Freesurfer

freesurfer@nmr.mgh.harvard.edu

30076 discussions

Start a nNew thread

DT_recon error
by m-maiworm＠web.de 11 May '22

11 May '22

2 1

VirtualBox Installation Password
by Viktor Pavliska 11 May '22

11 May '22

External Email - Use Caution Hello, please, where can I find the password of the VB image? I am following the instructions from the page: https://secure-web.cisco.com/1GwKqSd9gI16dUp0cqEmM-2_qILdbuXCQ2bXYCAxSOJGjE… Freesurfer 7.2.0 release in Ubuntu 18.04.06: FS_7_2_0_Ubuntu_18_04_06.ova.7z Best Regards -- RNDr. Viktor PAVLISKA, Ph. D. University of Ostrava Institute for Research and Applications of Fuzzy Modeling National Supercomputing Centre IT4Innovations 30. dubna 22 701 00 Ostrava 1 Czech Republic https://secure-web.cisco.com/1ERmDiIP2bUfj8wdW6dR7287YkQCoypPA35riqYyQKtdWM…

1 0

Compiling thalamic nuclei segmentation volumes
by O'Dor, Sarah Louise 11 May '22

11 May '22

Good morning, I apologize in advance that my background is not in coding. I have run the freesurfer thalamic segmentation tool on over 100 subjects. I am now trying to compile the data. I know that the instructions for this command are: quantifyThalamicNuclei.sh <output_file> <analysisID> <OPTIONAL_SUBJECTS_DIR> For <output_file>, I have specified the name and location for the text file it will generate. For <analysisID>, I’m using the T1 that was processed through freesurfer, so I simply put T1. For <OPTIONAL_SUBJECTS_DIR>, I specify the subject directory. When I run the script above as: quantifyThalamicNuclei.sh [complete path]/ThalamicSegSheet.txt T1 [complete path]/Subjects/ The response is: Gathering results from subjects in: [complete path]/Subjects And writing them to: [complete path]/ThalamicSegSheet.txt …but nothing is generated. Any advice? I’d hate to compile the date individually for over 100 subjects. Many thanks, Sarah

2 1

Re: [Freesurfer] VM Passcode
by fsbuild 10 May '22

10 May '22

External Email - Use Caution Sending the info to your email shortly. - R. On May 10, 2022, at 09:29, D R <deinrasenmaeher(a)gmx.de> wrote:       External Email - Use Caution        hello,I would like to get a passcode for the .7z file for the VM.Thank you in advance_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Recon-all Freezes on Parallel
by Joanna L Eckhardt 10 May '22

10 May '22

External Email - Use Caution Dear FreeSurfer Team, I have been trying to use the parallel command (following FreeSurfer tutorial) to run multiple subjects (Windows os running Ubuntu VM). I only have 2 cores, so I have it set to 2 jobs instead of 8 as in the tutorial. When I use the code from the tutorial, there is an error with the .nii, and I assume it is because my files are .nii.gz. developer@developer-VirtualBox:~/FreeSurfer/Cannabis_Reduced$ ls *.nii | parallel --jobs 3 recon-all -s {.} -i {} -all -qcache ls: cannot access '*.nii': No such file or directory So I changed the code to .gz with everything else the same, and FreeSurfer does nothing (it stalls/freezes). Is this just because my computer cannot handle the job? Is there anything else I can do to run parallel? If not, I can always just run 1 subject at a time, but I want to check and see if there is another way to get this to work. Thank you for your time! Joanna

2 2

VM Passcode
by D R 10 May '22

10 May '22

External Email - Use Caution hello, I would like to get a passcode for the .7z file for the VM. Thank you in advance

1 0

Re: [Freesurfer] Recon-all Freezes on Parallel
by fsbuild 09 May '22

09 May '22

External Email - Use Caution The VirtualBox settings indicate you host machine has 4 real and 4 virtual cores with 16G of RAM. You could try shutting down the VM, and then change the VirtualBox settings to give the VM 4 cores (instead of 2) and 12G of RAM (instead of 8G).  Then start the VM and try running your command again to see if performance improves maybe first with 2 jobs and then 4.   I would try not to run other applications on your host machine at this time. - R. On May 9, 2022, at 17:47, Joanna L Eckhardt <jeckhardt(a)health.ucsd.edu> wrote:        External Email - Use Caution        Oops, I meant to reply all: Hi R ,See below, I gave 8 GB and 2 CPU in settings.<image.png><image.png>--Joanna EckhardtNeurosciences Graduate ProgramUniversity of California, San DiegoSent: Monday, May 9, 2022 2:41 PMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Cc: Joanna L Eckhardt <jeckhardt@health.ucsd.edu>Subject: Re: [Freesurfer] Recon-all Freezes on Parallel In the VirtualBox settings, did you give the VM both cores to use?It would also be good to know much memory your machine has, and how much of that you gave to the VM in the VirtualBox settings.- R.On May 9, 2022, at 17:27, Joanna L Eckhardt <jeckhardt(a)health.ucsd.edu> wrote:        External Email - Use Caution        Dear FreeSurfer Team, I have been trying to use the parallel command (following FreeSurfer tutorial) to run multiple subjects (Windows os running Ubuntu VM).I only have 2 cores, so I have it set to 2 jobs instead of 8 as in the tutorial. When I use the code from the tutorial, there is an error with the .nii, and I assume it is because my files are .nii.gz.developer@developer-VirtualBox:~/FreeSurfer/Cannabis_Reduced$ ls *.nii | parallel --jobs 3 recon-all -s {.} -i {} -all -qcache ls: cannot access '*.nii': No such file or directory So I changed the code to .gz with everything else the same, and FreeSurfer does nothing (it stalls/freezes). Is this just because my computer cannot handle the job? Is there anything else I can do to run parallel? If not, I can always just run 1 subject at a time, but I want to check and see if there is another way to get this to work. Thank you for your time!Joanna_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_____________… mailing listFreesurfer@nmr.mgh..harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

