Freesurfer August 2019

freesurfer@nmr.mgh.harvard.edu

100 participants
144 discussions

timewindow parameter in mkanalysis-sess
by Caspar M. Schwiedrzik 13 Sep '19

13 Sep '19

External Email - Use Caution Hi! I am having difficulties setting the timewindow parameter in mkanalysis-sess in Freesurfer v5.3. I am trying to use 80 (data acquired with MION), but the parameter does not seem to affect analysis.info, where it is always 40. Is it possible to force a different timewindow? Below is some info from analysis.info. Thanks, Caspar # FSBUILD freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 # MKAVERSION $Id: mkanalysis-sess,v 1.64.2.5 2013/01/22 21:52:07 greve Exp $ # MKACMD /neuro_tools/freesurfer/fsfast/bin/mkanalysis-sess -fsd bold -native -timeoffset -2/2 -event-related -paradigm xxxx.para -nconditions 4 -TR 2 -gammafit 0 8 -gammaexp 0.3 *-timewindow 80* -refeventdur 0.5 -polyfit 2 -hpf 0.0109 -analysis xxxx -funcstem xxxx -runlistfile xxxx.list -nuisreg motion.dat 6 -tpef tpef.dat -acfbins 14 -acffwhm 0 -mask xxxx -force analysis xxxx mcstem fmc funcstem xxxx fsd bold runlistfile xxxx.list TR 2 RegDOF 6 PerSession 1 RawSpace volume native mask xxxx RawFWHM 0 RawSTC none UseB0DC 0 ApplySubCortMask 1 inorm 100 acfbins 14 fixacf 1 acffwhm 0 acfsvd 0 designtype event-related tpexclude tpef.dat nskip 0 polyfit 2 HPFCutoffHz 0.0109 HeteroGCor 0 nconditions 4 parname xxxx.para RefEventDur 0.5 *timewindow 40.000000* prestim 0 TER 0.050000 gamma 0 8 0.3 0 stimulusdelay -2/2 Condition 1 Condition01 Condition 2 Condition02 Condition 3 Condition03 Condition 4 Condition04 nuisreg motion.dat 6

2 6

Re: [Freesurfer] error in longitudinal stream command
by Alexandru Hanganu 10 Sep '19

10 Sep '19

External Email - Use Caution Hello Martin, I was wondering - how solved the "Unmatched" error ? In our case, this error appears for both 5.3, 6.0 and dev, on 2 different clusters. All folders exist, are filled with data and reecon-all finished without error, plus hippocampus and brainstem all folders and readable: drwxrwsrwx (chmod 777 -R) In the base-tps - all time points are listed correctly. Re-running -base - did not solve the issue. Name has no underscores '_' I didn't have this error on the local installation, so, I suspect it might be linked to sourcing some libraries/folders, since we had to source the mni folder to make it work. Best, Alexandru.

2 2

[WARNING: UNSCANNABLE EXTRACTION FAILED]Re: freeview crash -- petsc error when opening volume
by fsbuild 10 Sep '19

