External Email - Use Caution
Dear support I'm running the following command in Freesurfer 7.4: trac-all -nocorr -noqa -intra -tensor -inter -prior -debug -dontrun -c config_tracula.txt
I get the following error ERROR: Could not find thalamic nuclei segmentation in /nfsd/biopetmri4/Users/CauzzoOPA/FS_RECON/subjOPAPD01/mri/ ERROR: Thalamic nuclei segmentation is strongly recommended to use ERROR: for tracts that terminate in or travel near the thalamus ERROR: If there is good reason not to use it, set usethalnuc = 0
And this happens despite in that folder there are these files: thal_t1_fl.FSspace.mgz thal_t1_fl.thalamus.t2.stripped.bfcorr.mgz thal_t1_fl.thalamus.t2.mgz ThalamicNuclei.v13.thal_t1_fl.FSvoxelSpace.mgz ThalamicNuclei.v13.thal_t1_fl.volumes.txt ThalamicNuclei.v13.thal_t1_fl.mgz
then why isn't it finding the thalamic segmentation? I paste below the full output of the command Thank you
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INFO: SUBJECTS_DIR is /nfsd/biopetmri4/Users/CauzzoOPA/FS_RECON INFO: Diffusion root is /nfsd/biopetmri4/Users/CauzzoOPA/prove/tracula/res Actual FREESURFER_HOME /nfsd/opt/FSL/freesurfer-7.4.0 trac-preproc -c /nfsd/biopetmri4/Users/CauzzoOPA/prove/tracula/res/subjOPAPD01/scripts/dmrirc.local -log /nfsd/biopetmri4/Users/CauzzoOPA/prove/tracula/res/subjOPAPD01/scripts/trac-all.log -cmd /nfsd/biopetmri4/Users/CauzzoOPA/prove/tracula/res/subjOPAPD01/scripts/trac-all.cmd -dontrun -debug INFO: -dontrun flag is in effect so subsequent commands may not have accurate arguments! #------------------------------------- /nfsd/opt/FSL/freesurfer-7.4.0//bin/trac-preproc #------------------------------------- #@# DWI set selection Thu Jan 22 11:38:27 CET 2026 ln -sf dwi.nii.gz /nfsd/biopetmri4/Users/CauzzoOPA/prove/tracula/res/subjOPAPD01/dmri/data.nii.gz ln -sf dwi.bvecs /nfsd/biopetmri4/Users/CauzzoOPA/prove/tracula/res/subjOPAPD01/dmri/bvecs ln -sf dwi.bvals /nfsd/biopetmri4/Users/CauzzoOPA/prove/tracula/res/subjOPAPD01/dmri/bvals #------------------------------------- #@# Intra-subject registration Thu Jan 22 11:38:27 CET 2026 bbregister --s subjOPAPD01 --init-fsl --dti --6 --mov /nfsd/biopetmri4/Users/CauzzoOPA/prove/tracula/res/subjOPAPD01/dmri/lowb.nii.gz --reg /nfsd/biopetmri4/Users/CauzzoOPA/prove/tracula/res/subjOPAPD01/dmri/xfms/diff2anatorig.bbr.lta lta_convert --inlta /nfsd/biopetmri4/Users/CauzzoOPA/prove/tracula/res/subjOPAPD01/dmri/xfms/diff2anatorig.bbr.lta --invert --outlta /nfsd/biopetmri4/Users/CauzzoOPA/prove/tracula/res/subjOPAPD01/dmri/xfms/anatorig2diff.bbr.lta mri_convert /nfsd/biopetmri4/Users/CauzzoOPA/FS_RECON/subjOPAPD01/mri/aparc+aseg.mgz /nfsd/biopetmri4/Users/CauzzoOPA/prove/tracula/res/subjOPAPD01/dlabel/anatorig/aparc+aseg.nii.gz mri_binarize --i /nfsd/biopetmri4/Users/CauzzoOPA/prove/tracula/res/subjOPAPD01/dlabel/anatorig/aparc+aseg.nii.gz --min .5 --dilate 4 --erode 2 --o /nfsd/biopetmri4/Users/CauzzoOPA/prove/tracula/res/subjOPAPD01/dlabel/anatorig/aparc+aseg_mask.nii.gz ERROR: Could not find thalamic nuclei segmentation in /nfsd/biopetmri4/Users/CauzzoOPA/FS_RECON/subjOPAPD01/mri/ ERROR: Thalamic nuclei segmentation is strongly recommended to use ERROR: for tracts that terminate in or travel near the thalamus ERROR: If there is good reason not to use it, set usethalnuc = 0
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Simone Cauzzo