Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30065 discussions

Re: [Freesurfer] T2pial: Numerical argument out of domain
by AmirHussein Abdolalizadeh 07 Feb '23

07 Feb '23

External Email - Use Caution Hi again, An update: Repeating the analysis using 7.1.0 ends without any errors. Visually checking the results also seems totally fine. I think it is something specific to 7.3.2. Of note, my subjects are elderly with variable degrees of white matter hyperintensities. Any comments? Best, Amir

2 1

Help with script with 7.2 on an HPC
by Taylor, Lisa 07 Feb '23

07 Feb '23

External Email - Use Caution Hi there, I am trying to update my scripts on our university's HPC but am running into an issue. I am not too savvy when it comes to this, so I apologize. My guess is I will have to run my old 6.0 script but without the -hippocampal-subfields-T1 argument in the new 7.2 script that I copied over, but then run the 'segmentHA_T1.sh' separately? Is there a way to incorporate this script in the 7.2 script I currently have? Thank you for any help/insight you can give. Error I get when trying to run my updated 7.2 script: $cat slurm-19565158.out ERROR: the hippocampal subfield module is now in separate scripts: segmentHA_T1.sh segmentHA_T2.sh segmentHA_T1_long.sh 1 of 2 of the scripts used to run freesurfer on the HPC3: cat freesurfer_template_7.2.sub #!/bin/bash #SBATCH --job-name=fs_reconall_subid #SBATCH -A account #SBATCH -p user #SBATCH --nodes=1 #SBATCH --ntasks=1 #SBATCH --cpus-per-task=2 #SBATCH --error=slurm-reconall_subid.err #SBATCH --mem-per-cpu=18gb module load freesurfer/7.2.0 xport SUBJECTS_DIR=imagedir source $FREESURFER_HOME/SetUpFreeSurfer.sh # run freesurfer srun ${FREESURFER_HOME}/bin/recon-all -s imagedir/subid -no-isrunning -all -hippocampal-subfields-T1 -brainstem-structures -qcache 2 of 2 of the script used to run freesurfer on the HPC3: cat 7.2_freesurfer_prep_single_subj.sh #!/bin/sh # usage: sh freesurfer_prep_from_nii.sh [queue] [account_to_charge] [freesurfer_subj_folder] # [queue] = free | standard # [account_to_charge] = ltaylor2 # [freesurfer_subj_folder] = This is the subject directory created by freesurfer for processing # if [[ $# -lt 3 ]] ; then echo 'Usage: sh freesurfer_prep_from_nii.sh [queue] [account_to_charge] [freesurfer_subj_folder]' echo '[queue] = free | standard' echo '[account_to_charge] = ltaylor2' echo 'PLEASE ONLY USE THE FREE QUEUE UNLESS OTHERWISE INSTRUCTED'a echo '[freesurfer_subj_folder] = This is the subject directory created by freesurfer for processing' exit 0 fi subids=$3 imagedir=`echo $PWD` echo $subids if [ -d freesurfer_sub ]; then echo directory freesurfer_sub exists ...; else mkdir freesurfer_sub; fi for subid in ${subids}; do sed -e s/subid/${subid}/g -e s/user/${1}/g -e s/account/${2}/g -e s#imagedir#${imagedir}#g freesurfer_template_7.2.sub > freesurfer_sub/fs_${subid}.sub cd freesurfer_sub echo sbatch fs_${subid}.sub sbatch fs_${subid}.sub cd .. done Thank you! Lisa

2 1

creating a freesurfer guix package definition (aka compiling from source)
by Malte Frank Gerdes 07 Feb '23

