Freesurfer

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Re: [Freesurfer] segmenThalamicNuclei.sh exited with ERRORS
by fsbuild 15 Feb '23

15 Feb '23

External Email - Use Caution Hello Behçet, Are you saying the version of the Ubuntu operating system changed and now when you run the same command you get this error about the missing library ? If so, I would check with your system administrators to see if they have installed the freesurfer 7.1.1 .deb freesurfer package from https://secure-web.cisco.com/1kZqy9BcKMr7diHAAdkyYDg2sSQj5AQELQZUIDe_I964ho… which matches the version of Ubuntu you are now running.   Running the installer package should try to fix that missing library dependency. - R. On Feb 15, 2023, at 05:36, behçet ayyıldız <behcetayyildizz(a)gmail.com> wrote:        External Email - Use Caution        Dear All, I was using Linux Ubuntu to perform my analysis. However, they were changed with Linux ..... a couple of days ago. And while the segmentThalamicNuclei.sh command was running before the change, after the change it didn't run and I got the following message.drodriguez@causal:/data_august/Daniela/Behcet/Freesurfer_pulvinar_OCD$ segmentThalamicNuclei.sh con_HaJa93Setting ITK threads to 1#--------------------------------------------#@# Thalamic Nuclei processing Wed 15 Feb 2023 11:09:10 AM CET------------------------------------------Setting up environment variables---LD_LIBRARY_PATH is .:/sw/freesurfer/7.1.1//MCRv84//runtime/glnxa64:/sw/freesurfer/7.1.1//MCRv84//bin/glnxa64:/sw/freesurfer/7.1.1//MCRv84//sys/os/glnxa64:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/sw/freesurfer/7.1.1//bin/SegmentThalamicNuclei: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory127Linux causal.brain.mri.tu-muenchen.de 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/LinuxDo you guys have any idea how to fix it ?Thanks in advance.-- Behçet Ayyıldız.._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freeview Installation Error
by Carlos Alcocer 14 Feb '23

14 Feb '23

External Email - Use Caution Hi, I have been trying to install FreeSurfer and I went to test out the freeview command but received the following error. freeview: error while loading shared libraries: libGL.so.1: cannot open shared object file: No such file or directory I am unsure how to proceed. Thank you, Carlos

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Passcode for FS_7_2_0_Ubuntu_18_04_06.ova.7z
by Mehren, A. (Aylin) 14 Feb '23

14 Feb '23

External Email - Use Caution Hello, I would like to ask for the passcode for FS_7_2_0_Ubuntu_18_04_06.ova.7z to install the Freesurfer virtual image. Many thanks in advance!

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Suggested edit to Freesurfer wiki
by Tyler Ward 13 Feb '23

13 Feb '23

External Email - Use Caution Hi Freesurfer devs, Please consider the following small addition to the page: https://secure-web.cisco.com/1GiKElb-UIQGaju-zzhY7QIU2QYGQc4-VSdhVxQhcR0mYS… > *Note: If your subject surfaces are not yet available, then exclude the > --surf orig flag from tkregisterfv and add the flag --no-surfs* > tkregisterfv loads surface data by default, even when excluding "--surf orig". The flag "--no-surfs" is not in the help page and therefore difficult for a user to find. This is essential to fixing the talairach transform when freesurfer has not yet created surface data. Thanks, Tyler

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FS FAST
by Justin Oh 13 Feb '23

13 Feb '23

External Email - Use Caution Dear Freesurfer team, I am new to freesurfer and I'm working on learning how to pre process and analyze resting state fMRI. It's my understanding that MATLAB and FSL have to run in the background from what I took away from online tutorials. Is there a specific program within MATLAB that is necessary or will purchasing the basic student package from MATLAB be sufficient? Thank you for your time! -Justin Oh

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CT conversion from DICOM to MGZ
by Gonzalo Rojas Costa 13 Feb '23

13 Feb '23

External Email - Use Caution Hi: I am trying to convert CT images from DICOM to MGZ using mri_convert. When running it shows the message "INFO: applying rescale intercept and slope based on (0028,1052) (0028,1053). If you do not want this, then set FS_RESCALE_DICOM to 0 and rerun." Where can I find the FS_RESCALE_DICOM option ? Sincerely, Gonzalo Rojas Costa