Re: [Freesurfer] Recon-all Error
by fsbuild 09 May '22

09 May '22

External Email - Use Caution Hello Mouna, You should not need to set FREESURFER_HOME in the terminal window or source the setup script as that is already set in the environment to the pre-installed 7.2.0 release of freesurfer.  if the setup information listing FREESURFER_HOME etc. is not automatically displayed when you open a new terminal window, then something is not right with your current VM setup. Please see the online documentation https://secure-web.cisco.com/1gznVcTKDzEuwdybT3u9uoWvv2v… contains a link to the document Vbox_load_image showing how to setup the VM, i.e., page 12 says you can go to http://secure-web.cisco.com/1q0X87yBimuGRycgbM3K-M42AWFTRmdTzLmdSTP… obtain a license and how to use it in the terminal window. - R. On May 9, 2022, at 10:01, Mouna JABEUR <mouna.jabeur(a)enetcom.u-sfax.tn> wrote:        External Email - Use Caution        Hi,how can i solve this please ?<Capture d’écran 2022-05-09 145325.png><Capture d’écran 2022-05-09 145137.png><Capture d’écran 2022-05-09 145019.png>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Re: [Freesurfer] Recon-all Freezes on Parallel
by Joanna L Eckhardt 09 May '22

09 May '22

External Email - Use Caution Oops, I meant to reply all: Hi R , See below, I gave 8 GB and 2 CPU in settings. [cid:f2395341-7e91-40b6-bc1c-d89bca3e4876] [cid:32cfdb7f-40af-4c07-babd-c07a17f81269] -- Joanna Eckhardt Neurosciences Graduate Program University of California, San Diego ________________________________ From: fsbuild(a)convergenceservice.com <fsbuild(a)convergenceservice.com> Sent: Monday, May 9, 2022 2:41 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Cc: Joanna L Eckhardt <jeckhardt(a)health.ucsd.edu> Subject: Re: [Freesurfer] Recon-all Freezes on Parallel In the VirtualBox settings, did you give the VM both cores to use? It would also be good to know much memory your machine has, and how much of that you gave to the VM in the VirtualBox settings. - R. On May 9, 2022, at 17:27, Joanna L Eckhardt <jeckhardt(a)health.ucsd.edu> wrote: External Email - Use Caution Dear FreeSurfer Team, I have been trying to use the parallel command (following FreeSurfer tutorial) to run multiple subjects (Windows os running Ubuntu VM). I only have 2 cores, so I have it set to 2 jobs instead of 8 as in the tutorial. When I use the code from the tutorial, there is an error with the .nii, and I assume it is because my files are .nii.gz. developer@developer-VirtualBox:~/FreeSurfer/Cannabis_Reduced$ ls *.nii | parallel --jobs 3 recon-all -s {.} -i {} -all -qcache ls: cannot access '*.nii': No such file or directory So I changed the code to .gz with everything else the same, and FreeSurfer does nothing (it stalls/freezes). Is this just because my computer cannot handle the job? Is there anything else I can do to run parallel? If not, I can always just run 1 subject at a time, but I want to check and see if there is another way to get this to work. Thank you for your time! Joanna _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1D16OXl4F3D7EzPXJHwCPdzg7739Ei-nFn--qsir3PrQym…<https://secure-web.cisco.com/1gcVuUnsNGIajmH36BBP5ji4ZbVCz3onJbt4vYs8FHb4t2…>

1 0

Recon-all Error
by Mouna JABEUR 09 May '22

09 May '22

External Email - Use Caution Hi, how can i solve this please ? [cid:f249d482-90f9-43e9-a1f3-dc5a2f46ab7a] [cid:60b6d04d-5312-4ec4-a039-a79871a083a3][cid:6d8eb673-c4d0-472a-afa3-0e61e3bc4826]

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