Hi Jürgen - I suspect that the field map correction option is not very popular,
which is why you didn't find questions about it in the archives.
It fails because there's no number after the "--tediff" option. That's supposed
to be the difference in TE between the two scans that were used to compute your
field map (it's an option when you set up the field mapping sequence).
It normally tries to find the TEs from the header info that it extracts from
your field mapping DICOM and finds their difference in this line:
set dTE = `echo "($TE[2] - $TE[1])/1000" | bc -l`
Something in this sequence of events didn't work for your files. Let me know if
this helps debug it.
Best,
Anastasia.
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
juergen.haen...@upd.unibe.ch <juergen.haen...@upd.unibe.ch>
Sent: Wednesday, June 30, 2021 4:44 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] TRACULA: No b0info.dat file / error epidewarp.fsl
External Email - Use Caution
Dear Anastasia
thanks a lot for your answer. Meanwhile, the problem wrt reading magnitude and
phase files is solved, but a new error occurred that might be related to the
b0info.dat file and/or the epidewarp.fsl function.
After the b0mag.nii.gz and b0pha.nii.gz have successfully written, trac-preproc
is searching (grep) for the file b0info.dat, but there is no such file in the
subject’s dmri folder:
….
grep:
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/b0info.dat:
No such file or directory
TE: Subscript out of range.
I guess this file should be produced by trac-preproc, even if starting with
other than DICOM files, or?
Then, it reports that the flag "set echospacing = 0.58" is not recognized by
epidewarp.fsl (ERROR: Flag 0.58 unrecognized) although it seems that it is
recognized (because —esp 0.58 appears in the command line) and trac-preproc
exited with errors:
fslroi
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_eddy.nii.gz
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/lowb.nii.gz
0 1
epidewarp.fsl --mag
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/b0mag.nii.gz
--dph
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/b0pha.nii.gz
--exf
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/lowb.nii.gz
--epi
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_eddy.nii.gz
--tediff --esp 0.58 --vsm
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/vsm.nii.gz
--epidw
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi.nii.gz
ERROR: Flag 0.58 unrecognized.
--mag
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/b0mag.nii.gz
--dph
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/b0pha.nii.gz
--exf
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/lowb.nii.gz
--epi
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_eddy.nii.gz
--tediff --esp 0.58 --vsm
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/vsm.nii.gz
--epidw
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi.nii.gz
Darwin
upddkp224.unibe.ch<http://secure-web.cisco.com/14Watd0b29ADtjv2OJ5MtV2T8C_PX9vm76I5WFt8IPzxMqJsrk3XtGGBaD068yvyDnl79v7m1EBaYKdUZZZCok6fANRgIMH-V5KPxNWwMZSpm9VnmkpIO3Lb87Inqrl1VhsvzMaqYGW5mXskARsfXJN50hkDVaAD171DGShlYNvl1ID95_5v3avAt8M9ROaxOqfvizgCWTtnq6c9ZsCKfZc5GwXzgfXaBq1ZRJJDVF2v10NPnoX-8edRfdX1VJCkJV20tZNaXME5bBV07MSEbRA/http%3A%2F%2Fupddkp224.unibe.ch>
19.6.0 Darwin Kernel Version 19.6.0: Thu May 6 00:48:39 PDT 2021;
root:xnu-6153.141.33~1/RELEASE_X86_64 x86_64
trac-preproc exited with ERRORS at Wed Jun 30 08:48:48 CEST 2021
[upddkp224:Datenspeicher/01_IPS/04_C_DTI_TRACULA] jurgenhanggi%
Any idea why these errors occurred is highly appreciated.
I searched for these problems in the FS archive, but did not find any hint.
The whole trac-all.log file and the config file are attached.
Thanks in advance and good luck with your grant submission.
Regards
Jürgen
Am 29.06.2021 um 16:32 schrieb Yendiki, Anastasia
<ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>>:
Hi Jürgen - In principle they can be any format that mri_convert reads, so they
could be nifti. I suspect there's some glitch with where it's looking for the
files vs. where they are. Can you please attach your config file?
I have a grant deadline tomorrow, but will look after that. Thanks!
Anastasia.
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of juergen.haen...@upd.unibe.ch<mailto:juergen.haen...@upd.unibe.ch>
<juergen.haen...@upd.unibe.ch<mailto:juergen.haen...@upd.unibe.ch>>
Sent: Tuesday, June 29, 2021 8:27 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] trac-all -prep problem (error: corRead(): can't open file
PATH/TO/DCMROOT/COR-.info)
External Email - Use Caution
Dear TRACULA experts
I try to run trac-all -prep using the "Perform registration-based
B0-inhomogeneity compensation“ option, but the following error occurred:
mri_convert /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Prepared/
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/b0mag.nii.gz
mri_convert /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Prepared/
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/b0mag.nii.gz
reading from /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Prepared/...
