20

30 Mar '20

External Email - Use Caution Greetings 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 you Best regards Mina

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mri_vol2vol
by Benjamin Ineichen 30 Mar '20

30 Mar '20

External Email - Use Caution Dear Freesurfer experts, In order to transform a segmentation mask (example.mgz) from native so standard MNI space I ran: mri_vol2vol --talres 1 --interp nearest --mov example.mgz --s 001.mgz --targ $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz --regheader --o example.mni305.mgz the output example.mni305.mgz did somehow transform to a different space as you can see in Screenshot orig where the native mask is white and the transformed mask is red. However, the masks seems to be in a completely different brain region in the native MNI space (Screenshot MNI). But the point of transforming my segmentation mask is that the segmented mask should be in the same brain region but just transformed to the standard space. How can I correct this? Many thanks for the support! /Ben -- ____________________________________ Benjamin Victor Ineichen, MD PhD Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen(a)protonmail.ch +41 76 391 04 01 Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen(a)protonmail.ch +41 76 391 04 01

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libpng12.so.0
by Gonzalo Rojas Costa 30 Mar '20

30 Mar '20

External Email - Use Caution Hi: I tried to use the tkregisterfv command in Ubuntu 18.04.4 LTS, but I got the following error: "freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory". How can I solve it ? Sincerely, Gonzalo Rojas Costa

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PhD student position in Bordeaux, France
by Ismail Koubiyr 30 Mar '20

30 Mar '20

External Email - Use Caution Dear all, There is an open PhD student position at our lab (Neurocentre Magendie) at the University of Bordeaux, Bordeaux, France : "*Predictive factors of cognitive decline in multiple sclerosis*" Details can be found in the attached document. To apply, please contact Dr Aurélie Ruet (aurelie.ruet(a)chu-bordeaux.fr) with your CV before April 30,2020. Best Ismail Koubiyr

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Re: [Freesurfer] libpng12.so.0 (Freesurfer on Ubuntu)
by fsbuild 29 Mar '20

29 Mar '20

External Email - Use Caution Hello Gonzalo, Please try downloading and  installing the following, https://drive.google.com/file/d/1OWQSWL8a3Y8f1Weiauj9Lr2d3mtvZOm5/view?usp=… $ sudo apt install -y ./libpng12-0_1.2.54-1ubuntu1.1_amd64.deb https://drive.google.com/file/d/1Zdd-C3EQEEww180OzxEk1WV0h9obZYkD/view?usp=… sudo apt install -y ./libjpeg62_6b2-3_amd64.deb BTW - There is also an Ubuntu VM you can setup and use with freesurfer pre-installed, https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67 - R. On Mar 29, 2020, at 22:30, Gonzalo Rojas Costa <gonzalo.rojas.costa(a)gmail.com> wrote:        External Email - Use Caution        Hi:  I tried to use the tkregisterfv command in Ubuntu 18.04.4 LTS, but I got the following error:"freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory". How can I solve it ?  Sincerely,Gonzalo Rojas Costa_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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mri_vol2surf projections for subcortical structures
by Niels Janssen . 29 Mar '20

29 Mar '20

External Email - Use Caution Dear list I am working on a project in which we want to extract hippocampal surfaces using mri_tessellate and then overlay these surfaces with fmri activations from nifti files using mri_vol2surf. However, I am unclear whether mri_vol2surf can be used for surfaces derived from subcortical structures like the hippocampus. Crucially, these structures are unlike the cortex in that they have a closed shape and therefore the projection of activation to a surface may be more complex than in the case of cortex (which surface normal should one take?). So I guess my question is whether mri_vol2surf works for these kinds of surfaces or whether some other approach should be used. Thanks! Niels -- Niels Janssen Brain Imaging Laboratory Institute of Biomedical Technologies Institute of Neurosciences University of La Laguna Tenerife, Spain https://sites.google.com/view/nielsjanssen/

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thalamic segmentation analysis
by Parisi Veronica 28 Mar '20

28 Mar '20

External Email - Use Caution Hi there, I have been trying to learn and set-up Freesurfer for a research project I am working on, but I am having trouble with the set-up/installation process. Once Freesurfer is set-up, I will be using it to measure thalami and define their sub nuclei. I have followed the instructions online to the best of my ability but can't seem to figure this out. Any assistance would be very much appreciated. Thank you. Best, VP Rispetta l'ambiente: non stampare questa mail se non è necessario. Respect the environment: print this email only if necessary.

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Re: [Freesurfer] hippocampal-subfields-T1 error
by Iglesias Gonzalez, Juan E. 28 Mar '20

28 Mar '20

Dear Aleks, Please try: chmod u+x /rds/general/project/amyloidpet/live/freesurfer/bin/* Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Duvnjak, Aleksandar" <aleksandar.duvnjak16(a)imperial.ac.uk> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Friday, March 27, 2020 at 14:39 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] hippocampal-subfields-T1 error External Email - Use Caution Dear FreeSurfer Experts, FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 Platform: Secure Shell port of a high performance computer (HPC) accessed via Ubuntu 18.04 WSL Having processed a cohort of 1mm^3 MRI images via the recon-all command, we have had issues processing the hippocampal subfield command as described: https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields Although we eventually want to run the command in array, we are currently attempting it on individual subjects to ensure a good output. Upon running the command we receive a "permission denied" error. The HPC is a shared cluster, and the FreeSurfer 6.0.0 app is downloaded in a shared dir which we cannot edit, and thus couldn't download the Matlab runtime to. We initially thought this may be the issue, and so tried multiple workarounds, including copying the entirety of the FreeSurfer installation package from the shared directory to our own directory, within which we have editing permissions. This didn't help, even when setting our personal directory as the FREESURFER_HOME. As you can see from the end of the recon-all.log file, we tried numerous attempts with various workarounds and all have the same outcome. I appreciate this may still be more of an issue with running FreeSurfer via a secure shell port to a HPC cluster rather than an issue with FreeSurfer itself, but I'm sure you have many research labs asking questions regarding using HPC systems to run FreeSurfer, so any recommendations or thoughts would be welcome. Kind Regards, Aleks Duvnjak

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