External Email - Use Caution Dear TRACULA experts
I try to run TRACULA FS7.2 on a Linux machine and get the following error (see below). A similar problem has already been reported in the archives, but I found no solution. https://secure-web.cisco.com/15ekCi1WQB-CkH0WPGgECXGvPn99_mRmsow_C5M9nEA423BRbW-FKtNsZUbezZE_QDLB9tTrAhEngv6e3pZzRpvDIkIm6KXSCKMpikqqr8I7UzDhYNp9r4WMD_cNPQ1H9iJM_mZEjcL74q2XaK_BJMKcDCUR2IEVhTB14V-0-KDoDCIvf8avZH8sAQdlpf1AtWVaBOzP_a_q2ytmsXQq_z-VTqwl4kZhDQUh3pe3qM0Xq2I8WgvFw4OeT6omPBozJ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg71032.html Because the file "dwi_orig_las.1.bvals“ was renamed to „dwi_orig_las.bvals“ earlier in the run mv -f /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.1.bvals /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.bvals it cannot be found by awk and as a result, I guess, the index.txt file is empty and therefore eddy_openmp terminated. How can I fix this problem? The terminal output, log and config files are attached. Thank you for any advise in advance Regards Jürgen —————— error ———— awk: fatal: cannot open file `/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.1.bvals' for reading (No such file or directory) eddy_openmp --imain=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.nii.gz --mask=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/lowb_orig_las_brain_mask.nii.gz --bvecs=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.bvecs --bvals=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.bvals --acqp=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/acqp.txt --index=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/index.txt --data_is_shelled --out=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi EddyInputError: Error when attempting to read --index file /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/index.txt Terminating program Linux upd-159253 4.15.0-147-lowlatency #151-Ubuntu SMP PREEMPT Fri Jun 18 20:06:19 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Wed Oct 27 13:41:49 CEST 2021 upd-159253:/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test> ——————
upd-159253:/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test>
trac-all -prep -c
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/tracula_config_IPS_all_example.txt
INFO: SUBJECTS_DIR is
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_FS_subjects
INFO: Diffusion root is
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720
Actual FREESURFER_HOME /usr/local/freesurfer
trac-preproc -c
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/scripts/dmrirc.local
-log
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/scripts/trac-all.log
-cmd
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/scripts/trac-all.cmd
#-------------------------------------
/usr/local/freesurfer/bin/trac-preproc
#-------------------------------------
#@# Image corrections Wed Oct 27 13:41:01 CEST 2021
rm -f
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.bvals
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.bvecs
mri_convert --bvec-voxel
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Prepared_DICOMs_FS720//IPS_CO_007/DTI/32863323.dcm
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.nii.gz
mri_convert --bvec-voxel
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Prepared_DICOMs_FS720//IPS_CO_007/DTI/32863323.dcm
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.nii.gz
reading from
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Prepared_DICOMs_FS720//IPS_CO_007/DTI/32863323.dcm...
Getting Series No
INFO: Found 125 files in
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Prepared_DICOMs_FS720//IPS_CO_007/DTI
INFO: Scanning for Series Number 27
Scanning Directory
INFO: found 123 files in series
INFO: loading series header info.
RunNo = 26
WARNING: Run 1 appears to be truncated
Files Found: 123, Files Expected (lRep+1): 1
FileName
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Prepared_DICOMs_FS720//IPS_CO_007/DTI/32875290.dcm
Identification
NumarisVer syngo MR E11
ScannerModel Prisma_fit
PatientName ANONYMOUS
Date and time
StudyDate 20190410
StudyTime 080641.596000
SeriesTime 090254.994000
AcqTime 090128.605000
Acquisition parameters
PulseSeq *ep_b0
Protocol DQS_SCAN
PhEncDir COL
EchoNo 1
FlipAngle 90
EchoTime 82
InversionTime -1
RepetitionTime 4400
PhEncFOV 211
ReadoutFOV 211
Image information
RunNo 26
SeriesNo 27
ImageNo 1
NImageRows 768
NImageCols 768
NFrames 123
SliceArraylSize 64
IsMosaic 1
ImgPos 903.8222 801.9736 -66.6789
VolRes 2.1979 2.1979 2.2000
VolDim 96 96 64
Vc -0.9973 0.0723 0.0120
Vr -0.0715 -0.9958 0.0566
Vs 0.0160 0.0556 0.9983
VolCenter 0.0000 0.0000 0.0000
TransferSyntaxUID 1.2.840.10008.1.2.1
INFO: sorting.
