Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30071 discussions

FSLOUTPUTTYPE=NIFTI_PAIR: Command not found
by Deanna Aghbashian 15 Jul '22

15 Jul '22

External Email - Use Caution Hello FreeSurfer Developers, I have set up with terminal in tcsh, and it was working without error. However, when I logged on late last week I got an error in setting up environment for FreeSurfer on Mac OS Monterey Version 12.4 -------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSLOUTPUTTYPE=NIFTI_PAIR: Command not found. export: Command not found. FSL_DIR /usr/local/fsl [MacBook-Pro:~] deanna% nano ~/.cshrc Within my tcsh profile, I do not have anything to indicate to have FSLOUTPUTTYPE to be NIFTI_PAIR, nor do I have a line to export. I have also checked the SetUpFreeSurfer.csh, FreeSurferEnv.csh. I have tried clearing out my profile and recreating it, deleting and reinstalling FSL and FreeSurfer. When I use echo $FSLOUTPUTTYPE it comes back as NIFTI_GZ. My profile is below: # auto-inserted by @update.afni.binaries : setenv DYLD_LIBRARY_PATH /opt/X11/lib/flat_namespace # set up tab completion for AFNI programs if ( -f $HOME/.afni/help/all_progs.COMP ) then source $HOME/.afni/help/all_progs.COMP endif if ( $?DYLD_LIBRARY_PATH ) then setenv DYLD_LIBRARY_PATH ${DYLD_LIBRARY_PATH}:/opt/X11/lib/flat_namespace else setenv DYLD_LIBRARY_PATH /opt/X11/lib/flat_namespace endif set path = ( $path $HOME/abin ) # include directories for FSL setenv FSLDIR /usr/local/fsl source ${FSLDIR}/etc/fslconf/fsl.csh setenv PATH ${FSLDIR}/bin:${PATH} setenv FREESURFER_HOME /Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh Does anyone have any suggestions? Thanks, Deanna

1 0

Pass code
by Ulysses Bernardet 15 Jul '22

15 Jul '22

External Email - Use Caution Hi, I would like to request the pass code for the FreeSurfer Virtual VM image. Cheers, Ulysses Dr Ulysses Bernardet Assistant Professor of Computer Science cybernetic human lab cs.aston.ac.uk/chl College of Engineering and Physical Sciences Aston University, Birmingham, UK

1 0

[TRACULA] Auto-BIDS Config Variables Question
by Steven Meisler 15 Jul '22

15 Jul '22

External Email - Use Caution Hello, I am trying out the development dmri-bids-config script <https://secure-web.cisco.com/1w--1vLn2hIhDzN_sQmBI1_PGZkHehc5IsuQS_9ZRqntOo…> to set up my BIDS-formatted data for TRACULA. It runs fine without error, but I have some concerns about the automatically generated protocol variables. 1) For “echospacing”, should we be using the echo spacing as found in the scanner protocol, or effective echo spacing (as parsed from the BIDS json sidecar)? These values are fairly different from each other. It is also not clear what units the config file expects (I assume “ms” based on some of the examples and protocols I have looked at). 2) “epifactor” seems to be generated by a mathematical operation on the total readout time as parsed from the BIDS json file. The value I get from this operation is off by a few orders of magnitude. In my case, the predicted value from the BIDS json file is 127001, while the protocol epifactor is 128. What I imagine is happening here is that the script assumes the TotalReadoutTime is in different units, because it does some division by (0.001) and then adds 1 to the result. So if the units matched mine, then I would have ended up with 127+1 = 128 (which matches the protocol). In either case, I am happy to see this being configured for BIDS and am excited to see it deployed in 7.3! Best, Steven

2 1

Password for unzipping .7z file of virtual image
by Weilguny, Nicolas 14 Jul '22

14 Jul '22

External Email - Use Caution Hi FreeSurfer-Team, I hereby request the password for unzipping the FS_7_2_0_Ubuntu_18_04_06.ova.7z file. Thank you in advance! Best regards, Nicolas Weilguny

1 0

Freesurfer .7z password
by Kerezoudis, Panagiotis, M.D., M.S. 14 Jul '22

14 Jul '22

External Email - Use Caution Greetings, I would like to ask for the password to open and install the .7z file for Freesurfer on Windows. Thank you, Panos Panagiotis Kerezoudis, M.D., M.S. Resident | Department of Neurologic Surgery Mayo Clinic | Rochester, Minnesota<https://secure-web.cisco.com/1KQqKOxG8FySe-tB4is7yhyIC304BnfpZzLZiSpSYcMNmv…> 200 First Street SW, Rochester, MN, 55905 email: Kerezoudis.Panagiotis(a)mayo.edu<mailto:Kerezoudis.Panagiotis@mayo.edu> |phone: 5-6037<tel:5-6037> | pager: 17872<tel:17872>

1 0

Re: [Freesurfer] SynthSR: Illegal Hardware Instruction
by fsbuild 12 Jul '22

12 Jul '22

External Email - Use Caution Hello Ahmed, This can result from how the code was compiled and/or optimized for older versions of MacOS - which may not translate well to running on newer versions of MacOS.  In your case, the the Mac is also running the Rosetta environment to translate the Intel binary instructions to run on the arm M1 chip.   The code would probably have to be complied differently to address this. If you have an example command and file input you could share, you could send it along and we could try and reproduce it. - R.  environment to translate instructions compiled  On Jul 12, 2022, at 09:28, Abdelkarim, Ahmed <a.karam(a)ucl.ac.uk> wrote:        External Email - Use Caution        Hello I have an issue getting SynthSR working with FreeSurfer dev.I have MacBook Pro with apple M1 chip and MacOS Monterey. In bash terminal, after setting up FreeSurfer, and running the SynthSR command, I get this error ‘’Illegal instruction: 4’’. Have you had a similar issue before? Any advice? Many thanks in advance. RegardsAhmed  _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- This is a copy of a message which has been originally sent to: "To" field: freesurfer(a)nmr.mgh.harvard.edu "Copy" field: a..karam(a)ucl.ac.uk The message has been sent by https://secure-web.cisco.com/148oNXnm75KGvFGK5eicU0d_xOxYGERfT6ffGsller2qhI… and the used account name was: SSL

