Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Re: [Freesurfer] Processor speed/cores vs cache size
by fsbuild 15 Nov '19

15 Nov '19

External Email - Use Caution Hello Pradyumna, I have not read thru the mailing list posts so see what other comments there may be about this, but the posted system requirements,https://surfer.nmr.mgh.harvard.edu/fswiki/SystemRequirements- do not mention anything like Xeon class server chips. Desktop (non-server class) machines with a modern Intel i7 or i9 chip with base (non-turbo, non-overclocked) CPU speeds of ~3 GHz are common.  I’ve run a complete recon-all in about 7-8 hours on a mid-2016 MacBook Pro with a 2.9Ghz  i7 chip (4 physical, 8 virtual cores) with 16GB of old higher latency DDR3 memory using all SSD disk storage (with the machine doing nothing else). I don’t have any data w.r.t the pros/cons of L2 or L3 level cache.  I don’t know the details of how many threads the commands executed by recon-all can exploit.  From my own experience of running various commands, 4 or 8 physical cores (hyperthreaded to yield 8 or 16 cores) should be fine.   I’ve also found that 24G to 32G of RAM is helpful with performance.  Since data/files will be read/written from disk, at certain points performance could be I/O bound by how fast disk read/writes occur.  This can be helped by having your data stored on a 7200, 10,000 RPM disk drive (or better an SSD drive) to speed things up that is physically separate from the drive with the boot partition. But you could certainly meet or upgrade the specs to outfit a server machine with Xeon class chips and drives for multiple users. - R. On Nov 13, 2019, at 15:00, Pradyumna Bharadwaj <prad(a)email.arizona.edu> wrote:        External Email - Use Caution        Hello,For running recon-all or tracula on a local workstation, is it recommended to go for a higher processor speed/number of cores, or a larger cache size for the processor (Intel Xeon W series). Or is it likely to be a more complex interplay between the number of recon-all processes running at any given time?Thanks,Pradyumna_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Custom location of license file
by fsbuild 15 Nov '19

15 Nov '19

External Email - Use Caution Hello Karsten, I think the location for license.txt in the freesurfer 6 release needs to be under $FREESURFER_HOME, ie., $FREESURFER_HOME/license.txt, and cannot be relocated from there by an environment variable..  But you can try using a soft link to point to it in another location.   While it does not work to preserve $HOME/license.txt as a reference in another environment variable like FREESURFER_HOME or within a soft link, I believe the shorthand notation ~/license.txt does work in a soft link.   So in your common installation under $FREESURFER_HOME you could try, $ cd $FREESURFER_HOME$ ln -s ~/license.txt license.txt - and see if freesurfer complains if an individual users $HOME/license.txt (or ~/license.txt) is missing. In the newer code base on the freesurfer development branch, it should work to set the FS_LICENSE environment variable to point to the path of the license.txt file, but I don’t think that works in the 6.0.0 release. Ideally, I think the freesurfer group would prefer if each user signed up for their own license in order to track usage, so maybe try the soft link. - R. On Nov 14, 2019, at 12:58, Siller, Karsten H (khs3z) <khs3z(a)virginia.edu> wrote:        External Email - Use Caution        Hi, We’d like to install FreeSurfer globally for our users on a CentOS HPC system.  Is it possible to define an alternative location for the FreeSurfer license file, e.g.  ~/.license, so that users can use their individual license files with the globally installed software?  Perhaps the license file location and name can be customized via an environment variable at runtime? If that is not possible, is it ok to install a single “global” license file for all users in the shared FreeSurfer installation directory? Thanks,Karsten -- Karsten SillerResearch ComputingUniversity of Virginia _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Volume (WM Parcellation) of RightCerebralCortex -- Freesurfer 6.0
by An Lijun 15 Nov '19

15 Nov '19

External Email - Use Caution Dear Freesurfer experts, I am trying to use ADNI MERGE R package to get 'wholebrain' volume. It requires <Left/Right>CerebralCortex. The information I get from ADNI merge is "Volume (WM Parcellation) of RightCerebralCortex". But when I ran Freesurfer reconall 6.0, I could not find <Left/Right>CerebralCortex under 'stats' folder, do you know where it could be? Thanks so much. Best Regards, An Lijun

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Custom location of license file
by Siller, Karsten H (khs3z) 14 Nov '19

14 Nov '19

External Email - Use Caution Hi, We’d like to install FreeSurfer globally for our users on a CentOS HPC system. Is it possible to define an alternative location for the FreeSurfer license file, e.g. ~/.license, so that users can use their individual license files with the globally installed software? Perhaps the license file location and name can be customized via an environment variable at runtime? If that is not possible, is it ok to install a single “global” license file for all users in the shared FreeSurfer installation directory? Thanks, Karsten -- Karsten Siller Research Computing University of Virginia