INFO: ( 96 96 64), nframes = 123, ismosaic=1
sdfi->UseSliceScaleFactor 0
INFO: rescale not needed
datatype = 4, short=4, float=3
Could not parse NUMARIS version string syngo MR E11
found in dicom tag 18,1020 (len = 3 != 6)
Repetition Time = 4400, TR = 4400 ms
PE Dir COL COL
AutoAlign matrix detected
AutoAlign Matrix ---------------------
1.00000 0.00000 0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000;
0.00000 0.00000 1.00000 0.00000;
0.00000 0.00000 0.00000 1.00000;
FileName
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Prepared_DICOMs_FS720//IPS_CO_007/DTI/32875290.dcm
Identification
NumarisVer syngo MR E11
ScannerModel Prisma_fit
PatientName ANONYMOUS
Date and time
StudyDate 20190410
StudyTime 080641.596000
SeriesTime 090254.994000
AcqTime 090128.605000
Acquisition parameters
PulseSeq *ep_b0
Protocol DQS_SCAN
PhEncDir COL
EchoNo 1
FlipAngle 90
EchoTime 82
InversionTime -1
RepetitionTime 4400
PhEncFOV 211
ReadoutFOV 211
Image information
RunNo 26
SeriesNo 27
ImageNo 1
NImageRows 768
NImageCols 768
NFrames 123
SliceArraylSize 64
IsMosaic 1
ImgPos 114.5128 119.9261 -16.0192
VolRes 2.1979 2.1979 2.2000
VolDim 96 96 64
Vc -0.9973 0.0723 0.0120
Vr -0.0715 -0.9958 0.0566
Vs 0.0160 0.0556 0.9983
VolCenter 2.8832 26.4046 61.5000
TransferSyntaxUID 1.2.840.10008.1.2.1
UseSliceScaleFactor 0 (slice 0: 1)
IsDWI = 1
sagrev = 0, correv =0, trarev = 0
Vs = 0.0160358 0.0555939 0.998325
INFO: no Siemens slice order reversal detected (good!).
TR=4400.00, TE=82.00, TI=-1.00, flip angle=90.00
i_ras = (-0.997313, 0.0722762, 0.0119947)
j_ras = (-0.0714883, -0.995834, 0.0566035)
k_ras = (0.0160358, 0.0555939, 0.998325)
writing to
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.nii.gz...
Saving bvals and bvecs
mv -f
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.voxel_space.bvecs
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.bvecs
mri_probedicom --i
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Prepared_DICOMs_FS720//IPS_CO_007/DTI/32863323.dcm
>>
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dcminfo.dat
rm -f
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.bvals.tmp
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.bvecs.tmp
mv -f
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.bvecs.tmp
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.bvecs
mv -f
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.bvals.tmp
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.bvals
orientLAS
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.nii.gz
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.1.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 10.6278
mri_convert -oni 96 -onj 96 -onk 64 -oid -0.997313 0.0722762 0.0119947 -ojd
0.0714883 0.995834 -0.0566035 -okd 0.0160358 0.0555939 0.998325 -oc 3.04032
28.5934 61.3756 -rt nearest
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.nii.gz
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.1.nii.gz
mri_convert -oni 96 -onj 96 -onk 64 -oid -0.997313 0.0722762 0.0119947 -ojd
0.0714883 0.995834 -0.0566035 -okd 0.0160358 0.0555939 0.998325 -oc 3.04032
28.5934 61.3756 -rt nearest
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.nii.gz
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.1.nii.gz
normalizing out_i_direction: (-0.997313, 0.0722762, 0.0119947) -> (-0.997313,
0.0722762, 0.0119947)
normalizing out_j_direction: (0.0714883, 0.995834, -0.0566035) -> (0.0714883,
0.995834, -0.0566035)
normalizing out_k_direction: (0.0160358, 0.0555939, 0.998325) -> (0.0160358,
0.0555939, 0.998325)
reading from
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.nii.gz...
