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
######################################
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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