(base) user1s-iMac-Pro:Tracula_Test user1$ time trac-all -prep -c $base/tracula-outputs/${i}/${i}_config.txt domainname: Command not found. INFO: SUBJECTS_DIR is /Users/user1/Desktop/QA_Tracula/recon-all-outputs INFO: Diffusion root is /Users/user1/Desktop/QA_Tracula/tracula-outputs Actual FREESURFER_HOME /Applications/freesurfer/7.2.0 trac-preproc -c /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/scripts/dmrirc.local -log /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/scripts/trac-all.log -cmd /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/scripts/trac-all.cmd #------------------------------------- /Applications/freesurfer/7.2.0/bin/trac-preproc #------------------------------------- #@# Image corrections Wed Mar 2 08:55:51 EST 2022 rm -f /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig.1.bvals /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig.1.bvecs mri_convert --bvec-voxel /Users/user1/Desktop/QA_Tracula/raw-diffusion-data/QA_subj/dwi_preprocessed.nii /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig.1.nii.gz mri_convert --bvec-voxel /Users/user1/Desktop/QA_Tracula/raw-diffusion-data/QA_subj/dwi_preprocessed.nii /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig.1.nii.gz reading from /Users/user1/Desktop/QA_Tracula/raw-diffusion-data/QA_subj/dwi_preprocessed.nii... TR=8400.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.98918, -0.131599, -0.0648441) j_ras = (0.120405, 0.980758, -0.153676) k_ras = (0.08382, 0.144206, 0.985991) writing to /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig.1.nii.gz... rm -f /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig.1.bvals.tmp /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig.1.bvecs.tmp mv -f /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig.1.bvecs.tmp /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig.1.bvecs mv -f /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig.1.bvals.tmp /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig.1.bvals orientLAS /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig.1.nii.gz /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig_las.1.nii.gz INFO: input image orientation is RAS INFO: input image determinant is 15.625 mri_convert -oni 88 -onj 88 -onk 60 -oid -0.98918 0.131599 0.0648441 -ojd 0.120405 0.980758 -0.153676 -okd 0.08382 0.144206 0.985991 -oc 6.55566 26.9913 11.164 -rt nearest /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig.1.nii.gz /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig_las.1.nii.gz mri_convert -oni 88 -onj 88 -onk 60 -oid -0.98918 0.131599 0.0648441 -ojd 0.120405 0.980758 -0.153676 -okd 0.08382 0.144206 0.985991 -oc 6.55566 26.9913 11.164 -rt nearest /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig.1.nii.gz /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig_las.1.nii.gz normalizing out_i_direction: (-0.98918, 0.131599, 0.0648441) -> (-0.98918, 0.131599, 0.0648441) normalizing out_j_direction: (0.120405, 0.980758, -0.153676) -> (0.120405, 0.980758, -0.153676) normalizing out_k_direction: (0.08382, 0.144206, 0.985991) -> (0.08382, 0.144206, 0.985991) reading from /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig.1.nii.gz... TR=8400.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.98918, -0.131599, -0.0648441) j_ras = (0.120405, 0.980758, -0.153676) k_ras = (0.08382, 0.144206, 0.985991) Reslicing using nearest writing to /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig_las.1.nii.gz... INFO: found /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig.1.bvals, copying INFO: found /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig.1.bvecs, converting to LAS mv -f /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig_las.1.nii.gz /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig_las.nii.gz mv -f /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig_las.1.bvecs /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig_las.bvecs mv -f /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig_las.1.bvals /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig_las.bvals mv -f /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig_las.nii.gz /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi.nii.gz mv -f /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig_las.bvecs /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi.bvecs mv -f /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig_las.bvals /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi.bvals rm -f /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi.full.nii.gz /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi.bvecs.full /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi.bvals.full mri_convert --frame 0 /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi.nii.gz /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/lowb.nii.gz mri_convert --frame 0 /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi.nii.gz /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/lowb.nii.gz reading from /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi.nii.gz... TR=8400.