TR=4400.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.997313, 0.0722762, 0.0119947)
j_ras = (-0.0714883, -0.995834, 0.0566035)
k_ras = (0.0160358, 0.0555939, 0.998325)
Reslicing using nearest
writing to
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.1.nii.gz...
INFO: found
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.bvals,
copying
INFO: found
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig.1.bvecs,
converting to LAS
mv -f
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.1.nii.gz
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.nii.gz
mv -f
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.1.bvecs
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.bvecs
mv -f
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.1.bvals
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.bvals
mri_convert --frame 0
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.nii.gz
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/lowb_orig_las.nii.gz
mri_convert --frame 0
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.nii.gz
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/lowb_orig_las.nii.gz
reading from
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.nii.gz...
TR=4400.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.997313, 0.0722762, 0.0119947)
j_ras = (0.0714883, 0.995834, -0.0566035)
k_ras = (0.0160358, 0.0555939, 0.998325)
keeping frame 0
writing to
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/lowb_orig_las.nii.gz...
bet
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/lowb_orig_las.nii.gz
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/lowb_orig_las_brain.nii.gz
-m -f 0.3
awk: fatal: cannot open file
`/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.1.bvals'
for reading (No such file or directory)
eddy_openmp
--imain=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.nii.gz
--mask=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/lowb_orig_las_brain_mask.nii.gz
--bvecs=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.bvecs
--bvals=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.bvals
--acqp=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/acqp.txt
--index=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/index.txt
--data_is_shelled
--out=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi
EddyInputError: Error when attempting to read --index file
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/index.txt
Terminating program
Linux upd-159253 4.15.0-147-lowlatency #151-Ubuntu SMP PREEMPT Fri Jun 18
20:06:19 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Wed Oct 27 13:41:49 CEST 2021
upd-159253:/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test>
# FreeSurfer SUBJECTS_DIR # T1 images and FreeSurfer segmentations are expected to be found here # setenv SUBJECTS_DIR /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_FS_subjects # Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # set dtroot = /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720 # Subject IDs (n = 130 incl. IPS_SZ_024, excl. IPS_SZ_028 & IPS_SZ_068 due to missing fieldmap) # set subjlist = (IPS_CO_007) # In case you want to analyze only Huey and Louie # Default: Run analysis on all subjects # set runlist = (1) # Input diffusion DICOMs (file names relative to dcmroot) # If original DICOMs don't exist, these can be in other image format # but then the gradient table and b-value table must be specified (see below) # set dcmroot = /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Prepared_DICOMs_FS720/ set dcmlist = (IPS_CO_007/DTI/32863323.dcm) # Diffusion gradient tables (file names can be relative to dcmroot) # Must be specified only if they cannot be read from the DICOM headers # The tables must have either three columns, where each row is a gradient vector # or three rows, where each column is a gradient vector # There must be as many gradient vectors as volumes in the diffusion data set # Default: Read from DICOM header # #set bveclist = (TRACULA_Prepared/IPS_CO_007_test/DTI/bvecs.bvec) # Diffusion b-value tables (file names can be relative to dcmroot) # Must be specified only if they cannot be read from the DICOM headers # There must be as many b-values as volumes in the diffusion data set # Default: Read from DICOM header # #set bvallist = (TRACULA_Prepared/IPS_CO_007_test/DTI/bvals.bval) # Perform correction for B0 inhomogeneity distortions? # 0: No correction (default) # 1: Perform correction based on a field map # Requires additional inputs (see below): b0mlist, b0plist, echospacing # 2: Perform correction based on reverse-polarity images # Requires additional inputs (see below): echospacing, pedir, epifactor # set dob0 = 1 # Input B0 field map magnitude DICOMs (file names