[afrancis@AADL22137 Imaging]$ trac-all -prep -c dmrirc-111312-2
INFO: SUBJECTS_DIR is /home/afrancis/Imaging
INFO: Diffusion root is home/afrancis/Imaging/111312-2
Actual FREESURFER_HOME /usr/local/freesurfer/7.2.0-1
flirt: Command not found.
trac-preproc -c home/afrancis/Imaging/111312-2/111312-2/scripts/dmrirc.local -log home/afrancis/Imaging/111312-2/111312-2/scripts/trac-all.log -cmd home/afrancis/Imaging/111312-2/111312-2/scripts/trac-all.cmd
#-------------------------------------
/usr/local/freesurfer/7.2.0-1/bin/trac-preproc 
#-------------------------------------
#@# Image corrections Thu Aug 11 13:10:05 CDT 2022
rm -f home/afrancis/Imaging/111312-2/111312-2/dmri/dwi_orig.1.bvals home/afrancis/Imaging/111312-2/111312-2/dmri/dwi_orig.1.bvecs
mri_convert --bvec-voxel /home/afrancis/Imaging/111312-2/data.nii.gz home/afrancis/Imaging/111312-2/111312-2/dmri/dwi_orig.1.nii.gz
mri_convert --bvec-voxel /home/afrancis/Imaging/111312-2/data.nii.gz home/afrancis/Imaging/111312-2/111312-2/dmri/dwi_orig.1.nii.gz 
reading from /home/afrancis/Imaging/111312-2/data.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
writing to home/afrancis/Imaging/111312-2/111312-2/dmri/dwi_orig.1.nii.gz...
rm -f home/afrancis/Imaging/111312-2/111312-2/dmri/dwi_orig.1.bvals.tmp home/afrancis/Imaging/111312-2/111312-2/dmri/dwi_orig.1.bvecs.tmp
mv -f home/afrancis/Imaging/111312-2/111312-2/dmri/dwi_orig.1.bvecs.tmp home/afrancis/Imaging/111312-2/111312-2/dmri/dwi_orig.1.bvecs
mv -f home/afrancis/Imaging/111312-2/111312-2/dmri/dwi_orig.1.bvals.tmp home/afrancis/Imaging/111312-2/111312-2/dmri/dwi_orig.1.bvals
orientLAS home/afrancis/Imaging/111312-2/111312-2/dmri/dwi_orig.1.nii.gz home/afrancis/Imaging/111312-2/111312-2/dmri/dwi_orig_las.1.nii.gz
INFO: input image orientation is LAS
INFO: input image determinant is -1.15762
mri_convert -oni 173 -onj 207 -onk 173 -oid -1 0 0 -ojd 0 1 0 -okd 0 0 1 -oc -0.824997 -17.325 18.825 -rt nearest home/afrancis/Imaging/111312-2/111312-2/dmri/dwi_orig.1.nii.gz home/afrancis/Imaging/111312-2/111312-2/dmri/dwi_orig_las.1.nii.gz
mri_convert -oni 173 -onj 207 -onk 173 -oid -1 0 0 -ojd 0 1 0 -okd 0 0 1 -oc -0.824997 -17.325 18.825 -rt nearest home/afrancis/Imaging/111312-2/111312-2/dmri/dwi_orig.1.nii.gz home/afrancis/Imaging/111312-2/111312-2/dmri/dwi_orig_las.1.nii.gz 
reading from home/afrancis/Imaging/111312-2/111312-2/dmri/dwi_orig.1.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
writing to home/afrancis/Imaging/111312-2/111312-2/dmri/dwi_orig_las.1.nii.gz...
INFO: found home/afrancis/Imaging/111312-2/111312-2/dmri/dwi_orig.1.bvals, copying
INFO: found home/afrancis/Imaging/111312-2/111312-2/dmri/dwi_orig.1.bvecs, converting to LAS
mv -f home/afrancis/Imaging/111312-2/111312-2/dmri/dwi_orig_las.1.nii.gz home/afrancis/Imaging/111312-2/111312-2/dmri/dwi_orig_las.nii.gz
mv -f home/afrancis/Imaging/111312-2/111312-2/dmri/dwi_orig_las.1.bvecs home/afrancis/Imaging/111312-2/111312-2/dmri/dwi_orig_las.bvecs
mv -f home/afrancis/Imaging/111312-2/111312-2/dmri/dwi_orig_las.1.bvals home/afrancis/Imaging/111312-2/111312-2/dmri/dwi_orig_las.bvals
mv -f home/afrancis/Imaging/111312-2/111312-2/dmri/dwi_orig_las.nii.gz home/afrancis/Imaging/111312-2/111312-2/dmri/dwi.nii.gz
mv -f home/afrancis/Imaging/111312-2/111312-2/dmri/dwi_orig_las.bvecs home/afrancis/Imaging/111312-2/111312-2/dmri/dwi.bvecs
mv -f home/afrancis/Imaging/111312-2/111312-2/dmri/dwi_orig_las.bvals home/afrancis/Imaging/111312-2/111312-2/dmri/dwi.bvals
rm -f home/afrancis/Imaging/111312-2/111312-2/dmri/dwi.full.nii.gz home/afrancis/Imaging/111312-2/111312-2/dmri/dwi.bvecs.full home/afrancis/Imaging/111312-2/111312-2/dmri/dwi.bvals.full
mri_convert --frame 20 50 home/afrancis/Imaging/111312-2/111312-2/dmri/dwi.nii.gz home/afrancis/Imaging/111312-2/111312-2/dmri/lowb.nii.gz
mri_convert --frame 20 50 home/afrancis/Imaging/111312-2/111312-2/dmri/dwi.nii.gz home/afrancis/Imaging/111312-2/111312-2/dmri/lowb.nii.gz 
reading from home/afrancis/Imaging/111312-2/111312-2/dmri/dwi.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
keeping frames 20 50
writing to home/afrancis/Imaging/111312-2/111312-2/dmri/lowb.nii.gz...
mri_concat --i home/afrancis/Imaging/111312-2/111312-2/dmri/lowb.nii.gz --mean --o home/afrancis/Imaging/111312-2/111312-2/dmri/lowb.nii.gz
ninputs = 1
Checking inputs
nframestot = 2
Allocing output
Done allocing
nframes = 2
Computing mean across frames
Writing to home/afrancis/Imaging/111312-2/111312-2/dmri/lowb.nii.gz
bet home/afrancis/Imaging/111312-2/111312-2/dmri/lowb.nii.gz home/afrancis/Imaging/111312-2/111312-2/dmri/lowb_brain.nii.gz -m -f 0.3
bet: Command not found.
Linux AADL22137 4.18.0-372.9.1.el8.x86_64 #1 SMP Fri Apr 15 22:12:19 EDT 2022 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Thu Aug 11 13:14:11 CDT 2022