07 Feb '23

External Email - Use Caution Hi, I'm trying to create a freesurfer (v7.3.3) package definition for guix. I have some problems during freesurfers configure step though. I'm using the following definitions to build freesurfer (this may not help much if you don't know guix, but you may still see what might be wrong in the attached build log). ``` (use-modules (gnu packages algebra) (gnu packages check) (gnu packages commencement) (gnu packages compression) (gnu packages fontutils) (gnu packages geo) (gnu packages gl) (gnu packages image) (gnu packages image-processing) (gnu packages llvm) (gnu packages maths) (gnu packages pdf) (gnu packages perl) (gnu packages python) (gnu packages qt) (gnu packages serialization) (gnu packages shells) (gnu packages sqlite) (gnu packages tcl) (gnu packages vim) (gnu packages xiph) (gnu packages xml) (gnu packages xorg) (guix build-system cmake) (guix download) (guix gexp) (guix git-download) ((guix licenses) #:prefix license:) (guix packages)) (define-public itk (package (name "itk") (version "5.3.0") (source (origin (method git-fetch) (uri (git-reference (url "https://secure-web.cisco.com/1KgpkMc1pvHUPomaJMVqKQnZBVMErQsj49d1dySfD5xTF-…") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "1bx98lzafj83fxylm0qnxkn05rdlrvfc672f0n843hgis2wk0gfh")))) (build-system cmake-build-system) (arguments `(#:configure-flags (list "-DBUILD_EXAMPLES=OFF" "-DITK_FORBID_DOWNLOADS=ON" "-DITK_USE_KWSTYLE=OFF" ; requires git during build "-DITK_USE_SYSTEM_LIBRARIES=ON" "-DITK_USE_CLANG_FORMAT=OFF" (string-append "-DGTEST_ROOT=" (assoc-ref %build-inputs "googletest"))) #:phases ,#~(modify-phases %standard-phases (add-before 'configure 'unpack-test-data (lambda _ (invoke "tar" "xzf" #$(this-package-native-input "test-data") "--strip-components=1")))))) (native-inputs `(("cppcheck" ,cppcheck) ("eigen" ,eigen) ("googletest" ,(package-source googletest)) ("perl" ,perl) ("python" ,python) ("test-data" ,(origin (method url-fetch) (uri (string-append "https://secure-web.cisco.com/14JbcCit8VdllWuNGvNogUu6Rm4HBxrjFJ5eN_gcCfjbdt…" version "/InsightData-" version ".tar.gz")) (sha256 (base32 "1iyr037x7yqkdhd3w427pp6ba947l79acplq4cx9jicrbfgbxy2k")))))) (inputs (list expat hdf5 libjpeg-turbo libpng libtiff zlib)) (outputs (list "out" "debug")) (synopsis "Spatially-oriented architecture for processing, segmentation, and registration of scientific images") (description "The Insight Toolkit (ITK) is an open-source, cross-platform toolkit for N-dimensional scientific image processing, segmentation, and registration. Segmentation is the process of identifying and classifying data found in a digitally sampled representation. Typically the sampled representation is an image acquired from such medical instrumentation as CT or MRI scanners. Registration is the task of aligning or developing correspondences between data. For example, in the medical environment, a CT scan may be aligned with a MRI scan in order to combine the information contained in both.") (home-page "https://secure-web.cisco.com/1e3XSo-gh-p-0Y5bOrS4AAQKhvfMxcv9IpC5tdPa-bv-CJ…") (license license:asl2.0))) (define-public freesurfer (package (name "freesurfer") (version "7.3.3") (source (origin (method git-fetch) (uri (git-reference (url "https://secure-web.cisco.com/1wexvnLD388FTeoOYQDV62Yu0pE_NZYF0g3QWqMApqiUTs…") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "1vn9vs6q451qp8ak62fc21zv91gm2f0f5wiijh4xj4zys3fyvi93")) (modules '((guix build utils))) (snippet '(begin (substitute* "CMakeLists.txt" (("ARMADILLO") "Armadillo") (("OPENGL") "OpenGL")) (substitute* "cmake/FindOpenCV.cmake" (("opencv2 PATH_SUFFIXES include") "opencv2 opencv4/opencv2 PATH_SUFFIXES include")))))) (build-system cmake-build-system) (arguments `(#:configure-flags (list "-DMARTINOS_BUILD=OFF" "-DBUILD_GUIS=OFF"))) (native-inputs `(("gfortran-toolchain" ,gfortran-toolchain) ("gl2ps" ,gl2ps) ("googletest" ,(package-source googletest)) ("perl" ,perl) ("python" ,python) ("tcl" ,tcl) ("tcsh" ,tcsh) ("xxd" ,xxd))) (inputs (list armadillo openblas double-conversion eigen expat freetype hdf5 glew itk jsoncpp lapack libharu libjpeg-turbo libpng libtheora libtiff libx11 libxt libxml2 libxmu lz4 mesa netcdf opencv petsc proj qtbase-5 qtx11extras sqlite vtk zlib)) (outputs (list "out" "debug")) (synopsis "Software suite for processing human brain MRI") (description "FreeSurfer is a software package for the analysis and visualization of neuroimaging data from cross-sectional and longitudinal studies. It is developed by the Laboratory for Computational Neuroimaging at the Martinos Center for Biomedical Imaging. FreeSurfer provides full processing streams for structural and functional MRI and includes tools for linear and nonlinear registration, cortical and subcortical segmentation, cortical surface reconstruction, statistical analysis of group morphometry, diffusion MRI, PET analysis, and much more. It is also the structural MRI analysis software of choice for the Human Connectome Project.") (home-page "https://secure-web.cisco.com/1PZCRDcDOn3O1uoFNsBeYHfpLQY2DOO20fJU6mAm8xv-5H…") ;; it's an open source license but afaict it isn't free as in freedom. (license #f))) ``` The output of `guix describe`: ``` Generation 168 Feb 01 2023 13:00:36 (current) guix 14323ed repository URL: https://secure-web.cisco.com/15q8zTqQfZSwuvTajUs5f9N2aYltiq9edRi1PUyW8JzLdA… branch: master commit: 14323edcc37d9efaae2491cf5f57ea0621412d7e nonguix c694cf9 repository URL: https://secure-web.cisco.com/1XwNEBscgHWCPMrio9mZuc4l17saADnyXjvBec6Pavy9o8… branch: master commit: c694cf9211db3cc8673f0e73708d53b75d26518b ``` Now to my questions/remarks: - As i can see in the wiki i am actually supposed to set `FS_PACKAGES_DIR` but as far as i understand this setting it doesn't make sense in guix. What is the exact purpose of this variable? Every dependency of freesurfer that is specified in the `native-inputs` (which is for dependencies only used at build time) and `inputs` fields is available during the build (and _only_ what is specified there). The configure output in the log also clearly shows that all dependencies are actually found (besides ANN that isn't packaged and i haven't packaged it myself until now; i should probably do that...) - cmake searches for `FindARMADILLO.cmake` but the file is called `FindArmadillo.cmake` which results in CMake erroring out because it can't find `FindARMADILLO.cmake`. The find_package for Armadillo is commented out on dev though. - The actual error i hit currently are quite a bunch of these for different files, cmake reported earlier that it could find all X11 deps though. Googling for it seems to suggest that this could be due to transitive dependencies interfering with each other (vtk also imports libx11; but this is just a guess) ``` CMake Error at cmake/functions.cmake:234 (add_executable): Target "lineprof_test" links to target "X11::X11" but the target was not found. Perhaps a find_package() call is missing for an IMPORTED target, or an ALIAS target is missing? Call Stack (most recent call first): lineprof/CMakeLists.txt:31 (add_test_executable) ``` - even though i have lapack and openblas and the gfortran toolchain inside the build environment, i get: ``` CMake Error: The following variables are used in this project, but they are set to NOTFOUND. Please set them or make sure they are set and tested correctly in the CMake files: BLAS_LIBRARIES linked by target "lineprof_test" in directory /tmp/guix-build-freesurfer-7.3.3.drv-0/source/lineprof linked by target "surf2vol" in directory /tmp/guix-build-freesurfer-7.3.3.drv-0/source/fem_elastic GFORTRAN_LIBRARIES linked by target "lineprof_test" in directory /tmp/guix-build-freesurfer-7.3.3.drv-0/source/lineprof linked by target "surf2vol" in directory /tmp/guix-build-freesurfer-7.3.3.drv-0/source/fem_elastic LAPACK_LIBRARIES linked by target "lineprof_test" in directory /tmp/guix-build-freesurfer-7.3.3.drv-0/source/lineprof linked by target "surf2vol" in directory /tmp/guix-build-freesurfer-7.3.3.drv-0/source/fem_elastic ``` How am i supposed to let the build system know these variables? As the files are there i would have expected cmake to pick those up itself thanks in advance for any help :-) Malte

