Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

-qcache recon-all exciting with error
by Swanson,Clayton 10 Sep '19

10 Sep '19

External Email - Use Caution Hello FreeSurfer Developers, I am attempting to run -qcache on a cohort (55) of participants and two of them excited with error. It’s worth noting I am running recon-all -qcache after initial recon-all then correcting for errors and re-processing again. The error I am receiving is ERROR: number of vertices in /Users/claytonswanson/Desktop/Studies/Current_Studies/MS_Study/MRS_MRI/FreeSurfer/Subject_Dir_T1/Subj_010_T1/surf/lh.thickness does not match surface (154775,154624) ERROR: reading curvature file ERROR: number of vertices in /Users/claytonswanson/Desktop/Studies/Current_Studies/MS_Study/MRS_MRI/FreeSurfer/Subject_Dir_T1/Subj_008_T1/surf/lh.thickness does not match surface (141413,141431) ERROR: reading curvature file I have not been able to find anything in the mail archive to answer this particular question. I have attached the recon-all.log file if its of use. Thanks for your help, Clayton ________________________________ Clayton Swanson MS Graduate Research Assistant & PhD Student Sensorimotor Neuroimaging Laboratory Colorado State University Office: (970) 491-6160 Clayton.Swanson(a)colostate.edu

2 1

Re: [Freesurfer] freeview crash -- petsc error when opening volume
by fsbuild 10 Sep '19

10 Sep '19

External Email - Use Caution Hello Tristan, Please check to see that what is listed in the makefile.wiki under the section for Ubuntu is installed on your machine.   I would also try building with the instructions in the makefile if you have not already done so; that works on my Ubuntu 18.04 system, although I am not running the server distribution, e.g., type “make -f makefile.wiki help”.   The makefile based build will also save logs for the cmake command, build and install pass, so you could send me those directly - look for ./freesurfer/{cmake.log, make.log, install.log} - R. On Sep 10, 2019, at 13:52, TRISTAN J PAUTSCH <tpautsch(a)wisc.edu> wrote:        External Email - Use Caution        Thank you so much again for the detailed reply. I attempted your suggestion, following the instructions from the wiki to a T and compiled everything from scratch, and I still get the same PETSC error from my first post. To be thorough, I again tested on multiple machines, experiencing the same error on each.I also realized I've never posted the specs of the system on which I've been attempting all of this, so in case it's relevant to anyone else, here they are:OS: Ubuntu 18.04 ServerCPU: 4x Xeon Platinum 8164RAM: 512GB DDR4 ECC (16x32GB DIMMs)From: TRISTAN J PAUTSCH <tpautsch@wisc.edu>Sent: Thursday, August 29, 2019 10:27 AMTo: fsbuild <fsbuild@contbay.com>Cc: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume Thank you for the reply, I will try this when time permits!TristanFrom: fsbuild <fsbuild@contbay.com>Sent: Tuesday, August 27, 2019 4:25 PMTo: TRISTAN J PAUTSCH <tpautsch@wisc.edu>Cc: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume 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 treeThere 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-devI’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.tgzI’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_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

3 4

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

Opseq2 question
by Nasiriavanaki, Zahra 10 Sep '19

10 Sep '19

Hi Freesurfer experts I have a question about designing an event related task. We are designing a task for fear conditioning. Each stimuli presentation lasts 4 seconds. My question is if we set the TR to 2 (which is a multiply of 4), will it make the paradigm to have more power in signal detection? Or does it not matter if the TR and stimuli presentation be a multiply of each other or not? I appreciate if you give me your comments on that. Thanks a lot Mona Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

2 4

Custom Segmentation of the Cortex usable with mri_compute_volume_fractions
by Pfannmoeller, Joerg Peter 10 Sep '19

10 Sep '19

Hello, I would like to generate a custom segmentation of the cortex. That segmentation should be restricted to a certain labeled region (e.g. a Brodmann Area). If possible I would also like to restrict the region to the lower half or upper half of the cortex. Let's call these new segmentations sub-segmentations. I would like to use mri_compute_volume_fractions with this segmentation to compute the volume fractions of the voxels in a scan that overlap with these new sub-segmentations of the cortex. Are there tools for this purpose in FreeSurfer? Best Joerg

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

Convert nifti atlas into .annot file
by Dev vasu 10 Sep '19

10 Sep '19

External Email - Use Caution Dear all, How can i create .annot files for both left and right hemisphere from nifti atlases http://www.gin.cnrs.fr/en/tools/aal/ are there any specific guidelines or commands for surface based parcellation ? Thanks Vasudev

2 1

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

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