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bash: recon-all -İ : command not found
by behçet ayyıldız 13 Feb '23

13 Feb '23

External Email - Use Caution Hi dear all, I got the similar problem. I have freesurfer version 7.1.1 and when I was trying to run the "recon-all" it indicates me that the command not found. Here below you can find all that bash indicates. -------- freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /sw/freesurfer/7.1.1/ FSFAST_HOME /sw/freesurfer/7.1.1/ FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /sw/freesurfer/6.0.0//subjects MNI_DIR /sw/freesurfer/7.1.1//mni FSL_DIR /sw/fsl/6.0.5.1 drodriguez@causal:~$ cd ../../.. drodriguez@causal:/$ cd data_august/Daniela/Behcet/Freesurfer_pulvinar_OCD/ drodriguez@causal:/data_august/Daniela/Behcet/Freesurfer_pulvinar_OCD$ export SUBJECTS_DIR=`pwd` drodriguez@causal:/data_august/Daniela/Behcet/Freesurfer_pulvinar_OCD$ echo $SUBJECTS_DIR /data_august/Daniela/Behcet/Freesurfer_pulvinar_OCD drodriguez@causal:/data_august/Daniela/Behcet/Freesurfer_pulvinar_OCD$ recon-all-i pat_CoDa85.nii -s pat_CoDa85 -all bash: recon-all-i: command not found thanks.. -- *Behçet Ayyıldız..*

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ScLimbic: error: could not allocate memory for slice 1 out of 256error: mri_convert --conform failed!
by stdp82＠virgilio.it 13 Feb '23

13 Feb '23

External Email - Use Caution Hi list, the error is reported below. Of note I have just runned, with success, ScLimbic for another study. Thus, I do not understand which is the issue for this one. Thanks Stefano mri_sclimbic_seg --i FOLDER --o FOLDER --write_volumes --write_qa_stats --etiv --conform /Applications/freesurfer/7.3.2/sclimbic/python/scripts/mri_sclimbic_seg --i FOLDER --o FOLDER --write_volumes --write_qa_stats --etiv --conform Excluding seg [853]Using CPUUsing 1 thread(s)Loaded lookup table /Applications/freesurfer/7.3.2/sclimbic/models/sclimbic.ctab Loaded population stats /Applications/freesurfer/7.3.2/sclimbic/models/sclimbic.volstats.csv Loaded model weights /Applications/freesurfer/7.3.2/sclimbic/models/sclimbic.fsm+ad.t1.nstd00-50.nstd32-50.h5 Computing etiv from scratchmri_convert --conform FOLDER/subjID.mgz /var/folders/vd/g4zth0dn6nldcx62m0l827sr0000gn/T/tmpk6kr248m/nu.mgz reading from FOLDER/subjID.mgz...error: could not allocate memory for slice 1 out of 256error: mri_convert --conform failed!

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ERROR: Label BA1_exvivo does not exist in SUBJECTS_DIR fsaverage
by Lizanne Arnoldy 13 Feb '23

13 Feb '23

External Email - Use Caution Dear freesurfer Experts, I’ve been trying to run the fMRIPrep container on multiple subjects using two different versions of fmriprep (fmriprep-22.0.2.sif and fmriprep-22.1.0.sif) on a Linux computer. Most of the time, the container runs without errors, however occasionally, it exits with the error message: “ERROR: Label BA1_exvivo does not exist in SUBJECTS_DIR fsaverage! The fsaverage link probably points to an older freesurfer version” I have checked the mailing list where this error has been mentioned but haven’t found the solution yet. Here’s some additional information that might be helpful: - The …/fmriprep/sourcedata/freesurfer/sub-096/label directory, the rh.BA1_exvivo.label file is present (and has viewing permissions), but the lh.BA1.label file is missing (not sure if this needs to be included). * The recon-all log file has been attached I would appreciate any insight or guidance on what may be causing this error and hot to resolve it. Best, Lizanne

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(no subject)
by behçet ayyıldız 13 Feb '23

13 Feb '23

External Email - Use Caution behcetayyildizz(a)gmail.com -- *Behçet Ayyıldız..*

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