1 0

qcache morphometry measures are empty
by Steven Meisler 06 Feb '23

06 Feb '23

External Email - Use Caution Hello FreeSurfer developers, (This issue is described in detail at the following link: https://secure-web.cisco.com/19gHm_kiBwLabZG0kSzLCkZdl3RRluMPmh3eOd0r3KCWXL…) I am preparing a surface-based morphometry analysis. I ran recon-all v7.3.2 with qcache enabled. It completes without error and I do see the output files in fsaverage space at the various smoothing kernels, as expected. However, the fsaverage space smooth files appear to be empty, based upon trying to load their data with the Python package Nibabel. Some other notes: 1) When I load the QCACHE files, there are no errors in loading the file, but the data array returned is empty, so the files appear to be properly formatted morphological files. 2) When I load the native space thickness file (e.g. surf/lh.thickness), I get the expected full output with all data there, so I doubt it is a Nibabel issue. 3) This happens for all subjects, measurement types (e.g. area, volume, etc) and smoothing kernels. 4) All qcache outputs are the same file size (668.6 kb), which doesn’t seem like it should be right. I am planning on running models on the data outside of Freesurfer since I have to deal with complex tasks such as site harmonization and general additive modeling, which is why I cannot proceed using the typical mris_preproc method. Please let me know if I can provide any other helpful information in addressing this. Best, Steven

2 3

mapping from Desikan-Killiany regions to resting state networks
by Krieger, Donald N. 06 Feb '23