10 Sep '19

External Email - Use Caution Hello Tristan, Please try rebuilding the dev branch on your Ubuntu 18 machine using the makefile listed from the wiki, (wiki page, https://surfer.nmr.mgh.harvard.edu/fswiki/CMake) where the download link to makefile is https://drive.google.com/file/d/1IMEWQty_7zjsglbErQOlu_KpXb8Lmgmv/v… should go in the same subdirectory that contains the ./freesurfer tree There are some comments in there which recommend the following be installed for Ubuntu, so please check these are installed before building,       # sudo apt-get install build-essential       # sudo apt-get install libgl1-mesa-dev freeglut3-dev mesa-common-dev       # sudo apt-get install libblas-dev liblapack-dev       # sudo apt-get install ocl-icd-opencl-dev       # sudo apt-get install libxmu-dev libxi-dev       # sudo apt-get install libopencv-dev        # Ubuntu 16: sudo apt-get install gcc-4..9 g++-4.9 gfortran-4.9       # Ubuntu 18: sudo apt-get install gcc-4.8 g++-4.8 gfortran-4.8 <----       # sudo apt-get install xorg xorg-dev libx11-dev       # sudo apt-get install tcl tcl-dev tk tk-dev       # sudo apt-get install qt5-default qtcreator       # sudo apt-get install libqt5x11extras5-dev       # sudo apt-get install git-annex        # sudo apt-get install python3-dev I’ve attached an archive containing that makefile along with the cmake output/build logs from my Ubuntu 18.04 machine so you can see what it looks like for me, see cmake_make_install_ubuntu18.tgz I’ve run all the freeview tutorial commands using the 6.0.0 release on my Ubuntu 18.04 machine, but have not been able to reproduce a petsc error so far. - R. On Aug 27, 2019, at 11:27, TRISTAN J PAUTSCH <tpautsch(a)wisc.edu> wrote:        External Email - Use Caution        Some final bits of troubleshooting information for future readers, since I'm assuming this issue will now get lost in the sauce...I'll probably try compiling everything from scratch at some point, but my hopes aren't particularly highI manually compiled the missing libs to get the CentOS7 version of FS-dev freeview running on Ubuntu 18, and ultimately the same errors occur. As well, I replicated this behavior on a separate Ubuntu 18 machine in the environment, this time using a different lab's T1/brainmask/surface files. It would definitely seem like there is some sort of hard incompatibility with newer versions of freeview and loading surface files on top of volumes in Ubuntu 18. For what it's worth, it's not evident that any other part of FS has an issue; all CLI tools seem to work just fine.TristanFrom: TRISTAN J PAUTSCH <tpautsch@wisc.edu>Sent: Friday, August 23, 2019 11:38 AMTo: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume Good morning Ruopeng, thank you for your continued assistance!Unfortunately, I get the same error using the CentOS6 dev version. I tried the CentOS7 dev version, however this led to a series of library errors, the majority of which are unsolvable on Ubuntu 18 without individually compiling each necessary library (sym-linking newer libraries does not work).I wanted to ensure I provide the most details possible, so I also installed FS 5.3.0 and tested the files...interestingly, they opened just fine, no errors at all.This leads me to believe there is some strange incompatibility between Ubuntu 18 and the 6.x/dev version of FS (at least when it comes to surface files), specifically related to PETSC. Is there anything else I can do to help troubleshoot?TristanFrom: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Ruopeng Wang <rpwang@nmr.mgh.harvard.edu>Sent: Thursday, August 22, 2019 5:00 PMTo: Freesurfer support list <freesurfer@nmr..mgh.harvard.edu>Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume Hi Tristan,Thanks for the files. I have no problem loading them with the latest dev build and stable 6.0 build.. I do not have an Ubuntu system, though. If I’m not mistaken you use dev version of freeview binary along with stable 6.0 FS binary. Is that correct? Is there any chance you can try installing the whole FS dev package?RuopengOn Aug 22, 2019, at 12:20 PM, TRISTAN J PAUTSCH <tpautsch(a)wisc.edu> wrote:        External Email - Use Caution        Ruopeng,I've uploaded the files to the FTP drop (transfer/incoming/freesurfer_data.tar.gz). The command my user is running against these files is:freeview -v brainmask.mgz T1.mgz -f lh.white:edgecolor=yellow lh.pial:edgecolor=magenta rh.white:edgecolor=yellow rh.pial:edgecolor=magentaWe can also replicate the error by opening freeview and opening all the above files sequentially through the GUI.Thank you!TristanFrom: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Ruopeng Wang <rpwang@nmr.mgh..harvard.edu>Sent: Thursday, August 22, 2019 8:16 AMTo: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume Hi Tristan,Would it be possible to send us the files and the command-line you run? Best,RuopengOn Aug 21, 2019, at 12:18 PM, TRISTAN J PAUTSCH <tpautsch(a)wisc.edu> wrote:        External Email - Use Caution        Adding more details provided by my user:The crash only happens when loading surface files, either via the -f flag from the CLI or directly through the GUI. Could this be an issue with the surface files or the manner in which they are created?From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of TRISTAN J PAUTSCH <freesurfer-bounces@nmr.mgh.harvard.edu>Sent: Tuesday, August 20, 2019 2:35 PMTo: freesurfer@nmr..mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: [Freesurfer] freeview crash -- petsc error when opening volume         External Email - Use Caution        Greetings all, I'll try to keep this succinct. I'm attempting to deploy FreeSurfer on Ubuntu 18.04 servers here at the lab. I used the stable 6.0/CentOS 6 download, in addition to the dev version of freeview per the .../fswiki/UpdateFreeview instructions. All dependencies have ostensibly been satisfied, all libs from 'ldd freeview.bin' installed. Freeview launches fine and stays open when launched alone, however attempting to open a volume (either through the GUI or directly via the CLI) causes a crash and the following error about 5-8 seconds after launching (brain images begin to populate, then crash):---[0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger[0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshootin…: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash.[0]PETSC ERROR: --------------------- Error Message ------------------------------------[0]PETSC ERROR: Signal received![0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124[0]PETSC ERROR: See docs/changes/index.html for recent updates.[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.[0]PETSC ERROR: See docs/index.html for manual pages.[0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC ERROR: Unknown Name on a linux-gnu named xxxxxxx by xxxxxxx Tue Aug 20 13:44:15 2019[0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3[0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file[unset]: aborting job:application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0Segmentation fault (core dumped)---I've seen a number of other posts on the mailing list about this, but all of them I could find either end abruptly without a solution or with an unanswered request for more info. Happy to provide any additional information or anything that may aid in the resolution of this issue. Thanks everyone,~T_______________________________________________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