1 0

Passcode FreeSurfer 7.2.0
by Gomez,Julieth 12 Jul '22

12 Jul '22

External Email - Use Caution Hello Freesurfer family, Could you please share the passcode to unzip the folder for the following release: Freesurfer 7.2.0 release in Ubuntu 18.04.06: FS_7_2_0_Ubuntu_18_04_06.ova.7z<https://secure-web.cisco.com/19abC5jXMkA6x9Yd2W5e_hfVxltVss7cSjfS5uZCITfrgq…> ? I appreciate your help, >> Best regards, [cid:image001.png@01D89603.ED122FD0] Julieth Gómez Durán Ph.D. Student | Brain Mapping Lab J. Crayton Pruitt Family Department of Biomedical Engineering Herbert Wertheim College of Engineering University of Florida [Image result for phone icon](352) 226-6956

1 0

I need pass code for FS_7_2_0_ubuntu_18_04_06.ova.7z
by Vinod 12 Jul '22

12 Jul '22

External Email - Use Caution When I try to open it asks for pass code. Can you please give me the pass code. Thanks

1 0

Re: [Freesurfer] help troubleshooting lta_convert error
by fsbuild 12 Jul '22

12 Jul '22

External Email - Use Caution Hello Megan, The errors you list below usually result from running a version of Freesurfer that does not match the operating system you are using, i.e., it looks like you are trying to run the version built for Ubuntu linux, 7.2.0 (freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b) … on a CentOS6 system, Description:    CentOS release 6.7 (Final) If you have admin privileges on your system, then I would try installing the Freesurfer 7.2.0 CentOS6 rpm file on your CentOS6 system, which you can download from, https://secure-web.cisco.com/1_TrIriXqcfLg6YdYhz-fK97TtRKLaLawhDUmlefqUI_U6… If you do not have admin privs to install the RPM, then you can download and expand the tar archive from,https://secure-web.cisco.com/1Fhw7EkvdlF04-nFWgMtF44HHWjdGMGEq_-VbJMp1… The Freesurfer 7.2.0 distributions available for each operating system are currently listed on this page, https://secure-web.cisco.com/1Sbf8V045U7e_z5ui8AhyYxoVSIwU0U2msh… - R. On Jul 1, 2022, at 13:32, Megan Schendel <mschendel(a)mrn.org> wrote:        External Email - Use Caution        Hi all,I had a working distribution on an old system a few weeks ago, but now I'm getting an error.  Can anyone offer any troubleshooting ideas?I am working on a shared server with a freesurfer distribution that I own.Here is some system info:[mschendel@earth scripts]$ lsb_release -aLSB Version:    :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarchDistributor ID: CentOSDescription:    CentOS release 6.7 (Final)Release:        6.7Codename:       FinalOn the command line, the error looks like this:lta_convert: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by lta_convert)lta_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by lta_convert)lta_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.19' not found (required by lta_convert)lta_convert: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by lta_convert)The recon-all.log file contains the following:Fri Jul  1 11:08:24 MDT 2022cd /export/research/analysis/unm_psych/dquinn/Navigate_20673/MEG_source_analysis/M87124539setenv SUBJECTS_DIR /export/research/analysis/unm_psych/dquinn/Navigate_20673/MEG_source_analysis/export/research/analysis/human/jstephen/shared/programs/freesurfer_7.2/freesurfer//bin/recon-all -all -i /export/research/archive/human/dicom/prisma/dquinn/navigate_20673//M87124539/Study20210623at161830/mprage_5e_32ch_RMS_0003/SerieMR-0003-0001-1.dcm -s /export/research/analysis/unm_psych/dquinn/Navigate_20673/MEG_source_analysis//M87124539 -openmp 8subjid M87124539setenv SUBJECTS_DIR /export/research/analysis/unm_psych/dquinn/Navigate_20673/MEG_source_analysisFREESURFER_HOME /export/research/analysis/human/jstephen/shared/programs/freesurfer_7.2/freesurfer/Actual FREESURFER_HOME /export/research/analysis/human/jstephen/shared/programs/freesurfer_7.2/freesurferbuild-stamp.txt: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76bLinux earth.mind.unm.edu 2.6.32-573.26.1.el6.x86_64 #1 SMP Wed May 4 00:57:44 UTC 2016 x86_64 x86_64 x86_64 GNU/Linuxcputime      unlimitedfilesize     unlimiteddatasize     unlimitedstacksize    10240 kbytescoredumpsize 0 kbytesmemoryuse    unlimitedvmemoryuse   unlimiteddescriptors  1024memorylocked 64 kbytesmaxproc      unlimited########################################program versions used7.2.0 (freesurfer-linux-ubuntu18_x86_64-7..2.0-20210721-aa8f76b)ERROR: Executable 'lta_convert -all-info failed! Is it missing from the distribution?'MEG TechnicianPronouns: she/herThe Mind Research Network1101 Yale Blvd. NEAlbuquerque, New Mexico 87106_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Thalamus subnuclei ICC
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 11 Jul '22

11 Jul '22

External Email - Use Caution Hi, Can someone send me the full ICC for all of the thalamus subnuclei that are parcellated? Just want to have that ready if a reviewer asks. Thanks Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --

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