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.98918, 0.131599, 0.0648441) j_ras = (0.120405, 0.980758, -0.153676) k_ras = (0.08382, 0.144206, 0.985991) keeping frame 0 writing to /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/lowb.nii.gz... mri_concat --i /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/lowb.nii.gz --mean --o /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/lowb.nii.gz ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Computing mean across frames Writing to /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/lowb.nii.gz bet /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/lowb.nii.gz /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/lowb_brain.nii.gz -m -f 0.3 mv -f /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/lowb_brain_mask.nii.gz /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/diff #------------------------------------- #@# DWI set selection Wed Mar 2 08:56:23 EST 2022 ln -sf dwi.nii.gz /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/data.nii.gz ln -sf dwi.bvecs /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/bvecs ln -sf dwi.bvals /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/bvals #------------------------------------- #@# Image quality assessment Wed Mar 2 08:56:23 EST 2022 /Applications/freesurfer/7.2.0/bin/dmri_motion --dwi /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig.1.nii.gz --bval /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig.1.bvals --T 102.397758 --out /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_motion.txt --outf /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_motion_byvol.txt 7.2.0 cwd /Users/user1/Desktop/QA_Tracula cmdline /Applications/freesurfer/7.2.0/bin/dmri_motion --dwi /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig.1.nii.gz --bval /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig.1.bvals --T 102.397758 --out /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_motion.txt --outf /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_motion_byvol.txt sysname Darwin hostname user1s-iMac-Pro.wlan.musc.edu machine x86_64 user user1 Output motion measure file: /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_motion.txt Output frame-by-frame motion measure file: /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_motion_byvol.txt Input DWI file(s): /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig.1.nii.gz Input b-value table(s): /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig.1.bvals Low-b image intensity threshold: 102.398 Nominal diffusivity: 0.001 Loading DWI volume series from /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig.1.nii.gz Loading b-value table from /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/dwi_orig.1.bvals Computing within-volume head motion measures Done in 2.674 sec. dmri_motion done #------------------------------------- #@# Intra-subject registration Wed Mar 2 08:56:25 EST 2022 fslregister --s QA_subj --mov /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/lowb_brain.nii.gz --fsvol brain --out /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/lowb_brain_anat_orig.flt.nii.gz --reg /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/diff2anatorig.flt.dat --lta /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/diff2anatorig.flt.lta --cost mutualinfo --niters 2 --dof 12 --maxangle 90 Log file is /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/diff2anatorig.flt.dat.fslregister.log Wed Mar 2 08:56:26 EST 2022 --s QA_subj --mov /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/lowb_brain.nii.gz --fsvol brain --out /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/lowb_brain_anat_orig.flt.nii.gz --reg /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/diff2anatorig.flt.dat --lta /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/diff2anatorig.flt.lta --cost mutualinfo --niters 2 --dof 12 --maxangle 90 FreeSurferEnv.csh 7.2.0 user1s-iMac-Pro.wlan.musc.edu Darwin user1s-iMac-Pro.wlan.musc.edu 18.7.0 Darwin Kernel Version 18.7.0: Mon May 3 20:41:19 PDT 2021; root:xnu-4903.278.68~1/RELEASE_X86_64 x86_64 nIters 2 -------------------------------------- /Users/user1/Desktop/QA_Tracula mri_convert /Users/user1/Desktop/QA_Tracula/recon-all-outputs/QA_subj/mri/brain.mgz /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/tmp.fslregister.32005/refvol.fslregister.nii mri_convert /Users/user1/Desktop/QA_Tracula/recon-all-outputs/QA_subj/mri/brain.mgz /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/tmp.fslregister.32005/refvol.fslregister.nii reading from /Users/user1/Desktop/QA_Tracula/recon-all-outputs/QA_subj/mri/brain.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 3.72529e-09, -1.49012e-08) j_ras = (1.49012e-08, 0, -1) k_ras = (1.11759e-08, 1, 2.98023e-08) writing to /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/tmp.fslregister.32005/refvol.fslregister.nii... -------------------------------------- /Users/user1/Desktop/QA_Tracula mri_convert /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/lowb_brain.nii.gz /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/tmp.fslregister.32005/movvol.fslregister.nii --frame 0 mri_convert /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/lowb_brain.nii.gz /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/tmp.fslregister.32005/movvol.fslregister.nii --frame 0 reading from /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/lowb_brain.nii.gz... TR=8400.