mar 24 giu 2025, 10:51:38, CEST /home/gabriellam/Desktop/prova_tracula /usr/local/freesurfer/8.0.0/bin/trac-all -prep -c dmrirc.mio_config.tcsh Subject 002_S_6652 SUBJECTS_DIR /home/gabriellam/Desktop/prova_tracula/fs FREESURFER_HOME /usr/local/freesurfer/8.0.0/ Actual FREESURFER_HOME /usr/local/freesurfer/8.0.0 build-stamp.txt: freesurfer-linux-ubuntu22_x86_64-8.0.0-20250204-0f2bd3a gabriellam SN-CZC4487LYX Linux SN-CZC4487LYX 6.8.0-60-generic #63~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Apr 22 19:00:15 UTC 2 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 4065668 kbytes maxproc 126728 maxlocks unlimited maxsignal 126728 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 32525360 1694628 16409780 346916 14420952 30015380 Swap: 2097148 176640 1920508 ######################################## Program versions: trac-all 8.0.0 mri_convert --all-info ProgramName: mri_convert ProgramArguments: mri_convert --all-info ProgramVersion: 8.0.0 TimeStamp: 2025/06/24-08:51:38-GMT BuildTime: Feb 4 2025 01:21:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-20250204-0f2bd3a User: gabriellam Machine: SN-CZC4487LYX Platform: Linux PlatformVersion: 6.8.0-60-generic CompilerName: GCC CompilerVersion: 8.4.0 FLIRT version 6.0 bbregister 8.0.0 mri_cvs_register 8.0.0 ProgramName: dmri_motion ProgramArguments: /usr/local/freesurfer/8.0.0//bin/dmri_motion --all-info ProgramVersion: 8.0.0 TimeStamp: 2025/06/24-08:51:38-GMT BuildTime: Feb 4 2025 01:21:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-20250204-0f2bd3a User: gabriellam Machine: SN-CZC4487LYX Platform: Linux PlatformVersion: 6.8.0-60-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: dmri_train ProgramArguments: /usr/local/freesurfer/8.0.0//bin/dmri_train --all-info ProgramVersion: 8.0.0 TimeStamp: 2025/06/24-08:51:38-GMT BuildTime: Feb 4 2025 01:21:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-20250204-0f2bd3a User: gabriellam Machine: SN-CZC4487LYX Platform: Linux PlatformVersion: 6.8.0-60-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: dmri_paths ProgramArguments: /usr/local/freesurfer/8.0.0//bin/dmri_paths --all-info ProgramVersion: 8.0.0 TimeStamp: 2025/06/24-08:51:38-GMT BuildTime: Feb 4 2025 01:21:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-20250204-0f2bd3a User: gabriellam Machine: SN-CZC4487LYX Platform: Linux PlatformVersion: 6.8.0-60-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: dmri_pathstats ProgramArguments: /usr/local/freesurfer/8.0.0//bin/dmri_pathstats --all-info ProgramVersion: 8.0.0 TimeStamp: 2025/06/24-08:51:38-GMT BuildTime: Feb 4 2025 01:21:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-20250204-0f2bd3a User: gabriellam Machine: SN-CZC4487LYX Platform: Linux PlatformVersion: 6.8.0-60-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: dmri_mergepaths ProgramArguments: /usr/local/freesurfer/8.0.0//bin/dmri_mergepaths --all-info ProgramVersion: 8.0.0 TimeStamp: 2025/06/24-08:51:38-GMT BuildTime: Feb 4 2025 01:21:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-20250204-0f2bd3a User: gabriellam Machine: SN-CZC4487LYX Platform: Linux PlatformVersion: 6.8.0-60-generic CompilerName: GCC CompilerVersion: 8.4.0 ProgramName: dmri_group ProgramArguments: /usr/local/freesurfer/8.0.0//bin/dmri_group --all-info ProgramVersion: 8.0.0 TimeStamp: 2025/06/24-08:51:38-GMT BuildTime: Feb 4 2025 01:21:05 BuildStamp: freesurfer-linux-ubuntu22_x86_64-8.0.0-20250204-0f2bd3a User: gabriellam Machine: SN-CZC4487LYX Platform: Linux PlatformVersion: 6.8.0-60-generic CompilerName: GCC CompilerVersion: 8.4.0 New invocation of trac-preproc gabriellam SN-CZC4487LYX Linux SN-CZC4487LYX 6.8.0-60-generic #63~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Apr 22 19:00:15 UTC 2 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 4065668 kbytes maxproc 126728 maxlocks unlimited maxsignal 126728 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 32525360 1700908 16387476 346916 14436976 30009076 Swap: 2097148 176640 1920508 #------------------------------------- /usr/local/freesurfer/8.0.0/bin/trac-preproc #------------------------------------- #@# Image corrections mar 24 giu 2025, 10:51:38, CEST rm -f /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_orig.1.bvals /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_orig.1.bvecs mri_convert --bvec-voxel /home/gabriellam/Desktop/prova_tracula/bids/002_S_6652/dwi/eddy.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_orig.1.nii.gz mri_convert --bvec-voxel /home/gabriellam/Desktop/prova_tracula/bids/002_S_6652/dwi/eddy.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_orig.1.nii.gz INFO: using NIfTI-1 sform (sform_code=2) reading from /home/gabriellam/Desktop/prova_tracula/bids/002_S_6652/dwi/eddy.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/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_orig.1.nii.gz... rm -f /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_orig.1.bvals.tmp /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_orig.1.bvecs.tmp mv -f /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_orig.1.bvecs.tmp /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_orig.1.bvecs mv -f /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_orig.1.bvals.tmp /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_orig.1.bvals orientLAS /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_orig.1.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_orig_las.1.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -8 mri_convert -oni 116 -onj 116 -onk 81 -oid -1 0 0 -ojd 0 1 0 -okd 0 0 1 -oc 0 12 -19 -rt nearest /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_orig.1.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_orig_las.1.nii.gz mri_convert -oni 116 -onj 116 -onk 81 -oid -1 0 0 -ojd 0 1 0 -okd 0 0 1 -oc 0 12 -19 -rt nearest /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_orig.1.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_orig_las.1.nii.gz reading from /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/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) Reslicing using nearest writing to /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_orig_las.1.nii.gz... INFO: found /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_orig.1.bvals, copying INFO: found /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_orig.1.bvecs, converting to LAS mv -f /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_orig_las.1.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_orig_las.nii.gz mv -f /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_orig_las.1.bvecs /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_orig_las.bvecs mv -f /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_orig_las.1.bvals /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_orig_las.bvals mv -f /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_orig_las.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi.nii.gz mv -f /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_orig_las.bvecs /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi.bvecs mv -f /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_orig_las.bvals /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi.bvals rm -f /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi.full.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi.bvecs.full /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi.bvals.full mri_convert --frame 0 1 5 18 31 46 59 72 85 98 110 119 124 /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/lowb.nii.gz mri_convert --frame 0 1 5 18 31 46 59 72 85 98 110 119 124 /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/lowb.nii.gz reading from /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/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 0 1 5 18 31 46 59 72 85 98 110 119 124 writing to /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/lowb.nii.gz... mri_concat --i /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/lowb.nii.gz --mean --o /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/lowb.nii.gz ninputs = 1 Checking inputs nframestot = 13 Allocing output Done allocing nframes = 13 Computing mean across frames Writing to /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/lowb.nii.gz bet /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/lowb.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/lowb_brain.nii.gz -m -f 0.3 mv -f /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/lowb_brain_mask.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/diff #------------------------------------- #@# DWI set selection mar 24 giu 2025, 10:52:50, CEST ln -sf dwi.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/data.nii.gz ln -sf dwi.bvecs /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/bvecs ln -sf dwi.bvals /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/bvals #------------------------------------- #@# Image quality assessment mar 24 giu 2025, 10:52:50, CEST /usr/local/freesurfer/8.0.0//bin/dmri_motion --dwi /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_orig.1.nii.gz --bval /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_orig.1.bvals --T 1556.375244 --out /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_motion.txt --outf /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_motion_byvol.txt 8.0.0 cwd /home/gabriellam/Desktop/prova_tracula cmdline /usr/local/freesurfer/8.0.0//bin/dmri_motion --dwi /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_orig.1.nii.gz --bval /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_orig.1.bvals --T 1556.375244 --out /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_motion.txt --outf /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_motion_byvol.txt sysname Linux hostname SN-CZC4487LYX machine x86_64 user gabriellam Output motion measure file: /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_motion.txt Output frame-by-frame motion measure file: /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_motion_byvol.txt Input DWI file(s): /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_orig.1.nii.gz Input b-value table(s): /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_orig.1.bvals Low-b image intensity threshold: 1556.38 Nominal diffusivity: 0.001 Loading DWI volume series from /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_orig.1.nii.gz Loading b-value table from /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_orig.1.bvals Computing within-volume head motion measures Done in 6.369 sec. dmri_motion done #------------------------------------- #@# Intra-subject registration mar 24 giu 2025, 10:52:56, CEST bbregister --s 002_S_6652 --init-fsl --dti --6 --mov /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/lowb.nii.gz --reg /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/diff2anatorig.bbr.lta tmp /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513 Log file is /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/diff2anatorig.bbr.log mar 24 giu 2025, 10:52:56, CEST setenv SUBJECTS_DIR /home/gabriellam/Desktop/prova_tracula/fs cd /home/gabriellam/Desktop/prova_tracula /usr/local/freesurfer/8.0.0/bin/bbregister --s 002_S_6652 --init-fsl --dti --6 --mov /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/lowb.nii.gz --reg /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/diff2anatorig.bbr.lta bbregister 8.0.0 Linux SN-CZC4487LYX 6.8.0-60-generic #63~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Apr 22 19:00:15 UTC 2 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer/8.0.0/ mri_convert /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/lowb.