Freesurfer September 2024

freesurfer@nmr.mgh.harvard.edu

48 participants
58 discussions

Re: [Freesurfer] Question on using thalseg_1.1.h5
by Georgios Argyropoulos 23 May '25

23 May '25

External Email - Use Caution Many thanks and apologies, Henry - I figured it out... I stupidly replaced your improved segmentation script in both the scripts and the bin directory instead of only replacing the former. many thanks for your time, much appreciated g

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infantFS: expected outputs
by Marlene Staginnus 23 Oct '24

23 Oct '24

External Email - Use Caution Dear FreeSurfer Team, Apologies in case I missed this elsewhere, but I was wondering whether there is any information on what the expected outputs of running infant_ recon_all are, similar to this (https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllOutputFiles) for the adult pipeline? I am asking as after testing the pipeline using the example participant provided on openneuro (https://openneuro.org/datasets/ds004776/versions/1.0.0, I’ve noticed that some of the output differs from the adult version and I wanted to ensure that everything is running correctly before applying it to our data. For example, there is no ‘orig’ subdirectory or orig.mgz file in the ~/mri folder. Similarly, fewer files are included in the ~/stats folder (only: brainvol.stats, lh.aparc.stats, rh.aparc.stats) although I was able to able to generate other files (e.g., aseg.stats) using mri_segstats. Overall, only the following folders are generated following recon-all without errors: label, log, mri, stats, and surf. Is this correct or might there be something going wrong on my end? 1) FreeSurfer version: infant-dev-4a14499-20210109-4a14499 2) Platform: CentOS release 7 3) uname -a: Linux fhpc-1840 6.8.0-40-generic #40~22.04.3-Ubuntu SMP PREEMPT_DYNAMIC Tue Jul 30 17:30:19 UTC 2 x86_64 x86_64 x86_64 GNU/Linux 4) infant_recon_all log: see attached Thank you in advance! Best wishes, Marlene

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FreeSurfer - extract rigid parameters from .lta file
by noga.kertes＠campus.technion.ac.il 09 Oct '24

09 Oct '24

External Email - Use Caution Hello FreeSurfer Developers, I am using mri_robust_register to register a moving volume to a fixed one. The algorithm outputs the rigid transformation in a .lta file. I need to extract the rigid parameters (3 rotation angles in degrees and 3 translation parameters in millimeters). However, the transformation in the file doesn't seem right, as the translation parameters appear to be very large (I assume the values in the last column of the transformation are in millimeters). The moved image doesn’t seem to translate by more than a few millimeters. Is there a command for converting the .lta file into rotation and translation parameters? If not, could you provide more information on how to manually convert it using the transformation in the .lta file? Freesurfer version: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 Thank you, Noga

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petsurfer using brainstem subfields
by Sneha Pandya 01 Oct '24

01 Oct '24

External Email - Use Caution Dear team, We need to use PVC brainstem subfield which we intend to use as high binding region for MRTM based kinetic analysis. Can we run mri_gtmpvc using brainstemSsLabels.v12.mgz as input segmentation? Or is to possible to combine gtmseg and brainstem subfields and use this combined segmentation for mri_gtmpvc (will be using GTM or RBV for PVC). Thank you, Sneha

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BEDPOSTX Tracula Error
by Daniel Salinas 30 Sep '24