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.98918, 0.131599, 0.0648441) j_ras = (0.120405, 0.980758, -0.153676) k_ras = (0.08382, 0.144206, 0.985991) keeping frame 0 writing to /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/tmp.fslregister.32005/movvol.fslregister.nii... Mov determinant is -15.625 /Users/user1/Desktop/QA_Tracula tkregister2_cmdl --mov /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/tmp.fslregister.32005/movvol.fslregister.nii --reg /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/tmp.fslregister.32005/reg0.32005.dat --targ brain --fstarg --regheader --fslregout /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/diff2anatorig.flt.dat.fsl.mat0 --s QA_subj --noedit target volume brain movable volume /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/tmp.fslregister.32005/movvol.fslregister.nii reg file /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/tmp.fslregister.32005/reg0.32005.dat LoadVol 0 ZeroCRAS 0 7.2.0 Diagnostic Level -1 INFO: loading target /Users/user1/Desktop/QA_Tracula/recon-all-outputs/QA_subj/mri/brain.mgz Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/tmp.fslregister.32005/movvol.fslregister.nii Tmov: -------------------- -2.50000 0.00000 0.00000 110.00000; 0.00000 0.00000 2.50000 -75.00000; 0.00000 -2.50000 0.00000 110.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 0.98918 -0.13160 -0.06484 -0.63010; 0.08382 0.14421 0.98599 -24.24616; -0.12040 -0.98076 0.15368 3.82413; 0.00000 0.00000 0.00000 1.00000; --------------------------------------- ---- Input registration matrix -------- 0.98918 -0.13160 -0.06484 -0.63010; 0.08382 0.14421 0.98599 -24.24616; -0.12040 -0.98076 0.15368 3.82413; 0.00000 0.00000 0.00000 1.00000; Determinant 1 subject = QA_subj RegMat --------------------------- 0.98918 -0.13160 -0.06484 -0.63010; 0.08382 0.14421 0.98599 -24.24616; -0.12040 -0.98076 0.15368 3.82413; 0.00000 0.00000 0.00000 1.00000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -15.625, ref det = -1 Wed Mar 2 08:56:26 EST 2022 /Users/user1/Desktop/QA_Tracula flirt.fsl -ref /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/tmp.fslregister.32005/refvol.fslregister.nii -in /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/tmp.fslregister.32005/movvol.fslregister.nii -bins 256 -cost mutualinfo -dof 12 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/tmp.fslregister.32005/fslmat0.trans.mat -schedule /Applications/freesurfer/7.2.0/bin/fsl.5.0.2.xyztrans.sch -init /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/diff2anatorig.flt.dat.fsl.mat0 Wed Mar 2 08:56:30 EST 2022 /Users/user1/Desktop/QA_Tracula flirt.fsl -ref /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/tmp.fslregister.32005/refvol.fslregister.nii -in /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/tmp.fslregister.32005/movvol.fslregister.nii -bins 256 -cost mutualinfo -dof 12 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/diff2anatorig.flt.dat.fsl.mat -init /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/tmp.fslregister.32005/fslmat0.trans.mat -schedule /Applications/freesurfer/7.2.0/bin/flirt.newdefault.20080811.sch -o /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/tmp.fslregister.32005/outvol.fslregister.nii Iteration 2 Wed Mar 2 08:56:38 EST 2022 /Users/user1/Desktop/QA_Tracula flirt.fsl -ref /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/tmp.fslregister.32005/refvol.fslregister.nii -in /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/tmp.fslregister.32005/movvol.fslregister.nii -bins 256 -cost mutualinfo -dof 12 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/diff2anatorig.flt.dat.fsl.mat -init /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/tmp.fslregister.32005/fslmat0.trans.mat -schedule /Applications/freesurfer/7.2.0/bin/flirt.newdefault.20080811.sch -o /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/tmp.fslregister.32005/outvol.fslregister.nii -init /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/diff2anatorig.flt.dat.fsl.mat Wed Mar 2 08:56:47 EST 2022 /Users/user1/Desktop/QA_Tracula mri_convert /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/tmp.fslregister.32005/outvol.fslregister.nii /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/lowb_brain_anat_orig.flt.nii.gz mri_convert /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/tmp.fslregister.32005/outvol.fslregister.nii /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/lowb_brain_anat_orig.flt.nii.gz reading from /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/tmp.fslregister.32005/outvol.fslregister.