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/template.nii mri_convert /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/lowb.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/template.nii reading from /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/lowb.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/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/template.nii... fslregister --s 002_S_6652 --mov /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/template.nii --reg /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/reg.init.dat --niters 1 --maxangle 90 --tmp /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov Log file is /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/reg.init.dat.fslregister.log mar 24 giu 2025, 10:52:56, CEST --s 002_S_6652 --mov /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/template.nii --reg /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/reg.init.dat --niters 1 --maxangle 90 --tmp /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov fslregister 8.0.0 SN-CZC4487LYX Linux SN-CZC4487LYX 6.8.0-60-generic #63~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Apr 22 19:00:15 UTC 2 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /home/gabriellam/Desktop/prova_tracula mri_convert /home/gabriellam/Desktop/prova_tracula/fs/002_S_6652/mri/brainmask.mgz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/fslregister/refvol.fslregister.nii mri_convert /home/gabriellam/Desktop/prova_tracula/fs/002_S_6652/mri/brainmask.mgz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/fslregister/refvol.fslregister.nii reading from /home/gabriellam/Desktop/prova_tracula/fs/002_S_6652/mri/brainmask.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/fslregister/refvol.fslregister.nii... -------------------------------------- /home/gabriellam/Desktop/prova_tracula mri_convert /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/template.nii /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/fslregister/movvol.fslregister.nii --frame 0 mri_convert /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/template.nii /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/fslregister/movvol.fslregister.nii --frame 0 reading from /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/template.nii... 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 frame 0 writing to /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/fslregister/movvol.fslregister.nii... Mov determinant is -8 /home/gabriellam/Desktop/prova_tracula tkregister2_cmdl --mov /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/fslregister/movvol.fslregister.nii --reg /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/fslregister/reg0.96554.dat --targ brainmask --fstarg --regheader --fslregout /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/reg.init.dat.fsl.mat0 --s 002_S_6652 --noedit target volume brainmask movable volume /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/fslregister/movvol.fslregister.nii reg file /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/fslregister/reg0.96554.dat LoadVol 0 ZeroCRAS 0 8.0.0 Diagnostic Level -1 INFO: loading target /home/gabriellam/Desktop/prova_tracula/fs/002_S_6652/mri/brainmask.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 /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/fslregister/movvol.fslregister.nii Tmov: -------------------- -2.00000 0.00000 0.00000 116.00000; 0.00000 0.00000 2.00000 -81.00000; 0.00000 -2.00000 0.00000 116.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.00000 0.00000 0.00000 203.06610; 0.00000 0.00000 1.00000 538.52478; 0.00000 -1.00000 0.00000 -244.50000; 0.00000 0.00000 0.00000 1.00000; --------------------------------------- ---- Input registration matrix -------- 1.00000 0.00000 0.00000 203.06610; 0.00000 0.00000 1.00000 538.52478; 0.00000 -1.00000 0.00000 -244.50000; 0.00000 0.00000 0.00000 1.00000; Determinant 1 subject = 002_S_6652 RegMat --------------------------- 1.00000 0.00000 0.00000 203.06610; 0.00000 0.00000 1.00000 538.52478; 0.00000 -1.00000 0.00000 -244.50000; 0.00000 0.00000 0.00000 1.00000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -8, ref det = -1 mar 24 giu 2025, 10:52:57, CEST /home/gabriellam/Desktop/prova_tracula flirt.fsl -ref /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/fslregister/refvol.fslregister.nii -in /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/8.0.0//bin/fsl.5.0.2.xyztrans.sch -init /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/reg.init.dat.fsl.mat0 mar 24 giu 2025, 10:52:59, CEST /home/gabriellam/Desktop/prova_tracula flirt.fsl -ref /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/fslregister/refvol.fslregister.nii -in /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/reg.init.dat.fsl.mat -init /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/8.0.0//bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s 002_S_6652 --mov /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/template.nii --targ brainmask --fstarg --reg /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/reg.init.dat --fslreg /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/reg.init.dat.fsl.mat --noedit ---- FSL registration matrix -------- 0.99998 -0.00674 0.00000 13.54520; -0.00007 -0.00995 -0.99995 206.05701; 0.00674 0.99993 -0.00995 9.39832; 0.00000 0.00000 0.00000 1.00000; --------------------------------------- target volume brainmask movable volume /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/template.nii reg file /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/reg.init.dat LoadVol 0 ZeroCRAS 0 8.0.0 Diagnostic Level -1 INFO: loading target /home/gabriellam/Desktop/prova_tracula/fs/002_S_6652/mri/brainmask.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 /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/template.nii Tmov: -------------------- -2.00000 0.00000 0.00000 116.00000; 0.00000 0.00000 2.00000 -81.00000; 0.00000 -2.00000 0.00000 116.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -8, ref det = -1 ---- Input registration matrix (computed) -------- 0.99998 -0.00674 -0.00007 0.74362; -0.00000 -0.00995 0.99995 -4.12714; -0.00674 -0.99993 -0.00995 -2.59888; 0.00000 0.00000 0.00000 1.00000; --------------------------------------- ---- Input registration matrix -------- 0.99998 -0.00674 -0.00007 0.74362; -0.00000 -0.00995 0.99995 -4.12714; -0.00674 -0.99993 -0.00995 -2.59888; 0.00000 0.00000 0.00000 1.00000; Determinant 1 subject = 002_S_6652 RegMat --------------------------- 0.99998 -0.00674 -0.00007 0.74362; -0.00000 -0.00995 0.99995 -4.12714; -0.00674 -0.99993 -0.00995 -2.59888; 0.00000 0.00000 0.00000 1.00000; (standard_in) 1: illegal character: _ (standard_in) 1: syntax error (standard_in) 1: illegal character: _ Started at mar 24 giu 2025, 10:52:56, CEST Ended at mar 24 giu 2025, 10:53:07, CEST fslregister Done To check results, run: tkregisterfv --mov /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/template.nii --reg /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/reg.init.dat --surf orig mri_segreg --mov /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/template.nii --init-reg /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/reg.init.dat --out-reg /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 8.0.0 setenv SUBJECTS_DIR /home/gabriellam/Desktop/prova_tracula/fs cd /home/gabriellam/Desktop/prova_tracula mri_segreg --mov /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/template.nii --init-reg /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/reg.init.dat --out-reg /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Linux hostname SN-CZC4487LYX machine x86_64 user gabriellam movvol /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/template.nii regfile /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/reg.init.dat subject 002_S_6652 dof 6 outregfile /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1751253663 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99998 -0.00674 -0.00007 0.74362; -0.00000 -0.00995 0.99995 -4.12714; -0.00674 -0.99993 -0.00995 -2.59888; 0.00000 0.00000 0.00000 1.00000; Loading mov ExcludeZeroVoxels 1 Reading in targ vol /home/gabriellam/Desktop/prova_tracula/fs/002_S_6652/mri/orig.mgz Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 1.053645 1 -25.0 -25.0 25.0 0.992480 2 -25.0 25.0 -25.0 1.060579 3 -25.0 25.0 25.0 1.022314 4 25.0 -25.0 -25.0 1.035207 5 25.0 -25.0 25.0 1.033570 6 25.0 25.0 -25.0 1.012891 7 25.0 25.0 25.0 1.057702 REL: 8 0.882014 8.268388 1.033548 rel = 0.853385 Initial costs ---------------- Number of surface hits 2108 WM Intensity 1973.9369 +/- 338.5271 Ctx Intensity 2072.8717 +/- 441.1446 Pct Contrast 4.0983 +/- 21.3985 Cost 0.8820 RelCost 0.8534 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 1.0270 1.0270 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 1.0170 1.0170 0.0 5 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 4.0000 1.0162 1.0162 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.9953 0.9953 0.0 8 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 4.0000 0.9795 0.9795 0.0 9 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 -4.0000 0.9730 0.9730 0.0 12 -4.0000 -4.0000 -4.0000 0.0000 0.0000 -4.0000 0.9709 0.9709 0.0 13 -4.0000 -4.0000 -4.0000 0.0000 0.0000 0.0000 0.9378 0.9378 0.0 16 -4.0000 -4.0000 -4.0000 0.0000 4.0000 0.0000 0.8854 0.8854 0.0 40 -4.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.8527 0.8527 0.0 43 -4.0000 -4.0000 0.0000 0.0000 4.0000 0.0000 0.7885 0.7885 0.0 256 0.0000 -4.0000 -4.0000 0.0000 0.0000 0.0000 0.7572 0.7572 0.0 283 0.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.4109 0.4109 0.0 Brute Force -------------------------- Min cost was 0.410860 Number of iterations 729 Search time 0.438154 sec Parameters at best (transmm, rotdeg) 0.000 -4.