30 Sep '24

External Email - Use Caution Hello, I hope this email finds you well. I submitted this command to run the second part of tracula trac-all -bedp -c $SUBJECTS_DIR/tracula/tracula_config.txt And, before it would process, but then I was looking into SLURMS and somehow misconfigured it. Now I get: I tried to reconfig the file and got it running again, but still get the error: ----------------------------------------------------------------------------------- (base) danielsalinas@danielsalinas-linux:~$ trac-all -bedp -c $SUBJECTS_DIR/tracula/tracula_config.txt INFO: SUBJECTS_DIR is /home/danielsalinas/MRI-Data/Francis_HION/NCANDA-freesurfer/practice/freesurfer INFO: Diffusion root is /home/danielsalinas/MRI-Data/Francis_HION/NCANDA-freesurfer/practice/freesurfer/tracula/output Actual FREESURFER_HOME /usr/local/freesurfer ln -sf ../dlabel/diff/aparc+aseg_mask.bbr.nii.gz /home/danielsalinas/MRI-Data/Francis_HION/NCANDA-freesurfer/practice/freesurfer/tracula/output/NCANDA_S00033/dmri/nodif_brain_mask.nii.gz WARN: Running bedbostx locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 -model 1 /home/danielsalinas/MRI-Data/Francis_HION/NCANDA-freesurfer/practice/freesurfer/tracula/output/NCANDA_S00033/dmri subjectdir is /home/danielsalinas/MRI-Data/Francis_HION/NCANDA-freesurfer/practice/freesurfer/tracula/output/NCANDA_S00033/dmri Making bedpostx directory structure Queuing preprocessing stages srun: error: Invalid --mail-type specification Queuing parallel processing stage ----- Bedpostx Monitor ----- srun: error: Unable to allocate resources: Job dependency problem Queuing post processing stage srun: error: Unable to allocate resources: Job dependency problem ----------------------------------------------------------------------------------- I remade the config file: # Basic settings ControlMachine=danielsalinas-linux ClusterName=BakerLabCluster AuthType=auth/munge SlurmdPort=6818 SlurmctldPort=6817 SlurmUser=slurm SlurmdUser=root StateSaveLocation=/var/spool/slurmctld SlurmdSpoolDir=/var/spool/slurmd # Add or modify in your slurm.conf JobCompType=jobcomp/filetxt JobCompLoc=/var/log/slurm/jobcomp.log # Node settings NodeName=danielsalinas-linux CPUs=8 RealMemory=94000 Sockets=1 CoresPerSocket=4 ThreadsPerCore=2 State=IDLE # Partition settings PartitionName=normal Nodes=ALL Default=YES MaxTime=INFINITE State=UP

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Repost: NextBrain Segmentation PyTorch-GPU Compatibility Error
by AmirHussein Abdolalizadeh 30 Sep '24

30 Sep '24

External Email - Use Caution Hi, I am reposting an issue with NextBrain that I asked about a few months back: https://secure-web.cisco.com/1Ep1FaXAlpDcDJk3cT-fDgniEdtHQ5Fy30s9xstmgNRrAE… "NVIDIA H100 with CUDA capability sm_90 is not compatible with the current PyTorch installation. The current PyTorch install supports CUDA capabilities sm_37 sm_50 sm_60 sm_70 sm_75 sm_80 sm_86." There is a PyTorch incompatibility with the newer H100 nVidia GPUs. I had the same issue with FastBrain which was resolved by updating their torch dependencies in their release. See the discussion here: https://secure-web.cisco.com/1iI7S9ydIJfS44SEVzbqqTAOd5_M_tzx6bBulJhDsE0KOd… I think this can be a solution for this issue as well since many HPCs are moving towards these kinds of GPUs. Best, Amir

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Efficient printing of freeview screenshots through freeview [HPC]
by Camilo Castelblanco Riveros 30 Sep '24