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 3.72529e-09, -1.49012e-08) j_ras = (1.49012e-08, 0, -1) k_ras = (1.11759e-08, 1, 2.98023e-08) writing to /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/lowb_brain_anat_orig.flt.nii.gz... tkregister2_cmdl --s QA_subj --mov /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/lowb_brain.nii.gz --targ brain --fstarg --reg /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/diff2anatorig.flt.dat --fslreg /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/diff2anatorig.flt.dat.fsl.mat --noedit ---- FSL registration matrix -------- 0.95300 -0.08966 -0.04062 35.63118; -0.02585 0.16687 -0.95036 161.57115; 0.10043 0.96587 0.16649 4.58294; 0.00000 0.00000 0.00000 1.00000; --------------------------------------- target volume brain movable volume /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/lowb_brain.nii.gz reg file /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/diff2anatorig.flt.dat LoadVol 0 ZeroCRAS 0 7.2.0 Diagnostic Level -1 INFO: loading target /Users/user1/Desktop/QA_Tracula/recon-all-outputs/QA_subj/mri/brain.mgz Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/lowb_brain.nii.gz Tmov: -------------------- -2.50000 0.00000 0.00000 110.00000; 0.00000 0.00000 2.50000 -75.00000; 0.00000 -2.50000 0.00000 110.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -15.625, ref det = -1 ---- Input registration matrix (computed) -------- 1.03796 -0.10096 -0.02668 0.76939; 0.04579 0.17199 1.02015 -23.75528; -0.10003 -0.99519 0.17862 2.41191; 0.00000 0.00000 0.00000 1.00000; --------------------------------------- ---- Input registration matrix -------- 1.03796 -0.10096 -0.02668 0.76939; 0.04579 0.17199 1.02015 -23.75528; -0.10003 -0.99519 0.17862 2.41191; 0.00000 0.00000 0.00000 1.00000; Determinant 1.09755 subject = QA_subj RegMat --------------------------- 1.03796 -0.10096 -0.02668 0.76939; 0.04579 0.17199 1.02015 -23.75528; -0.10003 -0.99519 0.17862 2.41191; 0.00000 0.00000 0.00000 1.00000; (standard_in) 1: illegal character: _ (standard_in) 1: illegal character: Q (standard_in) 1: parse error lta_convert --inreg /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/diff2anatorig.flt.dat --outlta /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/diff2anatorig.flt.lta --src /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/lowb_brain.nii.gz --trg /Users/user1/Desktop/QA_Tracula/recon-all-outputs/QA_subj/mri/brain.mgz 7.2.0 --inreg: /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/diff2anatorig.flt.dat input TK REG transform. --outlta: /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/diff2anatorig.flt.lta output LTA. --src: /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/lowb_brain.nii.gz src image (geometry). --trg: /Users/user1/Desktop/QA_Tracula/recon-all-outputs/QA_subj/mri/brain.mgz trg image (geometry). INFO: This REGISTER_DAT transform is valid only for volumes between COR types with c_(r,a,s) = 0. LTA read, type : 1 0.95689 -0.03162 -0.03553 -1.13535; 0.03091 0.98451 0.02223 -0.83499; 0.03400 -0.02321 0.96436 -0.28325; 0.00000 0.00000 0.00000 1.00000; Writing LTA to file /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/diff2anatorig.flt.lta... lta_convert successful. Cleaning up Started at Wed Mar 2 08:56:26 EST 2022 Ended at Wed Mar 2 08:56:48 EST 2022 fslregister Done To check results, run: tkregisterfv --mov /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/lowb_brain.nii.gz --reg /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/diff2anatorig.flt.dat --surf orig lta_convert --inlta /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/diff2anatorig.flt.lta --invert --outlta /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/anatorig2diff.flt.lta 7.2.0 --inlta: /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/diff2anatorig.flt.lta input LTA transform. --invert: will invert transform. --outlta: /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/anatorig2diff.flt.lta output LTA. LTA read, type : 1 0.95689 -0.03162 -0.03553 -1.13535; 0.03091 0.98451 0.02223 -0.83499; 0.03400 -0.02321 0.96436 -0.28325; 0.00000 0.00000 0.00000 1.00000; Writing LTA to file /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/anatorig2diff.flt.lta... lta_convert successful. mri_convert /Users/user1/Desktop/QA_Tracula/recon-all-outputs/QA_subj/mri/aparc+aseg.mgz /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/aparc+aseg.nii.gz mri_convert /Users/user1/Desktop/QA_Tracula/recon-all-outputs/QA_subj/mri/aparc+aseg.mgz /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/aparc+aseg.nii.gz reading from /Users/user1/Desktop/QA_Tracula/recon-all-outputs/QA_subj/mri/aparc+aseg.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 3.72529e-09, -1.49012e-08) j_ras = (1.49012e-08, 0, -1) k_ras = (1.11759e-08, 1, 2.98023e-08) MRIcopyHeader(): source has ctab writing to /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/aparc+aseg.nii.gz... mri_binarize --i /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/aparc+aseg.nii.gz --min .5 --dilate 4 --erode 2 --o /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/aparc+aseg_mask.nii.gz 7.2.0 cwd /Users/user1/Desktop/QA_Tracula cmdline mri_binarize --i /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/aparc+aseg.nii.gz --min .5 --dilate 4 --erode 2 --o /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/aparc+aseg_mask.nii.gz sysname Darwin hostname user1s-iMac-Pro.wlan.musc.edu machine x86_64 user user1 input /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/aparc+aseg.nii.gz frame 0 nErode3d 2 nErode2d 0 output /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/aparc+aseg_mask.