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 -4 2 0 3 0 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000100 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.410860 9 -0.013 -4.000 0.000 0.000 0.000 0.000 0.4108384687 10 -0.009 -4.000 0.000 0.000 0.000 0.000 0.4108335969 12 -0.010 -4.000 0.000 0.000 0.000 0.000 0.4108335843 19 -0.010 -3.618 0.000 0.000 0.000 0.000 0.3904747033 21 -0.010 -3.644 0.000 0.000 0.000 0.000 0.3900019654 24 -0.010 -3.662 0.000 0.000 0.000 0.000 0.3898628806 25 -0.010 -3.664 0.000 0.000 0.000 0.000 0.3898571670 27 -0.010 -3.666 0.000 0.000 0.000 0.000 0.3898533262 40 -0.010 -3.666 0.021 0.000 0.000 0.000 0.3897614367 41 -0.010 -3.666 0.020 0.000 0.000 0.000 0.3897613090 51 -0.010 -3.666 0.020 0.011 0.000 0.000 0.3897280200 52 -0.010 -3.666 0.020 0.010 0.000 0.000 0.3897270956 58 -0.010 -3.666 0.020 0.010 -0.618 0.000 0.3840838819 60 -0.010 -3.666 0.020 0.010 -0.358 0.000 0.3754067505 63 -0.010 -3.666 0.020 0.010 -0.366 0.000 0.3753825596 64 -0.010 -3.666 0.020 0.010 -0.368 0.000 0.3753815232 71 -0.010 -3.666 0.020 0.010 -0.368 0.382 0.3744974688 72 -0.010 -3.666 0.020 0.010 -0.368 0.203 0.3714364366 74 -0.010 -3.666 0.020 0.010 -0.368 0.227 0.3713221115 75 -0.010 -3.666 0.020 0.010 -0.368 0.286 0.3711373610 77 -0.010 -3.666 0.020 0.010 -0.368 0.264 0.3710406816 78 -0.010 -3.666 0.020 0.010 -0.368 0.265 0.3710362344 79 -0.010 -3.666 0.020 0.010 -0.368 0.270 0.3710284132 81 -0.010 -3.666 0.020 0.010 -0.368 0.269 0.3710265948 powell nthiter 1: fret = 0.371027 89 0.372 -3.666 0.020 0.010 -0.368 0.269 0.3677543657 90 0.216 -3.666 0.020 0.010 -0.368 0.269 0.3611983663 91 0.200 -3.666 0.020 0.010 -0.368 0.269 0.3611379602 93 0.201 -3.666 0.020 0.010 -0.368 0.269 0.3611379424 102 0.201 -3.645 0.020 0.010 -0.368 0.269 0.3610477201 103 0.201 -3.641 0.020 0.010 -0.368 0.269 0.3610393089 105 0.201 -3.639 0.020 0.010 -0.368 0.269 0.3610383297 113 0.201 -3.639 -0.211 0.010 -0.368 0.269 0.3580703881 114 0.201 -3.639 -0.198 0.010 -0.368 0.269 0.3580703684 115 0.201 -3.639 -0.205 0.010 -0.368 0.269 0.3580615399 124 0.201 -3.639 -0.205 0.108 -0.368 0.269 0.3579650262 125 0.201 -3.639 -0.205 0.064 -0.368 0.269 0.3579081138 127 0.201 -3.639 -0.205 0.044 -0.368 0.269 0.3578437424 129 0.201 -3.639 -0.205 0.045 -0.368 0.269 0.3578431845 131 0.201 -3.639 -0.205 0.046 -0.368 0.269 0.3578429315 138 0.201 -3.639 -0.205 0.046 -0.490 0.269 0.3550162988 140 0.201 -3.639 -0.205 0.046 -0.464 0.269 0.3545768237 142 0.201 -3.639 -0.205 0.046 -0.457 0.269 0.3545389754 143 0.201 -3.639 -0.205 0.046 -0.455 0.269 0.3545330166 144 0.201 -3.639 -0.205 0.046 -0.453 0.269 0.3545316317 154 0.201 -3.639 -0.205 0.046 -0.453 0.276 0.3545067042 155 0.201 -3.639 -0.205 0.046 -0.453 0.278 0.3545052097 powell nthiter 2: fret = 0.354505 165 0.217 -3.639 -0.205 0.046 -0.453 0.278 0.3543073032 175 0.217 -3.664 -0.205 0.046 -0.453 0.278 0.3542699837 179 0.217 -3.669 -0.205 0.046 -0.453 0.278 0.3542697055 180 0.217 -3.667 -0.205 0.046 -0.453 0.278 0.3542696643 188 0.217 -3.667 -0.274 0.046 -0.453 0.278 0.3541764059 189 0.217 -3.667 -0.249 0.046 -0.453 0.278 0.3541163523 190 0.217 -3.667 -0.248 0.046 -0.453 0.278 0.3541137209 191 0.217 -3.667 -0.231 0.046 -0.453 0.278 0.3540883485 195 0.217 -3.667 -0.232 0.046 -0.453 0.278 0.3540880895 203 0.217 -3.667 -0.232 0.089 -0.453 0.278 0.3538251247 204 0.217 -3.667 -0.232 0.088 -0.453 0.278 0.3538230082 206 0.217 -3.667 -0.232 0.086 -0.453 0.278 0.3538213897 217 0.217 -3.667 -0.232 0.086 -0.456 0.278 0.3538181904 226 0.217 -3.667 -0.232 0.086 -0.456 0.343 0.3537339472 227 0.217 -3.667 -0.232 0.086 -0.456 0.317 0.3534689203 228 0.217 -3.667 -0.232 0.086 -0.456 0.313 0.3534510049 230 0.217 -3.667 -0.232 0.086 -0.456 0.310 0.3534465768 231 0.217 -3.667 -0.232 0.086 -0.456 0.309 0.3534460970 233 0.234 -3.694 -0.260 0.126 -0.458 0.340 0.3531670112 powell nthiter 3: fret = 0.353446 240 0.249 -3.667 -0.232 0.086 -0.456 0.309 0.3530048052 242 0.246 -3.667 -0.232 0.086 -0.456 0.309 0.3529946959 252 0.246 -3.701 -0.232 0.086 -0.456 0.309 0.3529502285 254 0.246 -3.688 -0.232 0.086 -0.456 0.309 0.3528733631 256 0.246 -3.689 -0.232 0.086 -0.456 0.309 0.3528723363 265 0.246 -3.689 -0.264 0.086 -0.456 0.309 0.3528359166 266 0.246 -3.689 -0.257 0.086 -0.456 0.309 0.3528047505 267 0.246 -3.689 -0.250 0.086 -0.456 0.309 0.3527876112 269 0.246 -3.689 -0.248 0.086 -0.456 0.309 0.3527847002 270 0.246 -3.689 -0.247 0.086 -0.456 0.309 0.3527844362 278 0.246 -3.689 -0.247 0.103 -0.456 0.309 0.3527091893 280 0.246 -3.689 -0.247 0.098 -0.456 0.309 0.3527002717 292 0.246 -3.689 -0.247 0.098 -0.457 0.309 0.3526978887 301 0.246 -3.689 -0.247 0.098 -0.457 0.328 0.3524668018 302 0.246 -3.689 -0.247 0.098 -0.457 0.338 0.3524410943 303 0.246 -3.689 -0.247 0.098 -0.457 0.337 0.3524406855 powell nthiter 4: fret = 0.352441 312 0.269 -3.689 -0.247 0.098 -0.457 0.337 0.3523712809 313 0.267 -3.689 -0.247 0.098 -0.457 0.337 0.3523567401 314 0.260 -3.689 -0.247 0.098 -0.457 0.337 0.3523318747 315 0.259 -3.689 -0.247 0.098 -0.457 0.337 0.3523315540 323 0.259 -3.659 -0.247 0.098 -0.457 0.337 0.3522363593 324 0.259 -3.664 -0.247 0.098 -0.457 0.337 0.3522017844 325 0.259 -3.670 -0.247 0.098 -0.457 0.337 0.3521880184 326 0.259 -3.669 -0.247 0.098 -0.457 0.337 0.3521878690 335 0.259 -3.669 -0.262 0.098 -0.457 0.337 0.3521540443 337 0.259 -3.669 -0.259 0.098 -0.457 0.337 0.3521517372 347 0.259 -3.669 -0.259 0.109 -0.457 0.337 0.3520896540 348 0.259 -3.669 -0.259 0.110 -0.457 0.337 0.3520881539 368 0.259 -3.669 -0.259 0.110 -0.457 0.355 0.3519621556 369 0.259 -3.669 -0.259 0.110 -0.457 0.357 0.3519607321 372 0.273 -3.649 -0.271 0.122 -0.457 0.377 0.3517687708 powell nthiter 5: fret = 0.351961 416 0.278 -3.663 -0.264 0.119 -0.457 0.357 0.3517381331 428 0.278 -3.663 -0.264 0.119 -0.458 0.357 0.3517379777 438 0.278 -3.663 -0.264 0.119 -0.458 0.371 0.3516685208 439 0.278 -3.663 -0.264 0.119 -0.458 0.370 0.3516678772 441 0.296 -3.657 -0.269 0.127 -0.459 0.383 0.3515505005 448 0.300 -3.656 -0.270 0.129 -0.460 0.386 0.3515465157 449 0.300 -3.656 -0.270 0.129 -0.460 0.386 0.3515464238 powell nthiter 6: fret = 0.351546 462 0.300 -3.656 -0.270 0.129 -0.460 0.389 0.3515378136 463 0.300 -3.656 -0.270 0.129 -0.460 0.392 0.3515335480 464 0.300 -3.656 -0.270 0.129 -0.460 0.393 0.3515333046 474 0.300 -3.660 -0.270 0.129 -0.460 0.393 0.3515256368 484 0.300 -3.660 -0.271 0.129 -0.460 0.393 0.3515222444 485 0.300 -3.660 -0.285 0.129 -0.460 0.393 0.3515214471 487 0.300 -3.660 -0.278 0.129 -0.460 0.393 0.3515105156 498 0.300 -3.660 -0.278 0.136 -0.460 0.393 0.3514909532 510 0.300 -3.660 -0.278 0.136 -0.461 0.393 0.3514901775 517 0.307 -3.658 -0.280 0.139 -0.461 0.398 0.3514822045 518 0.306 -3.658 -0.280 0.139 -0.461 0.397 0.3514820847 523 0.306 -3.658 -0.280 0.139 -0.461 0.397 0.3514820244 524 0.306 -3.658 -0.280 0.139 -0.461 0.397 0.3514820028 526 0.306 -3.658 -0.280 0.139 -0.461 0.397 0.3514819695 powell nthiter 7: fret = 0.351482 538 0.306 -3.658 -0.280 0.139 -0.461 0.398 0.3514806990 539 0.306 -3.658 -0.280 0.139 -0.461 0.400 0.3514794394 552 0.306 -3.657 -0.280 0.139 -0.461 0.401 0.3514789165 563 0.306 -3.657 -0.284 0.139 -0.461 0.401 0.3514729154 564 0.306 -3.657 -0.285 0.139 -0.461 0.401 0.3514720753 574 0.306 -3.657 -0.285 0.144 -0.461 0.401 0.3514663767 575 0.306 -3.657 -0.285 0.143 -0.461 0.401 0.3514659637 576 0.306 -3.657 -0.285 0.142 -0.461 0.401 0.3514657885 595 0.309 -3.656 -0.286 0.143 -0.461 0.403 0.3514645693 598 0.309 -3.656 -0.286 0.143 -0.461 0.403 0.3514645167 Powell done niters = 7 Computing relative cost 0 -25.0 -25.0 -25.0 1.039099 1 -25.0 -25.0 25.0 1.003201 2 -25.0 25.0 -25.0 1.015550 3 -25.0 25.0 25.0 1.036643 4 25.0 -25.0 -25.0 1.070733 5 25.0 -25.0 25.0 1.033145 6 25.0 25.0 -25.0 0.998654 7 25.0 25.0 25.0 1.012095 REL: 8 0.351465 8.209119 1.026140 rel = 0.342511 Number of iterations 7 Min cost was 0.351465 Number of FunctionCalls 607 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.340158 sec Parameters at optimum (transmm) 0.30930 -3.65556 -0.28625 Parameters at optimum (rotdeg) 0.14316 -0.46107 0.40306 Final costs ---------------- Number of surface hits 2108 WM Intensity 1800.2568 +/- 224.1097 Ctx Intensity 1994.3098 +/- 251.8228 Pct Contrast 10.0525 +/- 13.0721 Cost 0.3515 RelCost 0.8534 Reg at min cost was 0.99997 0.00136 -0.00704 1.10286; 0.00705 -0.00744 0.99995 -7.77071; 0.00131 -0.99997 -0.00745 -2.88937; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/bbr.pass1.dat, type = 14 Original Reg 0.99998 -0.00674 -0.00007 0.74362; -0.00000 -0.00995 0.99995 -4.12714; -0.00674 -0.99993 -0.00995 -2.59888; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00000 -0.00810 0.00697 -0.35924; -0.00705 -0.00251 0.00000 3.64357; -0.00805 0.00004 -0.00250 0.29049; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 3.944475 Computing change in rh position Surface-RMS-Diff-mm 3.728999 0.261096 4.264986 mri_segreg done mri_segreg --mov /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/template.nii --init-reg /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/bbr.pass1.dat --out-reg /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/diff2anatorig.bbr.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/diff2anatorig.bbr.dat.mincost --dof 6 --nmax 36 --param /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/diff2anatorig.bbr.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 8.0.0 setenv SUBJECTS_DIR /home/gabriellam/Desktop/prova_tracula/fs cd /home/gabriellam/Desktop/prova_tracula mri_segreg --mov /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/template.nii --init-reg /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/bbr.pass1.dat --out-reg /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/diff2anatorig.bbr.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/diff2anatorig.bbr.dat.mincost --dof 6 --nmax 36 --param /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/diff2anatorig.bbr.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname SN-CZC4487LYX machine x86_64 user gabriellam movvol /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/template.nii regfile /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/tmp.bbregister.96513/bbr.pass1.dat subject 002_S_6652 dof 6 outregfile /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/diff2anatorig.bbr.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1750939062 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99997 0.00136 -0.00704 1.10286; 0.00705 -0.00744 0.99995 -7.77071; 0.00131 -0.99997 -0.00745 -2.88937; 0.00000 0.00000 0.00000 1.00000; Loading mov ExcludeZeroVoxels 1 Reading in targ vol /home/gabriellam/Desktop/prova_tracula/fs/002_S_6652/mri/orig.mgz Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 1.049055 1 -25.0 -25.0 25.0 1.031155 2 -25.0 25.0 -25.0 1.032788 3 -25.0 25.0 25.0 1.042876 4 25.0 -25.0 -25.0 1.030401 5 25.0 -25.0 25.0 1.015761 6 25.0 25.0 -25.0 1.033820 7 25.0 25.0 25.0 1.033808 REL: 8 0.328426 8.269665 1.033708 rel = 0.317716 Initial costs ---------------- Number of surface hits 210684 WM Intensity 1797.2365 +/- 217.8083 Ctx Intensity 1995.4586 +/- 246.7057 Pct Contrast 10.2897 +/- 13.0224 Cost 0.3284 RelCost 0.3177 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.3590 0.3590 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.3554 0.3554 0.0 30 -0.1000 -0.1000 0.0000 -0.1000 0.0000 -0.1000 0.3549 0.3549 0.0 93 -0.1000 0.0000 -0.1000 0.0000 0.0000 -0.1000 0.3536 0.3536 0.0 256 0.0000 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.3536 0.3536 0.0 274 0.0000 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.3534 0.3534 0.0 333 0.0000 0.0000 -0.1000 0.0000 -0.1000 -0.1000 0.3530 0.3530 0.0 337 0.0000 0.0000 -0.1000 0.0000 0.0000 0.0000 0.3522 0.3522 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.3515 0.3515 0.0 Brute Force -------------------------- Min cost was 0.351465 Number of iterations 729 Search time 0.509197 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000000 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.328426 7 -0.071 0.000 0.000 0.000 0.000 0.000 0.3278329499 8 -0.067 0.000 0.000 0.000 0.000 0.000 0.3278253004 9 -0.062 0.000 0.000 0.000 0.000 0.000 0.3278218081 18 -0.062 0.046 0.000 0.000 0.000 0.000 0.3277414610 19 -0.062 0.029 0.000 0.000 0.000 0.000 0.3276821212 20 -0.062 0.028 0.000 0.000 0.000 0.000 0.3276815828 21 -0.062 0.026 0.000 0.000 0.000 0.000 0.3276813419 31 -0.062 0.026 0.005 0.000 0.000 0.000 0.3276765934 32 -0.062 0.026 0.008 0.000 0.000 0.000 0.3276762272 41 -0.062 0.026 0.008 0.002 0.000 0.000 0.3276547069 42 -0.062 0.026 0.008 0.031 0.000 0.000 0.3275580950 44 -0.062 0.026 0.008 0.026 0.000 0.000 0.3275530475 53 -0.062 0.026 0.008 0.026 -0.119 0.000 0.3263163415 54 -0.062 0.026 0.008 0.026 -0.109 0.000 0.3263007754 55 -0.062 0.026 0.008 0.026 -0.107 0.000 0.3263004137 63 -0.062 0.026 0.008 0.026 -0.107 0.150 0.3241506128 64 -0.062 0.026 0.008 0.026 -0.107 0.151 0.3241502961 65 -0.062 0.026 0.008 0.026 -0.107 0.152 0.3241502767 powell nthiter 1: fret = 0.324150 75 0.024 0.026 0.008 0.026 -0.107 0.152 0.3225952844 76 0.043 0.026 0.008 0.026 -0.107 0.152 0.3225450527 78 0.041 0.026 0.008 0.026 -0.107 0.152 