30 Sep '24

External Email - Use Caution Hi, I am trying to print screenshots of MR images efficiently with the freesurfer reconstruction with Freeview in an HPC. For an unknown reason, this code works for iterating over sagittal, not coronal or axial coordinates. It does not iterate over the coordinates in the coronal and axial cases even though the cmd file looks okay. Any help would be appreciated. -------- # Define the MRI and surface files for the current subject T1_IMAGE="${SUBJECT_DIR}/mri/T1.mgz" WM_IMAGE="${SUBJECT_DIR}/mri/wm.mgz" BRAINMASK_IMAGE="${SUBJECT_DIR}/mri/brainmask.mgz" ASEG_IMAGE="${SUBJECT_DIR}/mri/aseg.mgz" LH_WHITE="${SUBJECT_DIR}/surf/lh.white" LH_PIAL="${SUBJECT_DIR}/surf/lh.pial" RH_WHITE="${SUBJECT_DIR}/surf/rh.white" RH_PIAL="${SUBJECT_DIR}/surf/rh.pial" # Define number of slices and step size for each view (sagittal, coronal, axial) STEPS=15 # Increase this value for more plots/slices SAGITTAL_START=20 SAGITTAL_END=200 CORONAL_START=20 CORONAL_END=200 AXIAL_START=20 AXIAL_END=200 # Create a fresh cmd.txt file for the current subject echo "-v $T1_IMAGE \ $WM_IMAGE \ $BRAINMASK_IMAGE \ $ASEG_IMAGE:colormap=lut:opacity=0.2" > "$CMD_FILE" echo "-f $LH_WHITE:edgecolor=blue \ $LH_PIAL:edgecolor=red \ $RH_WHITE:edgecolor=blue \ $RH_PIAL:edgecolor=red" >> "$CMD_FILE" # Loop through slices in each dimension and add commands to cmd.txt #==================> Sagittal view slices (changes in X-coordinate) for ((i = 0; i <= STEPS; i++)); do slice=$(bc <<< "$SAGITTAL_START + ($SAGITTAL_END - $SAGITTAL_START) * $i / $STEPS") echo "-viewport sagittal -slice $slice 127 127 -viewsize 800 800 -ss ${ OUTPUT_DIR}/sagittal_slice_${slice}.png -noquit" >> "$CMD_FILE" done # Reset the view and Freeview instance to avoid cache issues between views echo "-quit" >> "$CMD_FILE" echo "Processing sagittal slices..." # Debug message freeview -cmd "$CMD_FILE" > freeview_log.txt 2>&1 sleep 2 # Wait for Freeview to close completely # If Freeview doesn't quit properly, use pkill as a fallback pkill freeview #%%%%%%%%%%%%%%%%%%%% # Create a fresh cmd.txt for coronal slices CMD_FILE="${OUTPUT_DIR}/cmd_coronal.txt" #================> Coronal view slices (changes in Y-coordinate) for ((i = 0; i <= STEPS; i++)); do slice=$(bc <<< "$CORONAL_START + ($CORONAL_END - $CORONAL_START) * $i / $STEPS") echo "-viewport coronal -slice 127 $slice 127 -viewsize 800 800 -ss ${ OUTPUT_DIR}/coronal_slice_${slice}.png -noquit" >> "$CMD_FILE" done ------- Best regards, Camilo *================================* *Camilo Castelblanco Riveros (He/His)* Integrative Neuroscience at Dartmouth (IND) Ph.D. Candidate Robertson Lab <https://secure-web.cisco.com/1QRdD2mxYtydinuoic7wn0eITgFhkqKqoGQdP-IFOAFtu5…> & Bujarski Lab <https://secure-web.cisco.com/1cOiHwMsWx3XS3cX7DjImdJuyBu3ix4ePXcP4xtelQK30A…> Student Interest Group in Neurology (SIGN <https://secure-web.cisco.com/1dq5CGYwmVLVUgtU1lI9vL6j7Qx4yi0AzfTjFxlK___c2G…>) Co-Leader Diversity Student Advisory Board Member e: ccastelblanco.gr(a)dartmouth.edu <camilo.a.castelblanco.riveros.gr(a)dartmouth.edu> Zoom <https://secure-web.cisco.com/14g7m031Cr0kkdNxX-rGazLPRk_s-3aNkJgXOZ6l_5Sf_8…> [image: Integrative Neuroscience at Dartmouth (IND) (@DartmouthNeuro) / Twitter]

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morphometry protocol - cross site/platform?
by Mira Michelle Raman 30 Sep '24

30 Sep '24

External Email - Use Caution Good afternoon, I was looking at the Morphometry Protocol on the wiki and was wondering if anyone has developed matching GE sequences (which they would be willing to share) that could be used in combination with these Siemens sequences (or equivalent) for a multi-site study. My proposed project: -multi-site (Siemens and GE), -participants under sedation (so minimum scan time is ideal), and - minimum images need T1w, T2w, and quantitative T1 at 1mm^3 resolution. Sincerely, Mira _______________________________________________________________________ Mira Michelle Raman BrIDGe Lab, Division of Interdisciplinary Brain Sciences Stanford University 1520 Page Mill Rd, 160.12 Palo Alto, CA 94304

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NextBrain with 333 labels
by Woo-Suk Tae 30 Sep '24