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Starting parallel 1 Found 1031654 values in range Dilating 4 voxels in 3d Eroding 2 voxels in 3d Counting number of voxels in first frame Found 1367867 voxels in final mask Writing output to /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/aparc+aseg_mask.nii.gz Count: 1367867 1367867.000000 16777216 8.153123 mri_binarize done printf: illegal option -- - usage: printf format [arguments ...] mri_binarize --i /Users/user1/Desktop/QA_Tracula/recon-all-outputs/QA_subj/mri/aparc+aseg.mgz --o /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz ERROR: must specify minimum and/or maximum threshold or match values mri_concat --i /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz --i /Users/user1/Desktop/QA_Tracula/recon-all-outputs/QA_subj/mri/ThalamicNuclei.v12.T1.FSvoxelSpace.mgz --max --o /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz ninputs = 2 Checking inputs error: niiRead(): error opening file /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz ERROR: reading /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz mri_binarize --i /Users/user1/Desktop/QA_Tracula/recon-all-outputs/QA_subj/mri/aparc+aseg.mgz --match 2 41 7 46 172 177 77 --o /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/White-Matter.nii.gz 7.2.0 cwd /Users/user1/Desktop/QA_Tracula cmdline mri_binarize --i /Users/user1/Desktop/QA_Tracula/recon-all-outputs/QA_subj/mri/aparc+aseg.mgz --match 2 41 7 46 172 177 77 --o /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/White-Matter.nii.gz sysname Darwin hostname user1s-iMac-Pro.wlan.musc.edu machine x86_64 user user1 input /Users/user1/Desktop/QA_Tracula/recon-all-outputs/QA_subj/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/White-Matter.nii.gz Binarizing based on matching values nMatch 7 0 2 1 41 2 7 3 46 4 172 5 177 6 77 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 MRIcopyHeader(): source has ctab Starting parallel 1 Found 452968 values in range Counting number of voxels in first frame Found 452967 voxels in final mask Writing output to /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/White-Matter.nii.gz Count: 452967 452967.000000 16777216 2.699894 mri_binarize done mri_binarize --i /Users/user1/Desktop/QA_Tracula/recon-all-outputs/QA_subj/mri/aparc+aseg.mgz --match 2 41 7 46 172 177 77 28 60 16 173 174 175 --o /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/White-Matter++.nii.gz 7.2.0 cwd /Users/user1/Desktop/QA_Tracula cmdline mri_binarize --i /Users/user1/Desktop/QA_Tracula/recon-all-outputs/QA_subj/mri/aparc+aseg.mgz --match 2 41 7 46 172 177 77 28 60 16 173 174 175 --o /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/White-Matter++.nii.gz sysname Darwin hostname user1s-iMac-Pro.wlan.musc.edu machine x86_64 user user1 input /Users/user1/Desktop/QA_Tracula/recon-all-outputs/QA_subj/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/White-Matter++.nii.gz Binarizing based on matching values nMatch 13 0 2 1 41 2 7 3 46 4 172 5 177 6 77 7 28 8 60 9 16 10 173 11 174 12 175 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 MRIcopyHeader(): source has ctab Starting parallel 1 Found 480681 values in range Counting number of voxels in first frame Found 480680 voxels in final mask Writing output to /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/White-Matter++.nii.gz Count: 480680 480680.000000 16777216 2.865076 mri_binarize done mri_convert -at /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/anatorig2diff.flt.lta -rt nearest /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/aparc+aseg.nii.gz /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/diff/aparc+aseg.flt.nii.gz mri_convert -at /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/anatorig2diff.flt.lta -rt nearest /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/aparc+aseg.nii.gz /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/diff/aparc+aseg.flt.nii.gz reading from /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/aparc+aseg.nii.gz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 3.72529e-09, -1.49012e-08) j_ras = (1.49012e-08, 0, -1) k_ras = (1.11759e-08, 1, 2.98023e-08) INFO: Reading transformation from file /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/anatorig2diff.flt.lta... Reading transform with LTAreadEx() INFO: Applying transformation from file /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/anatorig2diff.flt.