0.3225447592 87 0.041 0.062 0.008 0.026 -0.107 0.152 0.3224452364 88 0.041 0.053 0.008 0.026 -0.107 0.152 0.3224282484 89 0.041 0.052 0.008 0.026 -0.107 0.152 0.3224282226 98 0.041 0.052 0.010 0.026 -0.107 0.152 0.3224273295 108 0.041 0.052 0.010 0.047 -0.107 0.152 0.3223651636 110 0.041 0.052 0.010 0.045 -0.107 0.152 0.3223647754 118 0.041 0.052 0.010 0.045 -0.181 0.152 0.3220396692 119 0.041 0.052 0.010 0.045 -0.162 0.152 0.3219984359 121 0.041 0.052 0.010 0.045 -0.160 0.152 0.3219981588 131 0.041 0.052 0.010 0.045 -0.160 0.192 0.3218946835 132 0.041 0.052 0.010 0.045 -0.160 0.186 0.3218895603 133 0.041 0.052 0.010 0.045 -0.160 0.185 0.3218894193 134 0.041 0.052 0.010 0.045 -0.160 0.184 0.3218893345 138 0.145 0.077 0.013 0.065 -0.213 0.216 0.3215944466 144 0.105 0.067 0.012 0.057 -0.193 0.204 0.3214536318 146 0.105 0.067 0.012 0.057 -0.193 0.204 0.3214536122 152 0.106 0.067 0.012 0.058 -0.193 0.204 0.3214536101 powell nthiter 2: fret = 0.321454 160 0.106 0.067 0.012 0.058 -0.193 0.220 0.3214518464 161 0.106 0.067 0.012 0.058 -0.193 0.212 0.3214455837 181 0.106 0.068 -0.006 0.058 -0.193 0.212 0.3214169860 182 0.106 0.068 -0.005 0.058 -0.193 0.212 0.3214168516 191 0.106 0.068 -0.005 0.063 -0.193 0.212 0.3214143088 192 0.106 0.068 -0.005 0.062 -0.193 0.212 0.3214139893 201 0.106 0.068 -0.005 0.062 -0.196 0.212 0.3214115513 202 0.106 0.068 -0.005 0.062 -0.197 0.212 0.3214114547 210 0.110 0.070 -0.005 0.063 -0.200 0.214 0.3214106254 211 0.109 0.069 -0.005 0.062 -0.199 0.213 0.3214102473 214 0.109 0.069 -0.005 0.062 -0.199 0.213 0.3214102390 powell nthiter 3: fret = 0.321410 243 0.109 0.069 -0.010 0.062 -0.199 0.213 0.3214095092 244 0.109 0.069 -0.008 0.062 -0.199 0.213 0.3214092037 255 0.109 0.069 -0.008 0.063 -0.199 0.213 0.3214091776 277 0.109 0.069 -0.008 0.063 -0.199 0.213 0.3214091262 278 0.109 0.069 -0.008 0.063 -0.199 0.213 0.3214091058 287 0.109 0.069 -0.008 0.063 -0.199 0.213 0.3214090705 288 0.109 0.069 -0.009 0.064 -0.199 0.214 0.3214090514 289 0.109 0.069 -0.009 0.064 -0.199 0.214 0.3214089859 292 0.109 0.069 -0.009 0.064 -0.199 0.214 0.3214089719 294 0.109 0.069 -0.009 0.064 -0.199 0.214 0.3214089650 295 0.109 0.069 -0.009 0.064 -0.199 0.214 0.3214089599 powell nthiter 4: fret = 0.321409 Powell done niters = 4 Computing relative cost 0 -25.0 -25.0 -25.0 1.050689 1 -25.0 -25.0 25.0 1.032020 2 -25.0 25.0 -25.0 1.032628 3 -25.0 25.0 25.0 1.042043 4 25.0 -25.0 -25.0 1.030300 5 25.0 -25.0 25.0 1.015644 6 25.0 25.0 -25.0 1.033652 7 25.0 25.0 25.0 1.033948 REL: 8 0.321409 8.270923 1.033865 rel = 0.310881 Number of iterations 4 Min cost was 0.321409 Number of FunctionCalls 359 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 7.431782 sec Parameters at optimum (transmm) 0.10943 0.06935 -0.00894 Parameters at optimum (rotdeg) 0.06366 -0.19917 0.21352 Final costs ---------------- Number of surface hits 210684 WM Intensity 1796.9038 +/- 217.4417 Ctx Intensity 1996.4560 +/- 244.2868 Pct Contrast 10.3737 +/- 12.8981 Cost 0.3214 RelCost 0.3177 Reg at min cost was 0.99993 0.00486 -0.01075 1.25130; 0.01078 -0.00631 0.99992 -7.69394; 0.00479 -0.99997 -0.00637 -2.90310; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/diff2anatorig.bbr.dat, type = 14 Original Reg 0.99997 0.00136 -0.00704 1.10286; 0.00705 -0.00744 0.99995 -7.77071; 0.00131 -0.99997 -0.00745 -2.88937; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00004 -0.00350 0.00370 -0.14843; -0.00372 -0.00113 0.00003 -0.07677; -0.00348 -0.00000 -0.00109 0.01372; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.182318 Computing change in rh position Surface-RMS-Diff-mm 0.208888 0.082479 0.424722 mri_segreg done MinCost: 0.321409 1796.903841 1996.455983 10.373724 tkregister2_cmdl --mov /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/lowb.nii.gz --reg /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/diff2anatorig.bbr.dat --noedit --ltaout /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/diff2anatorig.bbr.lta INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/lowb.nii.gz reg file /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/diff2anatorig.bbr.dat LoadVol 0 ZeroCRAS 0 8.0.0 Diagnostic Level -1 ---- Input registration matrix -------- 0.99993 0.00486 -0.01075 1.25130; 0.01078 -0.00631 0.99992 -7.69394; 0.00479 -0.99997 -0.00637 -2.90310; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /home/gabriellam/Desktop/prova_tracula/fs/002_S_6652/mri/orig.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 /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/lowb.nii.gz Tmov: -------------------- -2.00000 0.00000 0.00000 116.00000; 0.00000 0.00000 2.00000 -81.00000; 0.00000 -2.00000 0.00000 116.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.99993 0.00486 -0.01075 1.25130; 0.01078 -0.00631 0.99992 -7.69394; 0.00479 -0.99997 -0.00637 -2.90310; 0.00000 0.00000 0.00000 1.00000; Determinant 1 subject = 002_S_6652 RegMat --------------------------- 0.99993 0.00486 -0.01075 1.25130; 0.01078 -0.00631 0.99992 -7.69394; 0.00479 -0.99997 -0.00637 -2.90310; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at mar 24 giu 2025, 10:52:56, CEST Ended at mar 24 giu 2025, 10:53:20, CEST BBR-Run-Time-Sec 24 bbregister Done To check results, run: tkregisterfv --mov /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/lowb.nii.gz --reg /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/diff2anatorig.bbr.lta --surfs --sd /home/gabriellam/Desktop/prova_tracula/fs lta_convert --inlta /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/diff2anatorig.bbr.lta --invert --outlta /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2diff.bbr.lta 8.0.0 --inlta: /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/diff2anatorig.bbr.lta input LTA transform. --invert: will invert transform. --outlta: /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2diff.bbr.lta output LTA. LTA read, type : 1 0.99993 -0.00479 0.01078 202.17401; 0.00486 0.99997 -0.00631 241.42270; -0.01075 0.00637 0.99992 546.13513; 0.00000 0.00000 0.00000 1.00000; Writing LTA to file /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2diff.bbr.lta... lta_convert successful. mri_convert /home/gabriellam/Desktop/prova_tracula/fs/002_S_6652/mri/aparc+aseg.mgz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/aparc+aseg.nii.gz mri_convert /home/gabriellam/Desktop/prova_tracula/fs/002_S_6652/mri/aparc+aseg.mgz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/aparc+aseg.nii.gz reading from /home/gabriellam/Desktop/prova_tracula/fs/002_S_6652/mri/aparc+aseg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/aparc+aseg.nii.gz... mri_binarize --i /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/aparc+aseg.nii.gz --min .5 --dilate 4 --erode 2 --o /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/aparc+aseg_mask.nii.gz 8.0.0 cwd /home/gabriellam/Desktop/prova_tracula cmdline mri_binarize --i /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/aparc+aseg.nii.gz --min .5 --dilate 4 --erode 2 --o /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/aparc+aseg_mask.nii.gz sysname Linux hostname SN-CZC4487LYX machine x86_64 user gabriellam input /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/aparc+aseg.nii.gz frame 0 nErode3d 0 nErode2d 0 output /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/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 Found 1365309 values in range Dilating 4 voxels in 3d Eroding 2 voxels using 3 ErodeEdges=0 Counting number of voxels in first frame Found 1629834 voxels in final mask Writing output to /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/aparc+aseg_mask.nii.gz Count: 1629834 1629834.000000 16777216 9.714568 mri_binarize done mri_binarize --i /home/gabriellam/Desktop/prova_tracula/fs/002_S_6652/mri/aparc+aseg.mgz --match 2 41 7 46 172 177 77 --o /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/White-Matter.nii.gz 8.0.0 cwd /home/gabriellam/Desktop/prova_tracula cmdline mri_binarize --i /home/gabriellam/Desktop/prova_tracula/fs/002_S_6652/mri/aparc+aseg.mgz --match 2 41 7 46 172 177 77 --o /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/White-Matter.nii.gz sysname Linux hostname SN-CZC4487LYX machine x86_64 user gabriellam input /home/gabriellam/Desktop/prova_tracula/fs/002_S_6652/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/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 Found 346986 values in range Counting number of voxels in first frame Found 346986 voxels in final mask Writing output to /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/White-Matter.nii.gz Count: 346986 346986.000000 16777216 2.068198 mri_binarize done mri_binarize --i /home/gabriellam/Desktop/prova_tracula/fs/002_S_6652/mri/aparc+aseg.mgz --match 2 41 7 46 172 177 77 28 60 16 173 174 # 175 --o /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/White-Matter++.nii.gz 8.0.0 cwd /home/gabriellam/Desktop/prova_tracula cmdline mri_binarize --i /home/gabriellam/Desktop/prova_tracula/fs/002_S_6652/mri/aparc+aseg.mgz --match 2 41 7 46 172 177 77 28 60 16 173 174 # 175 --o /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/White-Matter++.nii.gz sysname Linux hostname SN-CZC4487LYX machine x86_64 user gabriellam input /home/gabriellam/Desktop/prova_tracula/fs/002_S_6652/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/White-Matter++.nii.gz Binarizing based on matching values nMatch 14 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 0 13 175 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 15782159 values in range Counting number of voxels in first frame Found 15782159 voxels in final mask Writing output to /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/White-Matter++.nii.gz Count: 15782159 15782159.000000 16777216 94.068998 mri_binarize done mri_convert -at /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2diff.bbr.lta -rt nearest /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/aparc+aseg.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/diff/aparc+aseg.bbr.nii.gz mri_convert -at /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2diff.bbr.lta -rt nearest /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/aparc+aseg.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/diff/aparc+aseg.bbr.nii.gz reading from /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/aparc+aseg.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: Reading transformation from file /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2diff.bbr.lta... Reading transform with LTAreadEx() INFO: Applying transformation from file /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2diff.bbr.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 0.99993 0.00486 -0.01075 -197.46538; -0.00479 0.99997 0.00637 -243.92285; 0.01078 -0.00631 0.99992 -546.74719; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 0) writing to /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/diff/aparc+aseg.bbr.nii.gz... mri_convert -at /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2diff.bbr.lta -rt nearest /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/aparc+aseg_mask.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/diff/aparc+aseg_mask.bbr.nii.gz mri_convert -at /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2diff.bbr.lta -rt nearest /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/aparc+aseg_mask.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/diff/aparc+aseg_mask.bbr.nii.gz reading from /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/aparc+aseg_mask.