can be relative to dcmroot) # Only used if dob0 = 1 # Default: None # set b0mlist = (IPS_CO_007/Magnitude/33170637.dcm) # Input B0 field map phase DICOMs (file names can be relative to dcmroot) # Only used if dob0 = 1 # Default: None # set b0plist = (IPS_CO_007/Phase/33163229.dcm) # Echo spacing (this is found in the scanner protocol printout) # Only used if dob0 = 1 or 2 # Default: None # set echospacing = 0.29 set pedir = ( AP ) set epifactor = 96 # Perform correction for eddy-current distortions? # 0: No correction # 1: Perform registration-based correction with eddy_correct # 2: Perform model-based correction with eddy (default) # set doeddy = 2 # Rotate diffusion gradient vectors to match eddy-current compensation? # Only used if doeddy = 1 or 2 # Default: 1 (yes) # set dorotbvecs = 1 # Intra-subject (diffusion-to-T1) registration method # 1: Affine with a correlation ratio cost # 2: Affine with a mutual information cost # 3: Affine with a boundary-based cost (default) # set intrareg = 3 # Degrees of freedom for intra-subject registration # Can be 6 (rigid), 9 (rigid+scaling), or 12 (full affine) # Default: 6 for infants, 9 otherwise # set intradof = 9 # Maximum rotation angle (degrees) for intra-subject registration # Default: 3 for infants, 90 otherwise # set intrarot = 90 # Inter-subject registration method # 1: Affine T1-to-T1 with a correlation ratio cost # 2: Affine T1-to-T1 with a mutual information cost # 3: Affine T1-to-T1 with a robust cost (default for infants) # 4: Nonlinear T1-to-T1 with CVS # 5: Nonlinear FA-to-FA with SyN (default) # set interreg = 5 # Target brain for inter-subject registration # Default for affine T1-to-T1: # $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz # Default for nonlinear T1-to-T1: # $FREESURFER_HOME/subjects/cvs_avg35/ # Default for nonlinear FA-to-FA: # $FREESURFER_HOME/trctrain/hcp/MGH35_HCP_FA_template.nii.gz # #set intertrg = /path/to/a/duck/template.nii.gz # Whole-brain segmentation used to extract the anatomical neighborhood priors # of the pathways of interest # Must exist in each subject's FreeSurfer recon directory, under: # $SUBJECTS_DIR/$subjid/mri/$segname.mgz # Default: aparc+aseg # set segname = aparc+aseg # Use the thalamic nuclei segmentation? # This is highly recommended to use for any pathways that terminate in # or neighbor the thalamus # When used, it is merged with the whole-brain segmentation above # Must exist in each subject's FreeSurfer recon directory, under: # $SUBJECTS_DIR/$subjid/mri/ThalamicNuclei.v12.T1.FSvoxelSpace.mgz # Default: 1 (yes) # set usethalnuc = 1 # Use brain mask extracted from T1 image instead of low-b diffusion image? # Has no effect if there is no T1 data # Default: 1 (yes) # set usemaskanat = 1 # Fractional intensity threshold for BET mask extraction from low-b images # This mask is used only if usemaskanat = 0 # Default: 0.3 # set thrbet = 0.3 # Paths to reconstruct # Default: All paths in $FREESURFER_HOME/trctrain/hcp/pathlist.txt # #set pathlist = ( lh.cst_AS rh.cst_AS) # Number of path control points # It can be a single number for all paths or a different number for each of the # paths specified in pathlist (recommended, with more points for longer paths) # Default: As in $FREESURFER_HOME/trctrain/hcp/pathlist.txt # #set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5) # List of training subjects # This text file lists the locations of training subject directories # Default: $FREESURFER_HOME/trctrain/hcp/trainlist.txt # set trainfile = $FREESURFER_HOME/trctrain/hcp/trainlist.txt # Number of "sticks" (anisotropic diffusion compartments) in the bedpostx # ball-and-stick model # Default: 2 # set nstick = 2 # Number of MCMC burn-in iterations # (Path samples drawn initially by MCMC algorithm and discarded) # Default: 200 # set nburnin = 200 # Number of MCMC iterations # (Path samples drawn by MCMC algorithm and used to estimate path distribution) # Default: 7500 # set nsample = 7500 # Frequency with which MCMC path samples are retained for path distribution # Default: 5 (keep every 5th sample) # set nkeep = 5 # Reinitialize path reconstruction? # This is an option of last resort, to be used only if one of the reconstructed # pathway distributions looks like a single curve. This is a sign that the # initial guess for the pathway was problematic, perhaps due to poor alignment # between the individual and the atlas. Setting the reinit parameter to 1 and # rerunning "trac-all -prior" and "trac-all -path", only for the specific # subjects and pathways that had this problem, will attempt to reconstruct them # with a different initial guess. # Default: 0 (do not reinitialize) # set reinit = 0
trac-all.log
Description: trac-all.log
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
