External Email - Use Caution Hello to everyone!
I'm trying to run the preprocessing step of tracula to my subject and I keep getting the following error: mv: cannot stat '/home/ioannis/FFF/KORO/T1_nii/trc/Subj_koro/dmri/dwi_orig_las.1.bvecs': No such file or directory As a matter of fact this file was never created during the process. My files are in nifti format and I try to reconstruct the corticospinal tracts. I attach my configuration file and the log file. Thanks in advance for your help! Ioannis P.
dmrirc_nii
Description: Binary data
Κυρ 16 Ιαν 2022 12:19:38 μμ EET
/home/ioannis/FFF/KORO/T1_nii
/usr/local/freesurfer/7.2.0/bin/trac-all
-prep -c /home/ioannis/FFF/KORO/T1_nii/dmrirc_nii
Subject Subj_koro
SUBJECTS_DIR /home/ioannis/FFF/KORO/T1_nii
FREESURFER_HOME /usr/local/freesurfer/7.2.0
Actual FREESURFER_HOME /usr/local/freesurfer/7.2.0
build-stamp.txt: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
ioannis
ioannis-Latitude-E6230
Linux ioannis-Latitude-E6230 5.11.0-46-generic #51~20.04.1-Ubuntu SMP Fri Jan 7 06:51:40 UTC 2022 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 65536 kbytes
maxproc 15081
maxlocks unlimited
maxsignal 15081
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 3926440 1108092 1059136 216872 1759212 2346316
Swap: 2097148 2836 2094312
########################################
Program versions:
trac-all 7.2.0
mri_convert --all-info
ProgramName: mri_convert ProgramArguments: mri_convert --all-info ProgramVersion: 7.2.0 TimeStamp: 2022/01/16-10:19:38-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: ioannis Machine: ioannis-Latitude-E6230 Platform: Linux PlatformVersion: 5.11.0-46-generic CompilerName: GCC CompilerVersion: 4.8.5
FLIRT version 6.0
bbregister 7.2.0
mri_cvs_register 7.2.0
ProgramName: dmri_motion ProgramArguments: /usr/local/freesurfer/7.2.0/bin/dmri_motion --all-info ProgramVersion: 7.2.0 TimeStamp: 2022/01/16-10:19:38-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: ioannis Machine: ioannis-Latitude-E6230 Platform: Linux PlatformVersion: 5.11.0-46-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: dmri_train ProgramArguments: /usr/local/freesurfer/7.2.0/bin/dmri_train --all-info ProgramVersion: 7.2.0 TimeStamp: 2022/01/16-10:19:38-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: ioannis Machine: ioannis-Latitude-E6230 Platform: Linux PlatformVersion: 5.11.0-46-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: dmri_paths ProgramArguments: /usr/local/freesurfer/7.2.0/bin/dmri_paths --all-info ProgramVersion: 7.2.0 TimeStamp: 2022/01/16-10:19:39-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: ioannis Machine: ioannis-Latitude-E6230 Platform: Linux PlatformVersion: 5.11.0-46-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: dmri_pathstats ProgramArguments: /usr/local/freesurfer/7.2.0/bin/dmri_pathstats --all-info ProgramVersion: 7.2.0 TimeStamp: 2022/01/16-10:19:39-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: ioannis Machine: ioannis-Latitude-E6230 Platform: Linux PlatformVersion: 5.11.0-46-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: dmri_mergepaths ProgramArguments: /usr/local/freesurfer/7.2.0/bin/dmri_mergepaths --all-info ProgramVersion: 7.2.0 TimeStamp: 2022/01/16-10:19:39-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: ioannis Machine: ioannis-Latitude-E6230 Platform: Linux PlatformVersion: 5.11.0-46-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: dmri_group ProgramArguments: /usr/local/freesurfer/7.2.0/bin/dmri_group --all-info ProgramVersion: 7.2.0 TimeStamp: 2022/01/16-10:19:39-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: ioannis Machine: ioannis-Latitude-E6230 Platform: Linux PlatformVersion: 5.11.0-46-generic CompilerName: GCC CompilerVersion: 4.8.5
New invocation of trac-preproc
ioannis
ioannis-Latitude-E6230
Linux ioannis-Latitude-E6230 5.11.0-46-generic #51~20.04.1-Ubuntu SMP Fri Jan 7 06:51:40 UTC 2022 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 65536 kbytes
maxproc 15081
maxlocks unlimited
maxsignal 15081
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 3926440 1110440 1044320 216852 1771680 2343944
Swap: 2097148 2836 2094312
#-------------------------------------
/usr/local/freesurfer/7.2.0/bin/trac-preproc
#-------------------------------------
#@# Image corrections Κυρ 16 Ιαν 2022 12:19:39 μμ EET
rm -f /home/ioannis/FFF/KORO/T1_nii/trc/Subj_koro/dmri/dwi_orig.1.bvals /home/ioannis/FFF/KORO/T1_nii/trc/Subj_koro/dmri/dwi_orig.1.bvecs
mri_convert --bvec-voxel /home/ioannis/FFF/KORO/T1_nii//DWI_nii/DWI.nii.gz /home/ioannis/FFF/KORO/T1_nii/trc/Subj_koro/dmri/dwi_orig.1.nii.gz
mri_convert --bvec-voxel /home/ioannis/FFF/KORO/T1_nii//DWI_nii/DWI.nii.gz /home/ioannis/FFF/KORO/T1_nii/trc/Subj_koro/dmri/dwi_orig.1.nii.gz
reading from /home/ioannis/FFF/KORO/T1_nii//DWI_nii/DWI.nii.gz...