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: Reading transformation from file /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2diff.bbr.lta... Reading transform with LTAreadEx() INFO: Applying transformation from file /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2diff.bbr.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 0.99993 0.00486 -0.01075 -197.46538; -0.00479 0.99997 0.00637 -243.92285; 0.01078 -0.00631 0.99992 -546.74719; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 0) writing to /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/diff/aparc+aseg_mask.bbr.nii.gz... mri_convert -at /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2diff.bbr.lta -rt nearest /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/White-Matter.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/diff/White-Matter.bbr.nii.gz mri_convert -at /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2diff.bbr.lta -rt nearest /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/White-Matter.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/diff/White-Matter.bbr.nii.gz reading from /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/White-Matter.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: Reading transformation from file /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2diff.bbr.lta... Reading transform with LTAreadEx() INFO: Applying transformation from file /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2diff.bbr.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 0.99993 0.00486 -0.01075 -197.46538; -0.00479 0.99997 0.00637 -243.92285; 0.01078 -0.00631 0.99992 -546.74719; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 0) writing to /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/diff/White-Matter.bbr.nii.gz... mri_convert -at /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2diff.bbr.lta -rt nearest /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/White-Matter++.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/diff/White-Matter++.bbr.nii.gz mri_convert -at /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2diff.bbr.lta -rt nearest /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/White-Matter++.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/diff/White-Matter++.bbr.nii.gz reading from /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/White-Matter++.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: Reading transformation from file /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2diff.bbr.lta... Reading transform with LTAreadEx() INFO: Applying transformation from file /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2diff.bbr.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 0.99993 0.00486 -0.01075 -197.46538; -0.00479 0.99997 0.00637 -243.92285; 0.01078 -0.00631 0.99992 -546.74719; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 0) writing to /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/diff/White-Matter++.bbr.nii.gz... mri_convert -at /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2diff.bbr.lta -rt nearest /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/diff/aparc+aseg+thalnuc.bbr.nii.gz mri_convert -at /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2diff.bbr.lta -rt nearest /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/diff/aparc+aseg+thalnuc.bbr.nii.gz reading from /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: Reading transformation from file /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2diff.bbr.lta... Reading transform with LTAreadEx() INFO: Applying transformation from file /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2diff.bbr.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 0.99993 0.00486 -0.01075 -197.46538; -0.00479 0.99997 0.00637 -243.92285; 0.01078 -0.00631 0.99992 -546.74719; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 0) writing to /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/diff/aparc+aseg+thalnuc.bbr.nii.gz... fslstats -t /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi.nii.gz -k /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/diff/White-Matter++.bbr.nii.gz -m -s | awk '{print $1/$2}' > /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dwi_snr.txt mri_convert -at /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/diff2anatorig.bbr.lta -rt nearest /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/diff/lowb_brain_mask.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz mri_convert -at /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/diff2anatorig.bbr.lta -rt nearest /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/diff/lowb_brain_mask.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz INFO: using NIfTI-1 sform (sform_code=1) reading from /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/diff/lowb_brain_mask.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) INFO: Reading transformation from file /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/diff2anatorig.bbr.lta... Reading transform with LTAreadEx() INFO: Applying transformation from file /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/diff2anatorig.bbr.lta... --------------------------------- INFO: Transform Matrix (linear_vox_to_vox) 1.99986 0.00959 -0.02155 13.47922; -0.02149 -0.01273 -1.99984 203.29047; -0.00973 1.99994 -0.01263 10.12158; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 0) writing to /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz... #------------------------------------- #@# Tensor fit mar 24 giu 2025, 10:53:54, CEST dtifit -k /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/data.nii.gz -m /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/bvecs -b /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/bvals -o /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dtifit 0 116 0 116 0 81 0 slices processed 1 slices processed 2 slices processed 3 slices processed 4 slices processed 5 slices processed 6 slices processed 7 slices processed 8 slices processed 9 slices processed 10 slices processed 11 slices processed 12 slices processed 13 slices processed 14 slices processed 15 slices processed 16 slices processed 17 slices processed 18 slices processed 19 slices processed 20 slices processed 21 slices processed 22 slices processed 23 slices processed 24 slices processed 25 slices processed 26 slices processed 27 slices processed 28 slices processed 29 slices processed 30 slices processed 31 slices processed 32 slices processed 33 slices processed 34 slices processed 35 slices processed 36 slices processed 37 slices processed 38 slices processed 39 slices processed 40 slices processed 41 slices processed 42 slices processed 43 slices processed 44 slices processed 45 slices processed 46 slices processed 47 slices processed 48 slices processed 49 slices processed 50 slices processed 51 slices processed 52 slices processed 53 slices processed 54 slices processed 55 slices processed 56 slices processed 57 slices processed 58 slices processed 59 slices processed 60 slices processed 61 slices processed 62 slices processed 63 slices processed 64 slices processed 65 slices processed 66 slices processed 67 slices processed 68 slices processed 69 slices processed 70 slices processed 71 slices processed 72 slices processed 73 slices processed 74 slices processed 75 slices processed 76 slices processed 77 slices processed 78 slices processed 79 slices processed 80 slices processed #------------------------------------- #@# Inter-subject registration mar 24 giu 2025, 10:53:59, CEST mri_convert /home/gabriellam/Desktop/prova_tracula/fs/002_S_6652/mri/brain.mgz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/brain_anat_orig.nii.gz mri_convert /home/gabriellam/Desktop/prova_tracula/fs/002_S_6652/mri/brain.mgz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/brain_anat_orig.nii.gz reading from /home/gabriellam/Desktop/prova_tracula/fs/002_S_6652/mri/brain.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/brain_anat_orig.nii.gz... orientLAS /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/brain_anat_orig.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/brain_anat.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 mri_convert -oni 256 -onj 256 -onk 256 -oid -1 0 0 -ojd 0 1 0 -okd 0 0 1 -oc 203 256 520 -rt nearest /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/brain_anat_orig.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/brain_anat.nii.gz mri_convert -oni 256 -onj 256 -onk 256 -oid -1 0 0 -ojd 0 1 0 -okd 0 0 1 -oc 203 256 520 -rt nearest /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/brain_anat_orig.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/brain_anat.nii.gz reading from /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/brain_anat_orig.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) Reslicing using nearest writing to /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/brain_anat.nii.gz... flirt -in /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/brain_anat.nii.gz -ref /home/gabriellam/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/brain_anat_mni.nii.gz -omat /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anat2mni.mat -cost corratio lta_convert --infsl /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anat2mni.mat --src /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/brain_anat.nii.gz --trg /home/gabriellam/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz --outlta /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anat2mni.lta 8.0.0 --infsl: /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anat2mni.mat input FSL transform. --src: /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/brain_anat.nii.gz src image (geometry). --trg: /home/gabriellam/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz trg image (geometry). --outlta: /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anat2mni.lta output LTA. INFO: using NIfTI-1 sform (sform_code=4) FSLOUTPUTTYPE NIFTI_GZ fsl2TkReg: mov det = -1, ref det = -1 LTA read, type : 1 1.05065 0.01392 -0.02809 -200.99460; -0.02355 1.03612 0.38200 -463.35965; 0.02294 -0.34224 1.20110 -549.76233; 0.00000 0.00000 0.00000 1.00000; Writing LTA to file /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anat2mni.lta... lta_convert successful. tkregister2 --mov /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/brain_anat_orig.nii.gz --targ /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/brain_anat.nii.gz --regheader --noedit --reg /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2anat.dat --ltaout /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2anat.lta tkregister_tcl /usr/local/freesurfer/8.0.0//tktools/tkregister2.tcl target volume /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/brain_anat.nii.gz movable volume /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/brain_anat_orig.nii.gz reg file /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2anat.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ Diagnostic Level -1 INFO: loading target /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/brain_anat.nii.gz INFO: target does not conform to COR format, so I'm going to reslice to COR. This will not affect the final registration. 