06 Feb '23

External Email - Use Caution Dear list, I would like to find a reasonably good mapping from Desiken-Killiani ROIs and as many of the resting state networks as makes sense, e.g. salience, visual, etc. I have made a start using the network <----> ROI mapping in the Conn Toolbox but I think there is likely a better starting place. Any direction would be most welcome. Thanks - Don Don Krieger, PhD Research Scientist Department of Neurological Surgery University of Pittsburgh

1 2

Senior research position
by Aaron Tanenbaum 06 Feb '23

06 Feb '23

External Email - Use Caution Please see attached for a Senior research position job description. Please apply for the position at https://secure-web.cisco.com/1u02-AJuClQt7sTxQ63p9YV9P4EzHp2M0YbFhpmhtEnqyD… Do not apply for the position over email, email will be ignored. Aaron Tanenbaum

1 0

Re: [Freesurfer] FS FAST
by fsbuild 06 Feb '23

06 Feb '23

External Email - Use Caution Hello Justin, Depending upon the OS of the machine, there may not be a “python” installed by default on the system, i.e., you need to choose either python2 or python3.  Given some scripts may still look for “python”, then you can add an alias in your shell init file so “python” points to what’s available. - R. ubuntu20:~$ which python ubuntu20:~$ which python2 ubuntu20:~$ which python3 /bin/python3ubuntu20:~$ python3 --version Python 3.8.10 ubuntu20:~$ alias python='python3' ubuntu20:~$ python --version Python 3.8.10 On Feb 6, 2023, at 00:53, Justin Oh <ohjp89(a)gmail.com> wrote:        External Email - Use Caution        Hi all, I am trying to run preproc-sess on a resting state MRI. I believe my directory is set the way it should be. There was an error that stopped the pipeline: env: python: No such file or directoryCould anybody help me out? All the best,Justin Oh_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

FS FAST
by Justin Oh 06 Feb '23

06 Feb '23

External Email - Use Caution Hi all, I am trying to run preproc-sess on a resting state MRI. I believe my directory is set the way it should be. There was an error that stopped the pipeline: env: python: No such file or directory Could anybody help me out? All the best, Justin Oh

1 0

TRACULA cluster statistics visualization
by miracle ozzoude 04 Feb '23

04 Feb '23

External Email - Use Caution I have a similar question to this unanswer one (see link) https://secure-web.cisco.com/1TPpYYjX_nTrm6lqczxoG15eSKbWRPZCXEekOMWT-xtyur… *Also* 1) If I run along-tract stats with mri_glmfit/mri_glmfit-sim and I found a significant result, how do I know the entire length of the tract and how much was affected? Also, is it measured in mm? 2) When performing clusterwise correction for multiple comparison for along-tract analyses, should the bonferroni flag (--2spaces) be included? This is because it wasn't mentioned/included in the tracula statistics tutorial nor the publication "Using diffusion MRI data acquired with ultra-high gradient strength to improve tractography in routine-quality data ". Many thanks, Paul

1 0

Re: [Freesurfer] installation of two versions of freesurfer on same computer...
by fsbuild 03 Feb '23

03 Feb '23

External Email - Use Caution It should work to use multiple versions on the same machine.  You need to: (1) install them under different paths; (2) have enough disk space for each distribution; (3) change the setting of FREESURFER_HOME when you change the freesurfer version in use.   Then you need to re-source the SetUpFreeSurfer.[sh,csh] script each time you change FREESURFER_HOME to (re)set the shell environment. The package installers, *.rpm, *.deb, *.pkg, will install under a known path, i.e.., linux is /usr/local/freesurfer/<version> and for MacOS /Applications/freesurcer/<version>. The package management software on linux OS’s keeps track of the version that’s installed.  I think if you had  /usr/local/freesurfer/7.3.1 installed, then it would consider installing 7.3.2 as an upgrade to 7.3.1, and so it might remove 7.3.1 before installing 7.3.2 as  /usr/local/freesurfer/7.3.2.   There might be an option to tell the package tools to say to keep an old version.  You could make a copy of 7.3.1, install the 7.3.2 package, and then restore 7.3.1 so you have /usr/local/freesurfer/{7.3.1,7.3.2}.  I would try to have at least 1 version installed on Linux using the .deb or .rpm package installers.  That will have checked your machine and potentially installed dependencies fressurfer needs to run.  You could subsequently try using the tar archive for a different version located elsewhere, expanded as a non-root user. - R. On Feb 3, 2023, at 17:26, Gonzalo Rojas Costa <gonzalo.rojas.costa(a)gmail.com> wrote:        External Email - Use Caution        Hi:  How can I install two different versions of freesurfer on the same computer?  Sincerely,Gonzalo Rojas Costa_______________________________________________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