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 1.04261 0.03438 0.03762 1.22308; -0.03189 1.01413 -0.02456 0.80363; -0.03753 0.02319 1.03504 0.26993; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 0) writing to /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/diff/aparc+aseg.flt.nii.gz... mri_convert -at /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/anatorig2diff.flt.lta -rt nearest /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/aparc+aseg_mask.nii.gz /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/diff/aparc+aseg_mask.flt.nii.gz mri_convert -at /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/anatorig2diff.flt.lta -rt nearest /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/aparc+aseg_mask.nii.gz /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/diff/aparc+aseg_mask.flt.nii.gz reading from /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/aparc+aseg_mask.nii.gz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 3.72529e-09, -1.49012e-08) j_ras = (1.49012e-08, 0, -1) k_ras = (1.11759e-08, 1, 2.98023e-08) INFO: Reading transformation from file /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/anatorig2diff.flt.lta... Reading transform with LTAreadEx() INFO: Applying transformation from file /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/anatorig2diff.flt.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 1.04261 0.03438 0.03762 1.22308; -0.03189 1.01413 -0.02456 0.80363; -0.03753 0.02319 1.03504 0.26993; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 0) writing to /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/diff/aparc+aseg_mask.flt.nii.gz... mri_convert -at /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/anatorig2diff.flt.lta -rt nearest /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/White-Matter.nii.gz /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/diff/White-Matter.flt.nii.gz mri_convert -at /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/anatorig2diff.flt.lta -rt nearest /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/White-Matter.nii.gz /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/diff/White-Matter.flt.nii.gz reading from /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/White-Matter.nii.gz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 3.72529e-09, -1.49012e-08) j_ras = (1.49012e-08, 0, -1) k_ras = (1.11759e-08, 1, 2.98023e-08) INFO: Reading transformation from file /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/anatorig2diff.flt.lta... Reading transform with LTAreadEx() INFO: Applying transformation from file /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/anatorig2diff.flt.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 1.04261 0.03438 0.03762 1.22308; -0.03189 1.01413 -0.02456 0.80363; -0.03753 0.02319 1.03504 0.26993; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 0) writing to /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/diff/White-Matter.flt.nii.gz... mri_convert -at /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/anatorig2diff.flt.lta -rt nearest /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/White-Matter++.nii.gz /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/diff/White-Matter++.flt.nii.gz mri_convert -at /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/anatorig2diff.flt.lta -rt nearest /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/White-Matter++.nii.gz /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/diff/White-Matter++.flt.nii.gz reading from /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/White-Matter++.nii.gz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 3.72529e-09, -1.49012e-08) j_ras = (1.49012e-08, 0, -1) k_ras = (1.11759e-08, 1, 2.98023e-08) INFO: Reading transformation from file /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/anatorig2diff.flt.lta... Reading transform with LTAreadEx() INFO: Applying transformation from file /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/anatorig2diff.flt.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 1.04261 0.03438 0.03762 1.22308; -0.03189 1.01413 -0.02456 0.80363; -0.03753 0.02319 1.03504 0.26993; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 0) writing to /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/diff/White-Matter++.flt.nii.gz... mri_convert -at /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/anatorig2diff.flt.lta -rt nearest /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/diff/aparc+aseg+thalnuc.flt.nii.gz mri_convert -at /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dmri/xfms/anatorig2diff.flt.lta -rt nearest /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/diff/aparc+aseg+thalnuc.flt.nii.gz reading from /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz... error: niiRead(): error opening file /Users/user1/Desktop/QA_Tracula/tracula-outputs/QA_subj/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz Darwin user1s-iMac-Pro.wlan.musc.edu 18.7.0 Darwin Kernel Version 18.7.0: Mon May 3 20:41:19 PDT 2021; root:xnu-4903.278.68~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Wed Mar 2 08:57:08 EST 2022 real 1m18.445s user 1m14.294s sys 0m5.502s (base) user1s-iMac-Pro:Tracula_Test user1$