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 /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/brain_anat_orig.nii.gz Tmov: -------------------- -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; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.00000 0.00000 0.00000 -0.06610; 0.00000 1.00000 0.00000 -0.50000; 0.00000 0.00000 1.00000 0.47522; 0.00000 0.00000 0.00000 1.00000; --------------------------------------- ---- Input registration matrix -------- 1.00000 0.00000 0.00000 -0.06610; 0.00000 1.00000 0.00000 -0.50000; 0.00000 0.00000 1.00000 0.47522; 0.00000 0.00000 0.00000 1.00000; Determinant 1 subject = subject-unknown RegMat --------------------------- 1.00000 0.00000 0.00000 -0.06610; 0.00000 0.00000 -1.00000 -0.50000; 0.00000 1.00000 0.00000 0.47522; 0.00000 0.00000 0.00000 1.00000; mri_concatenate_lta /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2anat.lta /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anat2mni.lta /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2mni.lta Read individual LTAs Combining the two LTAs to get a RAS-to-RAS from src of LTA1 to dst of LTA2... Writing combined LTA to file /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2mni.lta... mri_concatenate_lta successful. lta_convert --inlta /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2mni.lta --invert --outlta /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/mni2anatorig.lta 8.0.0 --inlta: /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2mni.lta input LTA transform. --invert: will invert transform. --outlta: /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/mni2anatorig.lta output LTA. LTA read, type : 1 1.05065 0.01392 -0.02809 -200.99460; -0.02355 1.03612 0.38200 -463.35965; 0.02294 -0.34224 1.20110 -549.76239; 0.00000 0.00000 0.00000 1.00000; Writing LTA to file /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/mni2anatorig.lta... lta_convert successful. mri_concatenate_lta /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/diff2anatorig.bbr.lta /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2mni.lta /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/diff2mni.bbr.lta Read individual LTAs Combining the two LTAs to get a RAS-to-RAS from src of LTA1 to dst of LTA2... Writing combined LTA to file /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/diff2mni.bbr.lta... mri_concatenate_lta successful. lta_convert --inlta /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/diff2mni.bbr.lta --invert --outlta /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/mni2diff.bbr.lta 8.0.0 --inlta: /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/diff2mni.bbr.lta input LTA transform. --invert: will invert transform. --outlta: /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/mni2diff.bbr.lta output LTA. LTA read, type : 1 1.05094 0.00870 -0.01685 -0.56107; -0.02261 1.03863 0.37518 -9.35110; 0.00837 -0.33469 1.20342 28.21631; 0.00000 0.00000 0.00000 1.00000; Writing LTA to file /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/mni2diff.bbr.lta... lta_convert successful. mri_convert -at /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2mni.lta -rt nearest /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/aparc+aseg.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/mni/aparc+aseg.nii.gz mri_convert -at /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2mni.lta -rt nearest /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/aparc+aseg.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/mni/aparc+aseg.nii.gz reading from /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/aparc+aseg.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: Reading transformation from file /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2mni.lta... Reading transform with LTAreadEx() INFO: Applying transformation from file /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2mni.lta... --------------------------------- INFO: Transform Matrix (linear_vox_to_vox) 1.05065 -0.02809 -0.01392 -40.43967; 0.02355 -0.38200 1.03612 35.34348; -0.02294 -1.20110 -0.34224 263.59882; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 0) writing to /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/mni/aparc+aseg.nii.gz... mri_convert -at /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2mni.lta -rt nearest /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/aparc+aseg_mask.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/mni/aparc+aseg_mask.nii.gz mri_convert -at /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2mni.lta -rt nearest /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/aparc+aseg_mask.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/mni/aparc+aseg_mask.nii.gz reading from /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/aparc+aseg_mask.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: Reading transformation from file /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2mni.lta... Reading transform with LTAreadEx() INFO: Applying transformation from file /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2mni.lta... --------------------------------- INFO: Transform Matrix (linear_vox_to_vox) 1.05065 -0.02809 -0.01392 -40.43967; 0.02355 -0.38200 1.03612 35.34348; -0.02294 -1.20110 -0.34224 263.59882; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 0) writing to /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/mni/aparc+aseg_mask.nii.gz... mri_convert -at /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2mni.lta -rt nearest /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/White-Matter.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/mni/White-Matter.nii.gz mri_convert -at /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2mni.lta -rt nearest /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/White-Matter.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/mni/White-Matter.nii.gz reading from /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/White-Matter.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: Reading transformation from file /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2mni.lta... Reading transform with LTAreadEx() INFO: Applying transformation from file /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2mni.lta... --------------------------------- INFO: Transform Matrix (linear_vox_to_vox) 1.05065 -0.02809 -0.01392 -40.43967; 0.02355 -0.38200 1.03612 35.34348; -0.02294 -1.20110 -0.34224 263.59882; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 0) writing to /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/mni/White-Matter.nii.gz... mri_convert -at /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2mni.lta -rt nearest /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/White-Matter++.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/mni/White-Matter++.nii.gz mri_convert -at /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2mni.lta -rt nearest /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/White-Matter++.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/mni/White-Matter++.nii.gz reading from /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/White-Matter++.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: Reading transformation from file /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2mni.lta... Reading transform with LTAreadEx() INFO: Applying transformation from file /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2mni.lta... --------------------------------- INFO: Transform Matrix (linear_vox_to_vox) 1.05065 -0.02809 -0.01392 -40.43967; 0.02355 -0.38200 1.03612 35.34348; -0.02294 -1.20110 -0.34224 263.59882; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 0) writing to /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/mni/White-Matter++.nii.gz... mri_convert -at /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2mni.lta -rt nearest /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/mni/aparc+aseg+thalnuc.nii.gz mri_convert -at /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2mni.lta -rt nearest /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/mni/aparc+aseg+thalnuc.nii.gz reading from /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: Reading transformation from file /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2mni.lta... Reading transform with LTAreadEx() INFO: Applying transformation from file /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/anatorig2mni.lta... --------------------------------- INFO: Transform Matrix (linear_vox_to_vox) 1.05065 -0.02809 -0.01392 -40.43967; 0.02355 -0.38200 1.03612 35.34348; -0.02294 -1.20110 -0.34224 263.59882; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 0) writing to /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/mni/aparc+aseg+thalnuc.nii.gz... mri_convert -at /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/diff2mni.bbr.lta -rt nearest /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/diff/lowb_brain_mask.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/mni/lowb_brain_mask.bbr.nii.gz mri_convert -at /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/diff2mni.bbr.lta -rt nearest /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/diff/lowb_brain_mask.nii.gz /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/mni/lowb_brain_mask.bbr.nii.gz INFO: using NIfTI-1 sform (sform_code=1) reading from /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/diff/lowb_brain_mask.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) INFO: Reading transformation from file /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/diff2mni.bbr.lta... Reading transform with LTAreadEx() INFO: Applying transformation from file /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/diff2mni.bbr.lta... --------------------------------- INFO: Transform Matrix (linear_vox_to_vox) 2.10189 -0.01740 0.03370 -32.12867; 0.04523 2.07727 0.75036 -31.50981; -0.01674 -0.66937 2.40683 15.65302; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 0) writing to /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/mni/lowb_brain_mask.bbr.nii.gz... #------------------------------------- #@# Priors mar 24 giu 2025, 10:54:28, CEST /usr/local/freesurfer/8.0.0//bin/dmri_train --outdir /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/mni --out acomm_avg16_mni_bbr cc.bodyc_avg16_mni_bbr cc.bodyp_avg16_mni_bbr cc.bodypf_avg16_mni_bbr cc.bodypm_avg16_mni_bbr cc.bodyt_avg16_mni_bbr cc.genu_avg16_mni_bbr cc.rostrum_avg16_mni_bbr cc.splenium_avg16_mni_bbr mcp_avg16_mni_bbr lh.af_avg16_mni_bbr rh.af_avg16_mni_bbr lh.ar_avg16_mni_bbr rh.ar_avg16_mni_bbr lh.atr_avg16_mni_bbr rh.atr_avg16_mni_bbr lh.cbd_avg16_mni_bbr rh.cbd_avg16_mni_bbr lh.cbv_avg16_mni_bbr rh.cbv_avg16_mni_bbr lh.cst_avg16_mni_bbr rh.cst_avg16_mni_bbr lh.emc_avg16_mni_bbr rh.emc_avg16_mni_bbr lh.fat_avg16_mni_bbr rh.fat_avg16_mni_bbr lh.fx_avg16_mni_bbr rh.fx_avg16_mni_bbr lh.ilf_avg16_mni_bbr rh.ilf_avg16_mni_bbr lh.mlf_avg16_mni_bbr rh.mlf_avg16_mni_bbr lh.or_avg16_mni_bbr rh.or_avg16_mni_bbr lh.slf1_avg16_mni_bbr rh.slf1_avg16_mni_bbr lh.slf2_avg16_mni_bbr rh.slf2_avg16_mni_bbr lh.slf3_avg16_mni_bbr rh.slf3_avg16_mni_bbr lh.uf_avg16_mni_bbr rh.uf_avg16_mni_bbr --slist /tmp/tmp.cqWPp8.16.002_S_6652.txt --trk mni/acomm.bbr.prep.trk mni/cc.bodyc.bbr.prep.trk mni/cc.bodyp.bbr.prep.trk mni/cc.bodypf.bbr.prep.trk mni/cc.bodypm.bbr.prep.trk mni/cc.bodyt.bbr.prep.trk mni/cc.genu.bbr.prep.trk mni/cc.rostrum.bbr.prep.trk mni/cc.splenium.bbr.prep.trk mni/mcp.bbr.prep.trk mni/lh.af.bbr.prep.trk mni/rh.af.bbr.prep.trk mni/lh.ar.bbr.prep.trk mni/rh.ar.bbr.prep.trk mni/lh.atr.bbr.prep.trk mni/rh.atr.bbr.prep.trk mni/lh.cbd.bbr.prep.trk mni/rh.cbd.bbr.prep.trk mni/lh.cbv.bbr.prep.trk mni/rh.cbv.bbr.prep.trk mni/lh.cst.bbr.prep.trk