Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30130 discussions

Re: [Freesurfer] Bug in mri_convert reslice-like with 4D images
by fsbuild 06 Jun '24

06 Jun '24

External Email - Use Caution  It could help to see the core dump file.  If you are on a Mac it will probably display it.  If you are on Linux and you have core dumps enabled on the system, then you have to look in the logs. - R. On Jun 6, 2024, at 15:56, Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh..harvard.edu> wrote:Dear FS experts,We get a segfault when I try to resample images with the command:mri_convert input.mgz output.mgz -rl reference..mgz when reference.mgz has multiple frames (e.g., a RGB volume). Any idea of why this is happening?Cheers,/Eugenio (&Stefano & Pranav)_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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fs_temp_file: Command not found
by Cameron, Jack 06 Jun '24

06 Jun '24

External Email - Use Caution Hello FreeSurfer developers, I am in the process of learning how to use FreeSurfer and attempting to run the recon-all on FreeSurfer 7.4.1 on a 2019 MacBook Pro (Sonoma 14.5). The response is attached as a pdf, but I have also copied and pasted the environment and commands below. Last login: Thu Jun 6 14:07:57 on ttys000 jack@Jack-MacBook-Pro ~ % export FREESURFER_HOME=/Applications/freesurfer/7.4.1 jack@Jack-MacBook-Pro ~ % export SUBJECTS_DIR=$FREESURFER_HOME/subjects jack@Jack-MacBook-Pro ~ % echo $FREESURFER_HOME /Applications/freesurfer/7.4.1 jack@Jack-MacBook-Pro ~ % echo $SUBJECTS_DIR /Applications/freesurfer/7.4.1/subjects jack@Jack-MacBook-Pro ~ % source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer/7.4.1 FSFAST_HOME /Applications/freesurfer/7.4.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/7.4.1/subjects MNI_DIR /Applications/freesurfer/7.4.1/mni jack@Jack-MacBook-Pro ~ % which freeview /Applications/freesurfer/7.4.1/bin/freeview jack@Jack-MacBook-Pro ~ % which recon-all /Applications/freesurfer/7.4.1/bin/recon-all jack@Jack-MacBook-Pro ~ % cd SUBJECTS_DIR cd: no such file or directory: SUBJECTS_DIR jack@Jack-MacBook-Pro ~ % cd $SUBJECTS_DIR jack@Jack-MacBook-Pro subjects % ls HYPE_shared cvs_avg35_inMNI152 fsaverage_sym README fsaverage lh.EC_average Test.nii fsaverage3 rh.EC_average V1_average fsaverage4 sample-001.mgz bert fsaverage5 sample-002.mgz cvs_avg35 fsaverage6 tutorial_data_20190918_1558 jack@Jack-MacBook-Pro subjects % recon-all -all -i sample-001.mgz -s SAMPLE001J6 fs_temp_file: Command not found. fs-check-version --s SAMPLE001J6 --o ERROR: flag --o requires one argument I see that there is not an EXIT as is typical with FreeSurfer hard failures... Do you have any advice on where I might have gone wrong? I could not find any information posted/previous issues with this command online. I appreciate any help you can provide. Jack

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Freesurfer license
by Ayoub, Lizbeth 04 Jun '24

04 Jun '24

Hi, I am using singularity to run fmriprep, and it seems that it is not recognizing the location of my freesurfer license ( it is a new license). I have tried all three options for location, and none work: ERROR: a valid license file is required for FreeSurfer to run. fMRIPrep looked for an existing license file at several paths, in this order: 1) command line argument ``--fs-license-file``; 2) ``$FS_LICENSE`` environment variable; and 3) the ``$FREESURFER_HOME/license.txt`` path. Get it (for free) by registering at https://surfer.nmr.mgh.harvard.edu/registration.html I appreciate any insights on how to fix this error :) Thank you so much, Liz

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mri_fuse_segmentation error: could not open file
by Tommaso Cusolito S319624 04 Jun '24

