Freesurfer

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30130 discussions

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 - skull stripping error
by De Giorgi, Sara 29 Sep '24

29 Sep '24

Dear all, Skull stripping on Freesurfer failed due to MP2RAGE sequence. That’s the only sequence we have. This is how it looks: [cid:22ca1ab1-56b5-42b4-a482-23e883ecfab5] This is how the skull stripping appears: [cid:b3faf493-9947-4d50-a296-1f0456d5382d] Please find the log file as an attachment. I also tried to manually adjust brainmask.mgz , but also brain.mgz is incorrect. How can I solve this issue? Thanks, Sara

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Qt platform and lta_convert error
by Mohammad Amin Khodadadegan 28 Sep '24

28 Sep '24

External Email - Use Caution when I ran freeview ,I have encounter with this error: freeview This 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.oDwgAc Sat Sep 28 20:00:24 +0330 2024 setenv SUBJECTS_DIR /home/ubuntu/freesurfer/subjects cd /home/ubuntu freesurfer/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/Linux pid 6375 Current FS Version freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 Subject does not have a bstampfile, copying freesurfer/build-stamp.txt Subject FS Version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% fs-check-version match = 1 fs-check-version Done INFO: SUBJECTS_DIR is /home/ubuntu/freesurfer/subjects Actual FREESURFER_HOME /home/ubuntu/freesurfer 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/Linux lta_convert: Command not found. ERROR: Executable 'lta_convert -all-info failed! Is it missing from the distribution?'

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dev builds available for rocky Linux and silicon MacOS (M1, M2, M3 processors)
by fsbuild 27 Sep '24

27 Sep '24

External Email - Use Caution  In response to requests for freesurfer on Rocky8, Rocky9 linux and silicon macs (with M1, M2, M3 processors), there are updated, relatively stable development builds, i.e., builds that have gone thru some testing, available from https://secure-web.cisco.com/1GcRpXukAZA_u5fux2mIvH7rGNj6Iwz7089dTqiW5XwIhC… For Rocky8 or Rocky9 Linux, it should work to install the rpm, freesurfer-Rocky8-7.0.0-dev.x86_64.rpm For MacOS on Apple silicon machines with an M1, M2, M3 processor, you can try the .pkg installer, freesurfer-macOS-darwin_arm64-dev.pkg.  This has been tested on MacOS Monterey, Ventura and Sonoma, BUT NOT Sequoia which was just released. Please let us know if you run into issues. - R.

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trac-all longitudinal error
by Nelson, Eric (Campus) 23 Sep '24

23 Sep '24

External Email - Use Caution Hello all, I am trying to run trac-all prep longitudinally (testing it on a single subject for now with three timepoints and 2 scans per time point). I keep getting the below error. Can't figure out what is causing it and could use some advice. I've also attached the trac-all.log from my base file and the configuration file (configfile.test). Any help would be greatly appreciated Checking inputs error: niiRead(): error opening file /data/project/lahtilab/eanelson/FreeSurfer_7.1.1/Prisma_Data/OUTPUT/Freesurfer/Long/sessions_1-3/sub-control04_ses-01.long.sub-control04_base/dlabel/anatorig/aparc+aseg_mask.nii.gz ERROR: reading /data/project/lahtilab/eanelson/FreeSurfer_7.1.1/Prisma_Data/OUTPUT/Freesurfer/Long/sessions_1-3/sub-control04_ses-01.long.sub-control04_base/dlabel/anatorig/aparc+aseg_mask.nii.gz Linux c0231 3.10.0-1160.24.1.el7.x86_64 #1 SMP Thu Mar 25 21:21:56 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Tue Sep 17 13:48:41 CDT 2024 Best, Eric

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