mni/rh.cst.bbr.prep.trk mni/lh.emc.bbr.prep.trk mni/rh.emc.bbr.prep.trk mni/lh.fat.bbr.prep.trk mni/rh.fat.bbr.prep.trk mni/lh.fx.bbr.prep.trk mni/rh.fx.bbr.prep.trk mni/lh.ilf.bbr.prep.trk mni/rh.ilf.bbr.prep.trk mni/lh.mlf.bbr.prep.trk mni/rh.mlf.bbr.prep.trk mni/lh.or.bbr.prep.trk mni/rh.or.bbr.prep.trk mni/lh.slf1.bbr.prep.trk mni/rh.slf1.bbr.prep.trk mni/lh.slf2.bbr.prep.trk mni/rh.slf2.bbr.prep.trk mni/lh.slf3.bbr.prep.trk mni/rh.slf3.bbr.prep.trk mni/lh.uf.bbr.prep.trk mni/rh.uf.bbr.prep.trk --seg mni/aparc+aseg+thalnuc.nii.gz --cmask mni/cortex+2mm+crblm.nii.gz --lmask 0 0 0 0 0 0 0 0 0 0 0 0 10 49 10 49 0 0 0 0 16 16 0 0 0 0 28 60 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --bmask /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/mni/aparc+aseg_mask.nii.gz --fa /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dtifit_FA.nii.gz --cptdir /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/diff --reg /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/mni2diff.bbr.lta --ncpts 7 8 9 7 7 12 5 5 7 7 9 9 4 4 4 4 7 7 5 5 7 7 7 7 5 5 9 9 8 8 7 7 5 5 7 7 8 8 6 6 7 7 --trunc --aprior 8.0.0 cwd /home/gabriellam/Desktop/prova_tracula cmdline /usr/local/freesurfer/8.0.0//bin/dmri_train --outdir /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/mni --out acomm_avg16_mni_bbr cc.bodyc_avg16_mni_bbr cc.bodyp_avg16_mni_bbr cc.bodypf_avg16_mni_bbr cc.bodypm_avg16_mni_bbr cc.bodyt_avg16_mni_bbr cc.genu_avg16_mni_bbr cc.rostrum_avg16_mni_bbr cc.splenium_avg16_mni_bbr mcp_avg16_mni_bbr lh.af_avg16_mni_bbr rh.af_avg16_mni_bbr lh.ar_avg16_mni_bbr rh.ar_avg16_mni_bbr lh.atr_avg16_mni_bbr rh.atr_avg16_mni_bbr lh.cbd_avg16_mni_bbr rh.cbd_avg16_mni_bbr lh.cbv_avg16_mni_bbr rh.cbv_avg16_mni_bbr lh.cst_avg16_mni_bbr rh.cst_avg16_mni_bbr lh.emc_avg16_mni_bbr rh.emc_avg16_mni_bbr lh.fat_avg16_mni_bbr rh.fat_avg16_mni_bbr lh.fx_avg16_mni_bbr rh.fx_avg16_mni_bbr lh.ilf_avg16_mni_bbr rh.ilf_avg16_mni_bbr lh.mlf_avg16_mni_bbr rh.mlf_avg16_mni_bbr lh.or_avg16_mni_bbr rh.or_avg16_mni_bbr lh.slf1_avg16_mni_bbr rh.slf1_avg16_mni_bbr lh.slf2_avg16_mni_bbr rh.slf2_avg16_mni_bbr lh.slf3_avg16_mni_bbr rh.slf3_avg16_mni_bbr lh.uf_avg16_mni_bbr rh.uf_avg16_mni_bbr --slist /tmp/tmp.cqWPp8.16.002_S_6652.txt --trk mni/acomm.bbr.prep.trk mni/cc.bodyc.bbr.prep.trk mni/cc.bodyp.bbr.prep.trk mni/cc.bodypf.bbr.prep.trk mni/cc.bodypm.bbr.prep.trk mni/cc.bodyt.bbr.prep.trk mni/cc.genu.bbr.prep.trk mni/cc.rostrum.bbr.prep.trk mni/cc.splenium.bbr.prep.trk mni/mcp.bbr.prep.trk mni/lh.af.bbr.prep.trk mni/rh.af.bbr.prep.trk mni/lh.ar.bbr.prep.trk mni/rh.ar.bbr.prep.trk mni/lh.atr.bbr.prep.trk mni/rh.atr.bbr.prep.trk mni/lh.cbd.bbr.prep.trk mni/rh.cbd.bbr.prep.trk mni/lh.cbv.bbr.prep.trk mni/rh.cbv.bbr.prep.trk mni/lh.cst.bbr.prep.trk mni/rh.cst.bbr.prep.trk mni/lh.emc.bbr.prep.trk mni/rh.emc.bbr.prep.trk mni/lh.fat.bbr.prep.trk mni/rh.fat.bbr.prep.trk mni/lh.fx.bbr.prep.trk mni/rh.fx.bbr.prep.trk mni/lh.ilf.bbr.prep.trk mni/rh.ilf.bbr.prep.trk mni/lh.mlf.bbr.prep.trk mni/rh.mlf.bbr.prep.trk mni/lh.or.bbr.prep.trk mni/rh.or.bbr.prep.trk mni/lh.slf1.bbr.prep.trk mni/rh.slf1.bbr.prep.trk mni/lh.slf2.bbr.prep.trk mni/rh.slf2.bbr.prep.trk mni/lh.slf3.bbr.prep.trk mni/rh.slf3.bbr.prep.trk mni/lh.uf.bbr.prep.trk mni/rh.uf.bbr.prep.trk --seg mni/aparc+aseg+thalnuc.nii.gz --cmask mni/cortex+2mm+crblm.nii.gz --lmask 0 0 0 0 0 0 0 0 0 0 0 0 10 49 10 49 0 0 0 0 16 16 0 0 0 0 28 60 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --bmask /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/mni/aparc+aseg_mask.nii.gz --fa /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dtifit_FA.nii.gz --cptdir /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/diff --reg /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/mni2diff.bbr.lta --ncpts 7 8 9 7 7 12 5 5 7 7 9 9 4 4 4 4 7 7 5 5 7 7 7 7 5 5 9 9 8 8 7 7 5 5 7 7 8 8 6 6 7 7 --trunc --aprior sysname Linux hostname SN-CZC4487LYX machine x86_64 user gabriellam Output directory: /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/mni Output directory in test subject's space: /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/diff Training subject directory list: /tmp/tmp.cqWPp8.16.002_S_6652.txt Location of streamline files relative to base: mni/acomm.bbr.prep.trk mni/cc.bodyc.bbr.prep.trk mni/cc.bodyp.bbr.prep.trk mni/cc.bodypf.bbr.prep.trk mni/cc.bodypm.bbr.prep.trk mni/cc.bodyt.bbr.prep.trk mni/cc.genu.bbr.prep.trk mni/cc.rostrum.bbr.prep.trk mni/cc.splenium.bbr.prep.trk mni/mcp.bbr.prep.trk mni/lh.af.bbr.prep.trk mni/rh.af.bbr.prep.trk mni/lh.ar.bbr.prep.trk mni/rh.ar.bbr.prep.trk mni/lh.atr.bbr.prep.trk mni/rh.atr.bbr.prep.trk mni/lh.cbd.bbr.prep.trk mni/rh.cbd.bbr.prep.trk mni/lh.cbv.bbr.prep.trk mni/rh.cbv.bbr.prep.trk mni/lh.cst.bbr.prep.trk mni/rh.cst.bbr.prep.trk mni/lh.emc.bbr.prep.trk mni/rh.emc.bbr.prep.trk mni/lh.fat.bbr.prep.trk mni/rh.fat.bbr.prep.trk mni/lh.fx.bbr.prep.trk mni/rh.fx.bbr.prep.trk mni/lh.ilf.bbr.prep.trk mni/rh.ilf.bbr.prep.trk mni/lh.mlf.bbr.prep.trk mni/rh.mlf.bbr.prep.trk mni/lh.or.bbr.prep.trk mni/rh.or.bbr.prep.trk mni/lh.slf1.bbr.prep.trk mni/rh.slf1.bbr.prep.trk mni/lh.slf2.bbr.prep.trk mni/rh.slf2.bbr.prep.trk mni/lh.slf3.bbr.prep.trk mni/rh.slf3.bbr.prep.trk mni/lh.uf.bbr.prep.trk mni/rh.uf.bbr.prep.trk Location of cortex masks relative to base: mni/cortex+2mm+crblm.nii.gz Label ID's from aparc+aseg to add to cortex mask: 0 0 0 0 0 0 0 0 0 0 0 0 10 49 10 49 0 0 0 0 16 16 0 0 0 0 28 60 0 0 0 0 10 49 0 0 0 0 0 0 0 0 Location of aparc+aseg's relative to base: mni/aparc+aseg+thalnuc.nii.gz Brain mask for output subject: /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/mni/aparc+aseg_mask.nii.gz FA map for output subject: /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dtifit_FA.nii.gz Affine registration from atlas to base for output subject: /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/mni2diff.bbr.lta Number of control points for initial spline: 7 8 9 7 7 12 5 5 7 7 9 9 4 4 4 4 7 7 5 5 7 7 7 7 5 5 9 9 8 8 7 7 5 5 7 7 8 8 6 6 7 7 Exclude previously chosen center streamlines: 0 Use truncated streamlines: 1 Compute priors on underlying anatomy: 1 Compute priors on shape: 0 Loading segmentation from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1001/mni/aparc+aseg+thalnuc.nii.gz INFO: using NIfTI-1 sform (sform_code=1) Loading cortex mask from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1001/mni/cortex+2mm+crblm.nii.gz INFO: using NIfTI-1 sform (sform_code=1) Loading segmentation from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1006/mni/aparc+aseg+thalnuc.nii.gz INFO: using NIfTI-1 sform (sform_code=1) Loading cortex mask from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1006/mni/cortex+2mm+crblm.nii.gz INFO: using NIfTI-1 sform (sform_code=1) Loading segmentation from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1007/mni/aparc+aseg+thalnuc.nii.gz INFO: using NIfTI-1 sform (sform_code=1) Loading cortex mask from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1007/mni/cortex+2mm+crblm.nii.gz INFO: using NIfTI-1 sform (sform_code=1) Loading segmentation from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1008/mni/aparc+aseg+thalnuc.nii.gz INFO: using NIfTI-1 sform (sform_code=1) Loading cortex mask from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1008/mni/cortex+2mm+crblm.nii.gz INFO: using NIfTI-1 sform (sform_code=1) Loading segmentation from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1009/mni/aparc+aseg+thalnuc.nii.gz INFO: using NIfTI-1 sform (sform_code=1) Loading cortex mask from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1009/mni/cortex+2mm+crblm.nii.gz INFO: using NIfTI-1 sform (sform_code=1) Loading segmentation from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1010/mni/aparc+aseg+thalnuc.nii.gz INFO: using NIfTI-1 sform (sform_code=1) Loading cortex mask from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1010/mni/cortex+2mm+crblm.nii.gz INFO: using NIfTI-1 sform (sform_code=1) Loading segmentation from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1011/mni/aparc+aseg+thalnuc.nii.gz INFO: using NIfTI-1 sform (sform_code=1) Loading cortex mask from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1011/mni/cortex+2mm+crblm.nii.gz INFO: using NIfTI-1 sform (sform_code=1) Loading segmentation from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1012/mni/aparc+aseg+thalnuc.nii.gz INFO: using NIfTI-1 sform (sform_code=1) Loading cortex mask from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1012/mni/cortex+2mm+crblm.nii.gz INFO: using NIfTI-1 sform (sform_code=1) Loading segmentation from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1013/mni/aparc+aseg+thalnuc.nii.gz INFO: using NIfTI-1 sform (sform_code=1) Loading cortex mask from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1013/mni/cortex+2mm+crblm.nii.gz INFO: using NIfTI-1 sform (sform_code=1) Loading segmentation from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1015/mni/aparc+aseg+thalnuc.nii.gz INFO: using NIfTI-1 sform (sform_code=1) Loading cortex mask from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1015/mni/cortex+2mm+crblm.nii.gz INFO: using NIfTI-1 sform (sform_code=1) Loading segmentation from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1016/mni/aparc+aseg+thalnuc.nii.gz INFO: using NIfTI-1 sform (sform_code=1) Loading cortex mask from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1016/mni/cortex+2mm+crblm.nii.gz INFO: using NIfTI-1 sform (sform_code=1) Loading segmentation from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1017/mni/aparc+aseg+thalnuc.nii.gz INFO: using NIfTI-1 sform (sform_code=1) Loading cortex mask from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1017/mni/cortex+2mm+crblm.nii.gz INFO: using NIfTI-1 sform (sform_code=1) Loading segmentation from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1019/mni/aparc+aseg+thalnuc.nii.gz INFO: using NIfTI-1 sform (sform_code=1) Loading cortex mask from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1019/mni/cortex+2mm+crblm.nii.gz INFO: using NIfTI-1 sform (sform_code=1) Loading segmentation from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1021/mni/aparc+aseg+thalnuc.nii.gz INFO: using NIfTI-1 sform (sform_code=1) Loading cortex mask from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1021/mni/cortex+2mm+crblm.nii.gz INFO: using NIfTI-1 sform (sform_code=1) Loading segmentation from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1023/mni/aparc+aseg+thalnuc.nii.gz INFO: using NIfTI-1 sform (sform_code=1) Loading cortex mask from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1023/mni/cortex+2mm+crblm.nii.gz INFO: using NIfTI-1 sform (sform_code=1) Loading segmentation from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1024/mni/aparc+aseg+thalnuc.nii.gz INFO: using NIfTI-1 sform (sform_code=1) Loading cortex mask from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1024/mni/cortex+2mm+crblm.nii.gz INFO: using NIfTI-1 sform (sform_code=1) Loading brain mask of output subject from /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dlabel/mni/aparc+aseg_mask.nii.gz Loading FA map of output subject from /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/dtifit_FA.nii.gz INFO: using NIfTI-1 sform (sform_code=1) Loading affine registration from /home/gabriellam/Desktop/prova_tracula/trc/002_S_6652/dmri/xfms/mni2diff.bbr.lta LTA registration format detected FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -1, ref det = -8 Loading streamlines