04 Jun '24

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to extract cortical thickness from a fifth scan using a template based on only the first four scans (obtained by following the longitudinal pipeline available at https://secure-web.cisco.com/1S7BQNmF9HghVT1XkcD-pYvMmoQDm0WTjg3-N1bP-4anPW…) Unfortunately, I don't have the option to run the longitudinal processing from scratch including the fifth scan as I no longer have access to the cross-sectionally processed single scan data (in format patient_scan#) for scans 1 through 4 but only to the folders generated by the recon-all function (in format patient_scan#.long.patient_template). I've made sure to generate .lta files (through mri_robust_register) for forwards and backwards transformations from s5 to template and to add the scan 5 to the "base-tps" file, but recon-all reports a later error when using the function mri_fuse_segmentations as I no longer have access to files for single scans (norm.mgz, aseg.mgz,aseg.auto_noCCseg.mgz). I acknowledge that the template data will be biased towards the first four scans but I was looking for a way to use the function on only data belonging to the "patient_scan#.long.patient_template" folders together with the fifth scan data "patient_s5". Has anyone tried using this course of action and found a viable solution? I've attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 2) Platform: 3.10.0-1160.92.1.el7.x86_64 3) uname -a: Linux krusty 3.10.0-1160.92.1.el7.x86_64 #1 SMP Tue Jun 20 11:48:01 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached

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fmriprep and freesurfer license
by Patterson, Dianne K - (dkp) 03 Jun '24

03 Jun '24

External Email - Use Caution I use this on our HPC: apptainer run --cleanenv --bind ${MRIS}/data:/data:ro --bind ${MRIS}/derivatives/fmriprep:/outputs --bind ${MRIS}/fmriprep_work:/work ${APP} /data /outputs participant --participant_label ${Subject} --fs-license-file ${HOME}/license.txt -w /work --stop-on-first-crash --ignore slicetiming --cifti-output --output-spaces fsnative fsaverage MNI152NLin6Asym:res-2 This assumes license.txt is in my home directory. -Dianne Dianne Patterson, Ph.D<https://profiles.arizona.edu/person/dkp> dkp(a)arizona.edu Office: BSRL, Room 235 RII Neuroimaging Staff Scientist Program Coordinator Neuroimaging Methods Certificate<https://cogsci.arizona.edu/programs/certificate> Cognitive Science GIDP affiliate member Faculty Lead OpenClass.ai<https://openclass.ai> Mastodon: @dpat@scicomm.xyz

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Re: [Freesurfer] Contrast files - 2 groups, 4 covariates
by Liliana Wu 03 Jun '24

03 Jun '24

External Email - Use Caution Thank you Douglas. That’s much clearer. I do however, have a subject without a gender disclosure. Would I set up my class and contrasts as: 5 classes: PatentientsMale, PatientsFemale, HCMale, HCFemale, HCNa then use contrast [0.5 0.5 -0.33 -0.33 -0.33 0 0 0 0 0 ...]? Best, Liliana

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Call for applications: LINC fellows program 2024-25
by Yendiki, Anastasia 31 May '24

31 May '24

Dear FreeSurfers - Our BRAIN Initiative funded center for Large-scale Imaging of Neural Circuits (LINC)<https://connects.mgh.harvard.edu/> is seeking to name 2 undergrads and 2 postdocs from diverse backgrounds and/or under-resourced institutions “LINC fellows” for 2024-25. The applicants are expected to have a research mentor in their home institution, who will provide a letter of support for their application. During the LINC fellowship year, the LINC fellows will remain in their current program/institution, and engage in a research project that can benefit from remote access to the data and computational resources of the LINC project, and collaboration with the LINC investigative team. For eligibility and application materials, please see: https://connects.mgh.harvard.edu/outreach/<https://connects.mgh.harvard.edu/outreach/#research-teams> Thank you for sharing with any qualified applicants that you may know! Anastasia. | Anastasia Yendiki, Ph.D. | Associate Professor, Harvard Medical School | Associate Investigator, Massachusetts General Hospital | 149 13th St. Suite 2301 | Charlestown, MA 02129 | Tel: 617-726-9434 | Fax: 617-726-7422 | Web: http://dmri.mgh.harvard.edu/a-y

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Re: [Freesurfer] License for FreeSurfer 5.x
by fsbuild 30 May '24