30 Sep '24

External Email - Use Caution Dear FreeSurfer experts I tried to segment my brain MRI using NextBrain.in the most recent FreeSurfer-dev package. I followed the command in https://secure-web.cisco.com/150f92dNZNQHVJBK1fmC5Z4FYOqCYvgP1aIrq7dafQUxfy…, but, I got only the volumes of 101 labels How can I got the 333 labels and volumes using NextBrain? my command as follows mri_histo_atlas_segment ../subject/mri/orig.mgz ..subject/mri/histo_atlas_segmentation/ full 1 -1 Best regards Woo-Suk Tae Seoul, Korea -------------------------------------------------------------------- Woo-Suk, Tae Ph.D. Research Professor Brain Convergence Research Center, Korea University College of Medicine, Seoul, Korea mobile: 82-10-9120-4629 office: 82-2-920-6077 email: woosuk.tae(a)gmail.com, w <woosuk.tae(a)kumc.or.kr>stae(a)korea.ac.kr woostae(a)naver.com --------------------------------------------------------------------

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Re: [Freesurfer] Qt platform and lta_convert error
by fsbuild 29 Sep '24

29 Sep '24

External Email - Use Caution  You may be missing packages on your system freesurfer needs to run if you did not install freesurfer with the .deb package installer   You can download the 7.4.1 Ubuntu 22 installer from,https://secure-web.cisco.com/1Tsk98POal2iEABYPOiUI6g759awF8BwGwOezDnsI… … change directories to where you downloaded the file … … as root … $ apt install ./freesurfer_ubuntu22-7.4.1_amd64.deb… or as non-root user with sudo privileges …$ sudo apt install ./freesurfer_ubuntu22-7.4.1_amd64.deb … setup the freesurfer environment …$ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /usr/local/freesurfer/7.4.1FSFAST_HOME       /usr/local/freesurfer/7.4.1/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /usr/local/freesurfer/7.4.1/subjectsINFO: /home/rd521/matlab/startup.m does not exist ... creatingMNI_DIR           /usr/local/freesurfer/7.4.1/mni … check lta_convert is found and that it can at least run and display its help output …$ which lta_convert/usr/local/freesurfer/7..4.1/bin/lta_convert$ lta_convert —help<output deleted> - R. On Sep 28, 2024, at 13:40, Mohammad Amin Khodadadegan <godgivensma(a)gmail.com> wrote:        External Email - Use Caution        when I ran freeview ,I have encounter with this error:freeviewThis application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, webgl, xcb. Aborted (core dumped) when I run the reconstruction command,I encounter with this error: fs-check-version --s subj04 --o /tmp/tmp.oDwgAcSat Sep 28 20:00:24 +0330 2024 setenv SUBJECTS_DIR /home/ubuntu/freesurfer/subjectscd /home/ubuntufreesurfer/bin/fs-check-version --s subj04 --o /tmp/tmp.oDwgAc-rwxrwxr-x 1 1623927 1623927 18565 Jun 14 2023 freesurfer/bin/fs-check-version freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460$Id$Linux freesurferubuntu 5.15.0-122-generic #132-Ubuntu SMP Thu Aug 29 13:45:52 UTC 2024 x86_64 x86_64 x86_64 GNU/Linuxpid 6375Current FS Version freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460Subject does not have a bstampfile, copying freesurfer/build-stamp.txtSubject FS Version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460No constraints on version because REQ=UnSet and FsVerFile=NotThere#@#% fs-check-version match = 1fs-check-version DoneINFO: SUBJECTS_DIR is /home/ubuntu/freesurfer/subjectsActual FREESURFER_HOME /home/ubuntu/freesurferLinux freesurferubuntu 5.15.0-122-generic #132-Ubuntu SMP Thu Aug 29 13:45:52 UTC 2024 x86_64 x86_64 x86_64 GNU/Linuxlta_convert: Command not found.ERROR: Executable 'lta_convert -all-info failed! Is it missing from the distribution?' _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1jDQNFEChA6RnfhuCrwzZtv1Q1DkBnjuzgRahazq22iw7z…

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Freesurfer September 2024