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fspalm issue
by Isabelle Ye 13 Nov '19

13 Nov '19

External Email - Use Caution Hi FreeSurfer community, I’m using fspalm to correct multiple comparisons for vertex-based cortical thickness analysis. It ran successfully and several clusters survived after correction for multiple comparisons. Below is the code I used for permutation tests. fspalm --glmdir cth.glmdir --cft 4 --onetail --name palm-onetail-4 --iters 1000 --2spaces --cwp .05 After that, I would like to generate a surface map after permutation tests, which stores the original surface values except that vertices not assigned to a cluster are set to 0. I checked the fspalm and mri_surfcluster description but did not find any clue. I also tried to run the analysis below but I could not adjust the threshold of the output file (contrast.surfvalues.mgz) because it seems to be a binary file . mri_surfcluster --in fsp_clustere_tstat_fwep.mgz --thmin 1.301030 --subject fsaverage --hemi lh --annot aparc --no-fixmni --surf white --ocn contrast.ocn.mgz --oannot ./contrast.ocn.annot --sig2p-max --bonferroni-max 2 --o ./contrast.surfvalues.mgz Any help would be appreciated. Thanks, Isabelle

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Freesurfer6.0 hippocampal and amygdala segmentation-command not found error
by Isabella Leung 13 Nov '19

13 Nov '19

External Email - Use Caution To whom it may concern, I am trying to run hippocampal and amygdala segmentation https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm… I was able to run recon-all, however I am unable to run segmentHA_T1.sh and get the error message of "command doesn't exist". I'm not quite sure what the problem is. I have seen online that I should update the freesurfer to the development version? I'm not sure how to update my Freesurfer 6.0 to the development version. Could you please let me know how I can update my freesurfer 6.0 so that I can run segmentHA_T1.sh? I have run recon-all on all my participants through Freesurfer 6.0. Will it mean that I will have to redo my recon-all in the freesurfer development version for all my participants before I try to run the segmentHA_T1.sh? Thank you in advance for the help. Best wishes, Isabella Isabella Hoi Kei Leung | PhD Candidate Brain & Mind Centre | Central Clinical School | Faculty of Medicine THE UNIVERSITY OF SYDNEY Room 408, Level 4, Bldg M02K | 94 Mallett St, Camperdown NSW 2050 Australia M +61 404 066 903 E isabella.leung(a)sydney.edu.au

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Conference on “Emerging Topics in Artificial Intelligence”
by Joana Braga Pereira 13 Nov '19

13 Nov '19

External Email - Use Caution Dear all, We are organizing a conference on “Emerging Topics in Artificial Intelligence”, which will take place from 23-27 August 2020 in San Diego, USA. The aim of this conference is to bring together experts from different fields to discuss new applications of artificial intelligence to biomedicine, neuroimaging, microscopy, active matter and photonics. Importantly, this conference will also count with the participation of industry to foster commercialization and utilization opportunities. Please find more detailed information about the topics that will be covered at: https://spie.org/opn/conferencedetails/ai-machine-learning?SSO=1 The period for abstract submission is now open. Please forward this information to anyone who might be interested. Best wishes, Joana B. Pereira (Karolinska Institute) Giovanni Volpe (Gothenburg University) Aydogan Ozcan (University of California) Daniel Brunner (Institut Franche-Comte Electronique Mecanique Thermique et Optique)

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Re: [Freesurfer] Error "dyld: lazy symbol binding failed..." when some commands run via Matlab [system('fscmd')]
by fsbuild 13 Nov '19