2 2

question on GLM
by Barletta, Valeria 10 Sep '19

10 Sep '19

Good afternoon! I have a question on the Freesurfer GLM. The command: mri_glmfit-sim --glmdir ${glm_dir}/${hemi}_contrast-${contrast}_${surfname_cme} --cache 1.3 neg is giving me blue clusters (see attached picture). Do blue clusters mean that my variable y is LOWER in the FIRST or the SECOND group listed in the FSGD file? Thanks, Valeria

2 8

eTIV and brainmask mismatch on Philips data
by Agnieszka Sabisz 10 Sep '19

10 Sep '19

External Email - Use Caution Hi all! We are running FS v.6.0. on a supercomputer operating on Linux. We have two sets of data - one from 1.5T Aera Siemens, second from 3.0T Achieva TX Philips. The T1 images on both scanners have comparable CNR, with an isotropic resolution of 1mm3 each. The recon-all finished with no errors, but in approximately half of the Philips data there is a significant (up to 40%) difference between the brain mask volume and eTIV (no such problem on Siemens). We inspected the Talairach registration (as is pointed that eTIV is calculated upon it) in the mismatched data with: tkregister2 --mgz --s <subject> --fstal --surf orig and in the corrupted data the brain mask and the WM-GM borders align in terms of placement but are of a wrong scale (proportionate to the "brainmask-to-eTIV" difference). What may be the reason and how to cope with that? We cannot normalize the volume data to eTIV (as it is not proper), what value should we use instead? Attached you will find example tkregister2 output screenshots. Best regards, Agnieszka Sabisz

2 8

[FREESURFER] longitudinal processing base_tmps does not exist error
by Lee, Seonjoo 10 Sep '19

10 Sep '19

External Email - Use Caution Dear Freesurfer, Could you help me to resolve this error? I looked up the previous postings, but the recommendation (copying files in the same folder etc.) did not help. Thank you. $ recon-all -base template -tp 002_S_0295_S32678 -tp 002_S_0295_S567612 -sd $SUBJECTS_DIR Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c INFO: SUBJECTS_DIR is /Users/seonjoolee/ADNI_long/tmp Actual FREESURFER_HOME /Applications/freesurfer Darwin Seonjoos-iMac.nyspi.local 18.5.0 Darwin Kernel Version 18.5.0: Mon Mar 11 20:40:32 PDT 2019; root:xnu-4903.251.3~3/RELEASE_X86_64 x86_64 Started at Wed Aug 7 10:24:55 EDT 2019 Ended at Wed Aug 7 10:24:56 EDT 2019 #@#%# recon-all-run-time-hours 0.000 recon-all -s template finished without error at Wed Aug 7 10:24:56 EDT 2019 done $ recon-all -long 002_S_0295_S32678 template -all ERROR: file /Users/ll/ADNI_long/tmp/template/base-tps does not exist!

2 1

Re: [Freesurfer] recon_all cuda 9.1
by fsbuild 04 Sep '19

04 Sep '19

External Email - Use Caution Hello Vasudev, I think in January of 2018 it was possible to build the development branch of the freesurfer tree using cuda 5.  But I believe that was the last version we tried building the source with.  We no longer support building with cuda and instead favor using OpenMP..  Part of this is because of cuda’s dependencies on the Nvidia graphics hardware which is a moving target.  Some vendors have essentially stopped supporting Nvidia graphics card drivers, e.g., Apple as of Mac OS 10.14 onward.  The Freesurfer dev branch source is now compiled with C++ compilers, and I don’t know that anyone has tried building with cuda since we changed the compilers for freesurfer. - R. On Aug 30, 2019, at 11:39, Dev vasu <vasudevamurthy.devulapally(a)gmail.com> wrote:        External Email - Use Caution        Dear all,Does recon_all -use-gpu only works for CUDA 5.0, is there any way to make it work for CUDA 9.1.ThanksVasudev_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