from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1001/mni/acomm.bbr.prep.trk Pre-sorted training .trk file detected Loading streamlines from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1006/mni/acomm.bbr.prep.trk Pre-sorted training .trk file detected Loading streamlines from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1007/mni/acomm.bbr.prep.trk Pre-sorted training .trk file detected Loading streamlines from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1008/mni/acomm.bbr.prep.trk Pre-sorted training .trk file detected Loading streamlines from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1009/mni/acomm.bbr.prep.trk Pre-sorted training .trk file detected Loading streamlines from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1010/mni/acomm.bbr.prep.trk Pre-sorted training .trk file detected Loading streamlines from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1011/mni/acomm.bbr.prep.trk Pre-sorted training .trk file detected Loading streamlines from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1012/mni/acomm.bbr.prep.trk Pre-sorted training .trk file detected Loading streamlines from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1013/mni/acomm.bbr.prep.trk Pre-sorted training .trk file detected Loading streamlines from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1015/mni/acomm.bbr.prep.trk Pre-sorted training .trk file detected Loading streamlines from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1016/mni/acomm.bbr.prep.trk Pre-sorted training .trk file detected Loading streamlines from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1017/mni/acomm.bbr.prep.trk Pre-sorted training .trk file detected Loading streamlines from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1019/mni/acomm.bbr.prep.trk Pre-sorted training .trk file detected Loading streamlines from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1021/mni/acomm.bbr.prep.trk Pre-sorted training .trk file detected Loading streamlines from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1023/mni/acomm.bbr.prep.trk Pre-sorted training .trk file detected Loading streamlines from /usr/local/freesurfer/8.0.0//trctrain/hcp/mgh_1024/mni/acomm.bbr.prep.trk Pre-sorted training .trk file detected INFO: Rejected 0 streamlines for straying off mask INFO: Rejected 0 streamlines for reversing direction INFO: Have 717 total streamlines (min/mean/max length: 97/115/132) Processing pathway 1 of 42... INFO: Have 717 non-truncated streamlines (min/mean/max length: 97/115/132) Computing path histograms INFO: Total streamline volume is 14216 voxels Finding outlier streamlines Updating streamline distance ranking INFO: Split streamlines into 34 segments Computing prior on underlying anatomy (all streamlines) Selecting 7 points on center streamline INFO: Minimum allowable distance between dominant points is 11 INFO: Minimum allowable curvature at a dominant point is 0.0587567 INFO: Points where local peaks in curvature occur are 53 131 43 (curv = 0.0624143) 53 124 50 (curv = 0.078706) 56 119 59 (curv = 0.121317) 68 127 64 (curv = 0.0599172) 81 129 68 (curv = 0.0612147) 94 127 68 (curv = 0.0673169) 103 127 64 (curv = 0.111611) 116 118 62 (curv = 0.107492) 123 117 55 (curv = 0.109063) 126 124 45 (curv = 0.0803153) INFO: Intermediate dominant points are 56 145 38 56 119 59 68 127 64 81 129 68 103 127 64 123 117 55 122 140 35 INFO: Final dominant points are 56 145 38 56 119 59 69 127 64 81 129 68 103 127 64 123 117 55 122 140 35 WARN: Defaulting to equidistant control points INFO: Selected control points are 56 145 38 52 125 49 66 126 63 87 127 68 107 125 64 124 119 53 122 140 35 INFO: Distances between consecutive points are 23 20 22 20 21 28 INFO: Selected control points in test subject's space are 42 73 30 40 63 32 47 61 37 57 61 39 66 60 37 74 59 32 73 71 28 INFO: Distances between consecutive points in test subject's space are 10 9 10 9 9 13 WARN: Could not find satisfactory control point fit - try 1 Selecting 7 points on center streamline INFO: Minimum allowable distance between dominant points is 10 INFO: Minimum allowable curvature at a dominant point is 0.060296 INFO: Points where local peaks in curvature occur are 52 127 47 (curv = 0.0919104) 58 119 58 (curv = 0.137857) 77 130 66 (curv = 0.0738735) 88 126 68 (curv = 0.0991007) 102 128 64 (curv = 0.0783511) 116 120 61 (curv = 0.0610511) 122 117 57 (curv = 0.147883) 127 122 47 (curv = 0.098641) INFO: Intermediate dominant points are 56 145 36 58 119 58 69 127 64 88 126 68 102 128 64 122 117 57 121 139 35 INFO: Final dominant points are 56 145 36 58 119 58 77 130 66 88 126 68 102 128 64 122 117 57 121 139 35 WARN: Defaulting to equidistant control points INFO: Selected control points are 56 145 36 53 125 48 68 126 64 89 126 68 109 125 63 126 120 51 121 139 35 INFO: Distances between consecutive points are 24 22 21 21 21 25 INFO: Selected control points in test subject's space are 42 74 29 41 63 31 48 61 37 58 60 39 67 61 37 75 60 32 73 70 28 INFO: Distances between consecutive points in test subject's space are 11 9 10 9 9 11 WARN: Could not find satisfactory control point fit - try 2 Selecting 7 points on center streamline INFO: Minimum allowable distance between dominant points is 10 INFO: Minimum allowable curvature at a dominant point is 0.0556584 INFO: Points where local peaks in curvature occur are 52 133 42 (curv = 0.0638586) 55 121 53 (curv = 0.095738) 62 122 61 (curv = 0.0628582) 66 124 63 (curv = 0.0604113) 77 129 66 (curv = 0.066961) 80 129 68 (curv = 0.0696913) 90 127 69 (curv = 0.0623888) 103 127 64 (curv = 0.0606503) 113 123 63 (curv = 0.0615669) 121 117 58 (curv = 0.085444) 127 120 52 (curv = 0.0967067) INFO: Intermediate dominant points are 52 144 38 55 121 53 67 125 64 80 129 68 109 125 63 127 120 52 120 138 36 INFO: Final dominant points are 52 144 38 55 121 53 69 126 64 80 129 68 116 120 61 127 120 52 120 138 36 WARN: Defaulting to equidistant control points INFO: Selected control points are 52 144 38 52 127 47 65 124 63 84 128 68 105 126 63 125 119 54 120 138 36 INFO: Distances between consecutive points are 19 21 20 22 23 27 INFO: Selected control points in test subject's space are 40 73 30 40 64 31 46 61 37 55 61 39 65 61 37 75 59 33 73 70 28 INFO: Distances between consecutive points in test subject's space are 9 9 9 10 11 12 WARN: Could not find satisfactory control point fit - try 3 Selecting 7 points on center streamline INFO: Minimum allowable distance between dominant points is 10 INFO: Minimum allowable curvature at a dominant point is 0.0559287 INFO: Points where local peaks in curvature occur are 57 121 55 (curv = 0.0821615) 62 121 62 (curv = 0.102226) 75 127 65 (curv = 0.0587408) 80 128 67 (curv = 0.0660087) 87 126 70 (curv = 0.104106) 99 127 65 (curv = 0.0649333) 116 118 61 (curv = 0.0766163) 123 117 56 (curv = 0.161709) INFO: Intermediate dominant points are 52 144 38 54 126 48 62 121 62 87 126 70 99 127 65 123 117 56 125 134 38 INFO: Final dominant points are 52 144 38 55 123 51 62 121 62 87 126 70 99 127 65 123 117 56 125 134 38 WARN: Defaulting to equidistant control points INFO: Selected control points are 52 144 38 54 126 48 69 124 63 88 126 70 107 125 64 124 118 56 125 134 38 INFO: Distances between consecutive points are 21 21 20 20 20 24 INFO: Selected control points in test subject's space are 40 73 30 41 64 31 48 61 37 57 60 40 66 60 37 74 58 33 75 68 29 INFO: Distances between consecutive points in test subject's space are 9 10 10 9 9 11 WARN: Could not find satisfactory control point fit - try 4 Selecting 7 points on center streamline INFO: Minimum allowable distance between dominant points is 10 INFO: Minimum allowable curvature at a dominant point is 0.0606589 INFO: Points where local peaks in curvature occur are 52 125 47 (curv = 0.117534) 55 121 54 (curv = 0.086549) 62 122 62 (curv = 0.0677871) 71 129 64 (curv = 0.0794482) 82 129 68 (curv = 0.0684446) 88 127 68 (curv = 0.0744544) 103 127 64 (curv = 0.0653696) 113 121 63 (curv = 0.0768125) 126 117 54 (curv = 0.100204) 127 122 44 (curv = 0.0811123) INFO: Intermediate dominant points are 61 137 34 52 125 47 71 129 64 91 127 68 103 127 64 126 117 54 122 139 34 INFO: Final dominant points are 61 137 34 52 125 47 71 129 64 92 127 68 103 127 64 126 117 54 122 139 34 WARN: Defaulting to equidistant control points INFO: Selected control points are 61 137 34 53 123 50 70 128 64 89 127 68 110 123 63 127 119 50 122 139 34 INFO: Distances between consecutive points are 23 23 19 22 22 26 INFO: Selected control points in test subject's space are 44 70 27 41 62 32 48 62 38 58 61 39 68 60 37 76 59 31 73 70 28 INFO: Distances between consecutive points in test subject's space are 10 9 10 10 10 12 WARN: Could not find satisfactory control point fit - try 5 Selecting 7 points on center streamline INFO: Minimum allowable distance between dominant points is 10 INFO: Minimum allowable curvature at a dominant point is 0.0568541 INFO: Points where local peaks in curvature occur are 50 126 48 (curv = 0.112842) 53 120 54 (curv = 0.147599) 62 122 62 (curv = 0.0778598) 74 129 66 (curv = 0.0817401) 85 126 69 (curv = 0.0887861) 104 125 63 (curv = 0.0608636) 113 120 63 (curv = 0.0606978) 123 116 56 (curv = 0.109647) 127 121 50 (curv = 0.0652087) INFO: Intermediate dominant points are 53 141 36 53 120 54 67 125 63 85 126 69 104 125 63 123 116 56 122 139 34 INFO: Final dominant points are 53 141 36 53 120 54 73 129 65 85 126 69 104 125 63 123 116 56 122 139 34 WARN: Defaulting to equidistant control points INFO: Selected control points are 53 141 36 51 124 50 66 125 63 88 126 69 108 124 63 126 119 52 122 139 34 INFO: Distances between consecutive points are 22 20 23 21 22 27 INFO: Selected control points in test subject's space are 41 72 29 40 62 32 47 61 37 57 60 39 67 60 37 75 59 32 73 70 28 INFO: Distances between consecutive points in test subject's space are 10 9 10 10 9 12 WARN: Could not find satisfactory control point fit - try 6 Selecting 7 points on center streamline INFO: Minimum allowable distance between dominant points is 10 INFO: Minimum allowable curvature at a dominant point is 0.0583988 INFO: Points where local peaks in curvature occur are 52 125 46 (curv = 0.114059) 59 119 60 (curv = 0.151918) 75 129 66 (curv = 0.0698443) 90 126 68 (curv = 0.0725018) 102 126 64 (curv = 0.107196) 116 118 62 (curv = 0.0652751) 122 116 56 (curv = 0.098429) 126 121 46 (curv = 0.0716425) INFO: Intermediate dominant points are 60 136 36 59 119 60 75 129 66 90 126 68 102 126 64 122 116 56 123 139 34 INFO: Final dominant points are 60 136 36 59 119 60 75 129 66 91 126 68 102 126 64 122 116 56 123 139 34 WARN: Defaulting to equidistant control points INFO: Selected control points are 60 136 36 53 123 50 70 127 64 90 126 68 110 122 64 125 120 49 123 139 34 INFO: Distances between consecutive points are 20 22 20 21 21 24 INFO: Selected control points in test subject's space are 44 70 28 41 62 32 48 62 38 58 60 39 68 59 37 75 60 31 74 70 28 INFO: Distances between consecutive points in test subject's space are 9 9 10 10 9 10 WARN: Could not find satisfactory control point fit - try 7 Selecting 7 points on center streamline INFO: Minimum allowable distance between dominant points is 10 INFO: Minimum allowable curvature at a dominant point is 0.0552051 INFO: Points where local peaks in curvature occur are 53 132 42 (curv = 0.0553229) 53 122 51 (curv = 0.09522) 59 119 60 (curv = 0.0862954) 72 126 67 (curv = 0.0725406) 76 128 67 (curv = 0.0804444) 89 126 69 (curv = 0.0621606) 102 127 64 (curv = 0.0931208) [...goes on forever..]