TR=7693.49, 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/ioannis/FFF/KORO/T1_nii/trc/Subj_koro/dmri/dwi_orig.1.nii.gz...
rm -f /home/ioannis/FFF/KORO/T1_nii/trc/Subj_koro/dmri/dwi_orig.1.bvals.tmp /home/ioannis/FFF/KORO/T1_nii/trc/Subj_koro/dmri/dwi_orig.1.bvecs.tmp
mv -f /home/ioannis/FFF/KORO/T1_nii/trc/Subj_koro/dmri/dwi_orig.1.bvecs.tmp /home/ioannis/FFF/KORO/T1_nii/trc/Subj_koro/dmri/dwi_orig.1.bvecs
mv -f /home/ioannis/FFF/KORO/T1_nii/trc/Subj_koro/dmri/dwi_orig.1.bvals.tmp /home/ioannis/FFF/KORO/T1_nii/trc/Subj_koro/dmri/dwi_orig.1.bvals
orientLAS /home/ioannis/FFF/KORO/T1_nii/trc/Subj_koro/dmri/dwi_orig.1.nii.gz /home/ioannis/FFF/KORO/T1_nii/trc/Subj_koro/dmri/dwi_orig_las.1.nii.gz
INFO: input image orientation is LAS
INFO: input image determinant is -6.25
mri_convert -oni 192 -onj 192 -onk 55 -oid -1 0 0 -ojd 0 1 0 -okd 0 0 1 -oc -1 7 -31 -rt nearest /home/ioannis/FFF/KORO/T1_nii/trc/Subj_koro/dmri/dwi_orig.1.nii.gz /home/ioannis/FFF/KORO/T1_nii/trc/Subj_koro/dmri/dwi_orig_las.1.nii.gz
mri_convert -oni 192 -onj 192 -onk 55 -oid -1 0 0 -ojd 0 1 0 -okd 0 0 1 -oc -1 7 -31 -rt nearest /home/ioannis/FFF/KORO/T1_nii/trc/Subj_koro/dmri/dwi_orig.1.nii.gz /home/ioannis/FFF/KORO/T1_nii/trc/Subj_koro/dmri/dwi_orig_las.1.nii.gz
reading from /home/ioannis/FFF/KORO/T1_nii/trc/Subj_koro/dmri/dwi_orig.1.nii.gz...
TR=7693.49, 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/ioannis/FFF/KORO/T1_nii/trc/Subj_koro/dmri/dwi_orig_las.1.nii.gz...
mv -f /home/ioannis/FFF/KORO/T1_nii/trc/Subj_koro/dmri/dwi_orig_las.1.nii.gz /home/ioannis/FFF/KORO/T1_nii/trc/Subj_koro/dmri/dwi_orig_las.nii.gz
mv -f /home/ioannis/FFF/KORO/T1_nii/trc/Subj_koro/dmri/dwi_orig_las.1.bvecs /home/ioannis/FFF/KORO/T1_nii/trc/Subj_koro/dmri/dwi_orig_las.bvecs
mv: cannot stat '/home/ioannis/FFF/KORO/T1_nii/trc/Subj_koro/dmri/dwi_orig_las.1.bvecs': No such file or directory
Linux ioannis-Latitude-E6230 5.11.0-46-generic #51~20.04.1-Ubuntu SMP Fri Jan 7 06:51:40 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Κυρ 16 Ιαν 2022 12:19:54 μμ EET
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