30 May '24

External Email - Use Caution  Hello Rafa, If you take a look under, https://secure-web.cisco.com/1dfxSJC8JWSEz6n8dSa8oPi0pnwDlx9137h03BernH-2Q8… - you will see there is a Virtual Box ..vdi file for the 5.3.0 release,  https://secure-web.cisco.com/1RcGOCq2p6BYFO6rvNlcGnNuDdMKQaAC7luBVOPnx9yiqM… - but I think that Virtual Box image will be running CentOS6 (or some old version of CentOS).  At that time we did not build or provide releases for Ubuntu linux.  The version of CentOS in the VM and Ubuntu12 may use different versions of glibc so I’m not sure the packages with 5.3.0 binaries listed above will run on Ubuntu12. We advertise the following caveat about switching to newer/different OS versions, or upgrading to a different (newer) Freesurfer release built with different compilers.  Either of those changes will likely produce some difference in floating point math results. Important Note: When processing a group of subjects for your study, it is essential to process all your subjects with the same version of FreeSurfer, on the same OS platform and vendor, and for safety, even the same version of the OS. While we continue to work to ensure that results match across platforms, there are none-the-less system-level libraries that are OS dependent. An exception to this rule is that you may view and edit files across any platform or version, and run some post-processing tools (outside the recon-all stream) if you check with us first (for instance you may run the longitudinal processing with newer versions). But if it’s not an issue for you to run on an old version of CentOS instead of Ubuntu linux, then your best bet is to try and run the existing .vdi file listed above in the VirtualBox client - which you would need to download and install on your current Linux machine. -R. On May 30, 2024, at 12:34, Rafael Navarro <rafa.navarrogo(a)gmail.com> wrote:        External Email - Use Caution        Hello everyone,  I am working with a neuroimage model that uses the FreeSurfer 5.3 version as preprocessing (only autorecon-I). I have tried to install Freesurfer 5.3, but after reading previous messages in the mailing list It seems the license file format changed from FreeSurfer 5.3 to 6.0 due to an update of the Ubuntu libcrypt. Do you think that migrating the autorecon-I from v5.3 to v6.0 might affect the final results? Is there any alternative? Does a docker container running Ubuntu 12 with FreeSurfer 5.3 could work? Is still possible to get a license with the old format?  Regards! Rafa Navarro  _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1rQmyzrBzuTiOfJNym0JFZOqwWej3pdzcvkhiXJWLyPV3L…

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License for FreeSurfer 5.x
by Rafael Navarro 30 May '24

30 May '24

External Email - Use Caution Hello everyone, I am working with a neuroimage model that uses the FreeSurfer 5.3 version as preprocessing (only autorecon-I). I have tried to install Freesurfer 5.3, but after reading previous messages in the mailing list It seems the license file format changed from FreeSurfer 5.3 to 6.0 due to an update of the Ubuntu libcrypt. Do you think that migrating the autorecon-I from v5.3 to v6.0 might affect the final results? Is there any alternative? Does a docker container running Ubuntu 12 with FreeSurfer 5.3 could work? Is still possible to get a license with the old format? Regards! Rafa Navarro

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Re: [Freesurfer] SynthSR problem
by fsbuild 28 May '24

28 May '24

External Email - Use Caution  Some commands such as mri_synthsr in previous releases, e.g., 7.4.1, use code built with Intel processor specific instructions that cannot run on an arm processor, i.e., there is not full backwards binary compatibility in that case using the Rosetta emulation environment on MacOS.  Hence the “illegal instruction” error. We do have a (more recent) development build on a Silicon Mac you can download via the link,  https://secure-web.cisco.com/1lWnZREm3JXXMeuMNsb_hOkyb2ipaBFlFN8u43RUzyQ6-c… .... it has not yet gone the the same testing as done for a release.  Please let us know if you run into issues trying it. - R. On May 28, 2024, at 16:08, Tabasi, Farhad <farhad-tabasi(a)uiowa.edu> wrote:        External Email - Use Caution        Hello FreeSurfer developers, I am trying to use mri_synthsr to improve the quality of clinical scans, but this is the error I encountered: Illegal instruction: 4 (I followed the instructions on SynthSR page, using mri_synthsr --i input.nii --o output_synthT1.nii command) FreeSurfer version: freesurfer-darwin-macOS-7.3.2-20220804-6354275OS: macOS Ventura (13.2.1) on iMac M1 (116 GB) This is likely related to binary problems or CPU compatibility (especially with M1).Is there any solution to the issue? Thanks,Farhad Farhad Tabasi, MD (he/him/his)Postdoctoral ScholarHuman Brain Research Lab, Department of Neurosurgery, Carver College of Medicine, University of IowaCell: (858)588-2779_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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