Freesurfer June 2024

freesurfer@nmr.mgh.harvard.edu

47 participants
51 discussions

Issue with cortical data extraction for mkanalysis-sess
by O'Dor, Sarah 11 Jun '24

11 Jun '24

We are trying to run resting state connectivity analyses using amygdala ROI. The left hemisphere ran fine, but for the right hemisphere, something is clearly off. When we export the results into a table, the unknown column, which should be zero, has values, and one of the regions instead has zeroes. It’s as if something is shifted, but we’ve checking the coding. Briefly, the commands we used were mri_vol2vol, fcseed-config, fcseed-sess, mkanalysis-sess, selxavg3-sess, mri_glmfit, mri_segstats. Any ideas on where/which commend we should be troubleshooting? We’ve run it twice and gotten the same results. Thanks, Sarah

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negative values converting mgz files to nifty
by Nina Rouhani 11 Jun '24

11 Jun '24

External Email - Use Caution hello! after freesurfer segmentation (through fmriprep v23), i converted the aparc+aseg.mgz file into a nifty file using the below code (freesurfer v7.4.1): -rl $fs_dir/mri/rawavg.mgz -rt nearest $fs_dir/mri/aparc+aseg.mgz $sub_dir/rois/anatomical/aparc_aseg2mprage.nii.gz however, the voxel values of the aparc_aseg2mprage.nii.gz range between 31000-32000 and -31000- -32000. consequently, the label values for particular regions no longer correspond to what’s in the freesurfer manuals (like those listed here: FsTutorial/AnatomicalROI/FreeSurferColorLUT - Free Surfer Wiki <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurf…> ). would be incredibly grateful if i could be pointed to what i’m missing or what could be going wrong! thank you!

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Bug in mri_convert reslice-like with 4D images
by Iglesias Gonzalez, Juan E. 11 Jun '24

11 Jun '24

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)

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INTERNATIONAL CONFERENCE ON ARTIFICIAL INTELLIGENCE IN HEALTHCARE (AIiH)
by Jiaxiang ZHANG 11 Jun '24

11 Jun '24

External Email - Use Caution [apologies for cross-posting] *INTERNATIONAL CONFERENCE ON ARTIFICIAL INTELLIGENCE IN HEALTHCARE (AIiH)* 4 - 6 September 2024, Swansea, UK https://aiih.cc (*2nd CALL FOR ABSTRACT*) Submission deadline: Monday 1 July (FIRM) *1. INTRODUCTION * https://aiih.cc/abstracts/ AIiH 2024 welcomes late-breaking short abstract submissions to be included as poster or short spot-light presentation at the conference. This is to both enable fast dissemination of promising preliminary findings and encourage attendance by a broader audience of early career researchers (including research students), healthcare professionals, and industrial practitioners. AIiH 2024 is a single-track conference with oral and poster presentations and will include a conference tutorial on generative DNNs and 5 keynote presentations. The conference will also feature a plenary session, which consists of 3 invited speakers who have extensive experience in related areas. AIiH aims to provide a prominent platform for researchers and practitioners who are devoted to improving healthcare using modern artificial intelligence. We recognise that healthcare applications present complex and sometimes unique challenges across a wide spectrum, from ethics to technical developments, that generic AI methods are often inadequate. By creating this dedicated forum, we encourage discussions and disseminations of efficient and effective AI solutions and technologies for healthcare, and in turn we hope to influence the research, technology adoption, and decision making in healthcare. *2. CONFERENCE TUTORIAL* Title: Deep Generative Neural Networks https://aiih.cc/tutorial-generative-dnn/ Dr. Amir Atapour-Abarghouei University of Durham *3. KEYNOTE SPEAKERS* https://aiih.cc/keynote-speakers/ Prof. Hao Ni University College London Dr. Timothy Rittman Cambridge University Dr. Konstantinos Kamnitsas Oxford University Prof. Jacques Fleuriot Edinburgh University Prof. Eiichiro Tanaka Waseda University, Japan *4. PLENARY SESSION ON TRANSLATING AI RESEARCH INTO PRACTICE* https://aiih.cc/plenary-session/ Dr. Alba Di Pardo IRCCS Istituto Neurologico Mediterraneo Neuromed Dr. Noura Al Moubayed Durham University & Evergreen Life Dr. Haoda Fu Eli Lilly and Company *5. ABSTRACT SUBMISSION* Submission instructions are available at the conference website: https://aiih.cc/abstracts/ IMPORTANT DATES Abstract deadline: Monday 1 July (FIRM) Abstract notification: Monday 8 July (FIRM) Abstract registration: Monday 15 July Late registration: Monday 12 August Main conference: Wednesday 4 – Friday 6 September 2024 *6. ORGANISERS* CONFERENCE GENERAL CHAIRS Xianghua Xie, Swansea University, UK Iain Styles, Queen’s University Belfast, UK PROGRAMME CHAIRS Gibin Powathil, Swansea University, UK Marco Ceccarelli, University of Rome Tor Vergata, Italy SPECIAL SESSION CHAIRS Jiaxiang Zhang, Swansea University, UK Rex Ying, Yale University, USA SPONSORSHIP CHAIRS Daniele Cafolla, Swansea University, UK Raoul van Loon, Swansea University, UK PUBLICITY CHAIRS Lu Zhang, Swansea University, UK Beiyu Lin, University of Nevada, USA PUBLICATION CHAIR Jingjing Deng, Durham University, UK *7. SPONSORS* Gold: - Technis Blu - Infordata Silver: - Amicus Therapeutics Bronze: - Zienkiewicz Institute for Modelling, Data and AI - IET Institution of Engineering and Technology Your Researcher Sponsor: - Elsevier Journal of Theoretical Biology Best Paper Award Sponsor: - Springer *8. CONTACT* contact(a)aiih.cc <contact(a)aiih.cc>

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Incoporating synthstrip and synthseg into recon-all
by Dan Levitas 07 Jun '24

07 Jun '24

External Email - Use Caution Hello, I am using freesurfer version 7.4.1, and would like to incorporate the recently introduced synthstrip and synthseg functions into my recon-all command, if that's possible. From this archive message ( https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg75148.html) it seems that adding the -synthstrip option enables synthstrip; however, I don't see this as an option in the recon-all documentation ( https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all) nor as a command line option for recon-all. Assuming that both synthstrip and synthseg can be used in recon-all, would the command need to look something like this: *recon-all -subjid sub-${sub}_ses-${ses} -i $anat_file -3T -synthstrip --no-csf -synthseg -qcache -all* I'm adding the *--no-csf* synthstrip option based on this comment ( https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg75172.html) I should also note that I'm performing a longitudinal analysis, so this specific recon-all pertains to the cross-sectional portion of the workflow. Thanks, Dan

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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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Freesurfer June 2024