13 Nov '19

External Email - Use Caution Hello hj23, If you are running the 6.0.0 freesurfer Mac release, then you can try downloading this patch.  You will need to double click on the archive to expand it and then follow the instructions in README.patch.  I think you will also need admin privileges though to make the changes described there. https://drive.google.com/file/d/1ezjiNIbGNrNAiYD5ciYxMO2SK-R5vz9A/view?usp=… - R. On Nov 13, 2019, at 03:39, hj23 <hj23(a)nyu.edu> wrote:        External Email - Use Caution        Hello FreeSurfer Developers,I’m attempting to run FreeSurfer commands via Matlab [system(‘fscmd’)]. Some of the commands work but some don’t, though all the commands work well when run in Terminal.Commands work in both Terminal and Matlab:When I run “tksurfer” in Terminal or system(’tksurfer’) in Matlab, I will get the help information for ’tksurfer'.Commands do not work in Matlab, but work in Terminal:For example, when I run “mri_info" in terminal, I will get the help information for “mri_info”. However, when I run system(‘mri_info’) in Matlab, I got the following error (screeshot also attached):===================================================================dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address  Referenced from: /Applications/freesurfer_6.0/bin/../lib/gcc/lib/libgomp.1.dylib  Expected in: /usr/lib/libSystem.B.dylibdyld: Symbol not found: ___emutls_get_address  Referenced from: /Applications/freesurfer_6.0/bin/../lib/gcc/lib/libgomp.1.dylib  Expected in: /usr/lib/libSystem.B.dylibmri_info: Abortedans =   134===================================================================I randomly tried some FreeSurfer commands and the commands do not work in Matlab (but work in Terminal) are: ‘mri_info’ ‘mri_coreg’  Commands work in both terminal and Matlab are: ’tksurfer’ ‘mri_convert’ ‘mri_head’I did search for the error in FreeSurfer Archive and found the recommendation of disable System Integrity Protection. Before doing that, I wonder if there is any other solution to this.Also, I tried to run these commands in both FreeSurfer 5.3-HCP and FreeSurfer 6.0 (on the same computer), and interestingly, the commands via Matlab work well in FS 5.3 (except that ‘mri_coreg’ cannot be found in FS 5.3) but the error will show in FS 6.0. Additional information:1) FreeSurfer version: error show for freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c, but not for freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0-HCP2) Platform: macOS Mojave (version 10.14.5) iMac Pro (2017)3) uname -a Darwin ADUAED07785WKMX.local 18.6.0 Darwin Kernel Version 18.6.0: Thu Apr 25 23:16:27 PDT 2019; root:xnu-4903.261.4~2/RELEASE_X86_64 x86_64Please let me know if there is any other information will help.Thanks in advance,Haiyang<Screen Shot 2019-11-13 at 12.15.09 PM.png>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Recon all hard failure,
by Vicente Ferrer 13 Nov '19

13 Nov '19

External Email - Use Caution Hello, I was runnning reconall in one of my images and it got stucked fixing surface defects, since i run it on a cluster it stopped when it runned out from cpu time. As you will see in the log the command started in SUNday 16 14:59:32 CEST 2019 and ended in Mon Jun 17 05:10:16 CEST 2019 which is more than usual for a recon-all duration. I have checked some of the previous images and there is clearly an alignment problem as you can check in this image: Vicente Ferrer Predoctoral Researcher BCBL www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

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Error "dyld: lazy symbol binding failed..." when some commands run via Matlab [system('fscmd')]
by hj23 13 Nov '19

13 Nov '19

External Email - Use Caution Hello FreeSurfer Developers, I’m attempting to run FreeSurfer commands via Matlab [system(‘fscmd’)]. Some of the commands work but some don’t, though all the commands work well when run in Terminal. Commands work in both Terminal and Matlab: When I run “tksurfer” in Terminal or system(’tksurfer’) in Matlab, I will get the help information for ’tksurfer'. Commands do not work in Matlab, but work in Terminal: For example, when I run “mri_info" in terminal, I will get the help information for “mri_info”. However, when I run system(‘mri_info’) in Matlab, I got the following error (screeshot also attached): =================================================================== dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer_6.0/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer_6.0/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib mri_info: Aborted ans = 134 =================================================================== I randomly tried some FreeSurfer commands and the commands do not work in Matlab (but work in Terminal) are: ‘mri_info’ ‘mri_coreg’ Commands work in both terminal and Matlab are: ’tksurfer’ ‘mri_convert’ ‘mri_head’ I did search for the error in FreeSurfer Archive and found the recommendation of disable System Integrity Protection. Before doing that, I wonder if there is any other solution to this. Also, I tried to run these commands in both FreeSurfer 5.3-HCP and FreeSurfer 6.0 (on the same computer), and interestingly, the commands via Matlab work well in FS 5.3 (except that ‘mri_coreg’ cannot be found in FS 5.3) but the error will show in FS 6.0. Additional information: 1) FreeSurfer version: error show for freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c, but not for freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0-HCP 2) Platform: macOS Mojave (version 10.14.5) iMac Pro (2017) 3) uname -a Darwin ADUAED07785WKMX.local 18.6.0 Darwin Kernel Version 18.6.0: Thu Apr 25 23:16:27 PDT 2019; root:xnu-4903.261.4~2/RELEASE_X86_64 x86_64 Please let me know if there is any other information will help. Thanks in advance, Haiyang

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