3 2

qdec contrast and data extraction
by Maximo, Jose Omar 03 Sep '19

03 Sep '19

External Email - Use Caution Hi, I have a question: My design is 2 groups (HC and Patients in that respective order) and 2 nuisance factors (age and eTIV). When I look at the average volume difference between the 2 groups, I get blue and red clusters. I presume the color coding is where each group is greater than the other (Blue = Patients > HC and Red = HC > Patients). Then, I processed to extract individual values from each cluster in order to plot them. When I extract data from the blue clusters and plot them, the two groups show no difference in thickness at all, whereas when I look at volume, HC show more than patients in blue clusters (see attached figure). I would assume that both figures would show patients > HC based on the negative statistic. Am I interpreting the colors wrong? Or am I doing something wrong? These are my steps 1) After applying montecarlo correction, I drew my ROIs to extract the data from; 2) map it onto every single subject; and then 3) used mris_anatomical_stats to extract the data from each subject. Any suggestions are welcome. Best, Omar Jose O. Maximo, Ph.D. | Postdoctoral Fellow Department of Psychiatry & Behavioral Neurobiology UAB School of Medicine University of Alabama at Birmingham Cell Phone: (619) 252-3492 Email: jomaximo(a)uabmc.edu<mailto:jomaximo@uabmc.edu>

2 1

syntax error near unexpected token 'newline'
by michele rizzi 31 Aug '19

31 Aug '19

External Email - Use Caution Dear All during freesurfer installation, I type export FREESURFER_HOME=/Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh and I have this error syntax error near unexpected token 'newline' can you help me? thanks Mike

5 7

Re: [Freesurfer] R: R: syntax error near unexpected token 'newline'
by fsbuild 31 Aug '19

31 Aug '19

External Email - Use Caution Yes, as Viviana said, you need to specify the path to the Applications folder by using a leading slash “/“ character. You can test that path /Applications/freesurfer/subjects is OK by opening the terminal application and then typing at the dollar sign prompt, $ ls /Applications/freesurfer/subjects ... which should not give you an error and show some files are there. Unless someone changed the shell preferences for your account on the Mac, then the default shell at the $ prompt in the terminal window is bash shell for Mac OS 10.14.  There should be no need to type “bash” again (and start another shell). So in the terminal window it should work for you to type the lines after the dollar sign prompt  (you could cut and paste the below), and then see if you get the same output. $ ls -d /Applications/freesurfer/Applications/freesurfer $ export FREESURFER_HOME=/Applications/freesurfer$ echo $FREESURFER_HOME/Applications/freesurfer $ ls $FREESURFER_HOME/SetUpFreeSurfer.sh/Applications/freesurfer/SetUpFreeSurfer.sh $ source $FREESURFER_HOME/SetUpFreeSurfer.sh If the “source" command results in an error, then you can try to see what failed by running the shell script with “sh -x” instead of “source”. $ sh -x $FREESURFER_HOME/SetUpFreeSurfer.sh If running the script with “sh -X” does not end with a “return 0” statement displayed on the terminal, then you cost cut and paste the last several lines before the error and email it back to us. - R. On Aug 31, 2019, at 00:04, Viviana Siless <viviana.siless(a)gmail.com> wrote:        External Email - Use Caution        Hi, I think you are just mistyping it, if the subjects dir is in "/Applications/freesurfer/subjects/ " the command  should be:export SUBJECTS_DIR=/Applications/freesurfer/subjects/ ( instead of  export SUBJECTS_DIR=<Applications/freesurfer/subjects>)Viv On Fri, Aug 30, 2019 at 4:35 PM Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote:oh, the export command is failing? You mentioned you weren't running bash (which is the shell that knows what to do with an export command). Can you install bash? If not, you can use setenv instead of export and the .csh file instead of the .shOn Fri, 30 Aug 2019, michele rizzi wrote:> >         External Email - Use Caution        > > > I put > > > export SUBJECTS_DIR=<Applications/freesurfer/subjects>> > > > but again I get > > > > -bash: syntax error near unexpected token `newline'> > > > > > >_______________________________________________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

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer August 2019