error: corRead(): can't open file
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Prepared/COR-.info
Darwin
upddkp224.unibe.ch<http://secure-web.cisco.com/1SV0wPuNBydK7FxGu_z7xu1JTzd0pdxL_zr2NIs20D16nNkpJAQm-UZ_vY4A-rpC0RBPlOPiQq3Kw2qTFp5IR8m-fjDDOYMZOu5dp4LU-nRvZzN9e-23JKj3gUoqyqDXBQqYdS7XjnB7fC4QKUHKlvCNNZILcHUwSmKJR4qgoFJQwODsMyARCZ4GiikdLRxQOYXbbRTBcZzQ1stu8aG5R953WACkK1pyUOTOaYZEZ9XzLj9X_oSbmR1AsRxvatSbIrVYqPiM67JUIvHOkAtFfQA/http%3A%2F%2Fupddkp224.unibe.ch%2F>
19.6.0 Darwin Kernel Version 19.6.0: Thu May 6 00:48:39 PDT 2021;
root:xnu-6153.141.33~1/RELEASE_X86_64 x86_64
trac-preproc exited with ERRORS at Tue Jun 29 13:55:16 CEST 2021
My magnitude and phase images are in NIFTI format.
Do the magnitude and phase images have to be in DICOM format or does NIFTI
format should also work?
The full trac-all.log output is pasted below.
Thanks in advance for any advise
Regards
Jürgen
———————————————
Tue Jun 29 13:52:16 CEST 2021
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA
/Applications/freesurfer/bin/trac-all
-prep -c
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/tracula_config_IPS_all_with_eddy_with_fieldmap_test.txt
Subject IPS_CO_007
SUBJECTS_DIR /Applications/freesurfer/subjects
FREESURFER_HOME /Applications/freesurfer
Actual FREESURFER_HOME /Applications/freesurfer
build-stamp.txt: freesurfer-darwin-macOS-7.1.1-20200811-8b40551
jurgenhanggi
upddkp224.unibe.ch<http://secure-web.cisco.com/1SV0wPuNBydK7FxGu_z7xu1JTzd0pdxL_zr2NIs20D16nNkpJAQm-UZ_vY4A-rpC0RBPlOPiQq3Kw2qTFp5IR8m-fjDDOYMZOu5dp4LU-nRvZzN9e-23JKj3gUoqyqDXBQqYdS7XjnB7fC4QKUHKlvCNNZILcHUwSmKJR4qgoFJQwODsMyARCZ4GiikdLRxQOYXbbRTBcZzQ1stu8aG5R953WACkK1pyUOTOaYZEZ9XzLj9X_oSbmR1AsRxvatSbIrVYqPiM67JUIvHOkAtFfQA/http%3A%2F%2Fupddkp224.unibe.ch%2F>
Darwin
upddkp224.unibe.ch<http://secure-web.cisco.com/1SV0wPuNBydK7FxGu_z7xu1JTzd0pdxL_zr2NIs20D16nNkpJAQm-UZ_vY4A-rpC0RBPlOPiQq3Kw2qTFp5IR8m-fjDDOYMZOu5dp4LU-nRvZzN9e-23JKj3gUoqyqDXBQqYdS7XjnB7fC4QKUHKlvCNNZILcHUwSmKJR4qgoFJQwODsMyARCZ4GiikdLRxQOYXbbRTBcZzQ1stu8aG5R953WACkK1pyUOTOaYZEZ9XzLj9X_oSbmR1AsRxvatSbIrVYqPiM67JUIvHOkAtFfQA/http%3A%2F%2Fupddkp224.unibe.ch%2F>
19.6.0 Darwin Kernel Version 19.6.0: Thu May 6 00:48:39 PDT 2021;
root:xnu-6153.141.33~1/RELEASE_X86_64 x86_64
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 8192 kbytes
coredumpsize 0 kbytes
memoryuse unlimited
descriptors 256
memorylocked unlimited
maxproc 11136
PhysMem: 64G used (5040M wired), 7908M unused.
########################################
Program versions:
FreeSurferEnv.csh 7.1.1
mri_convert --all-info
ProgramName: mri_convert ProgramArguments: mri_convert --all-info
ProgramVersion: 7.1.1 TimeStamp: 2021/06/29-11:52:17-GMT BuildTime: Aug 11
2020 19:06:41 BuildStamp: freesurfer-darwin-macOS-7.1.1-20200811-8b40551
User: jurgenhanggi Machine:
upddkp224.unibe.ch<http://secure-web.cisco.com/1SV0wPuNBydK7FxGu_z7xu1JTzd0pdxL_zr2NIs20D16nNkpJAQm-UZ_vY4A-rpC0RBPlOPiQq3Kw2qTFp5IR8m-fjDDOYMZOu5dp4LU-nRvZzN9e-23JKj3gUoqyqDXBQqYdS7XjnB7fC4QKUHKlvCNNZILcHUwSmKJR4qgoFJQwODsMyARCZ4GiikdLRxQOYXbbRTBcZzQ1stu8aG5R953WACkK1pyUOTOaYZEZ9XzLj9X_oSbmR1AsRxvatSbIrVYqPiM67JUIvHOkAtFfQA/http%3A%2F%2Fupddkp224.unibe.ch%2F>
Platform: Darwin PlatformVersion: 19.6.0 CompilerName: Clang
CompilerVersion: 10.0.1
FLIRT version 6.0
bbregister 7.1.1
mri_cvs_register 7.1.1
ProgramName: dmri_motion ProgramArguments:
/Applications/freesurfer/bin/dmri_motion --all-info ProgramVersion: 7.1.1
TimeStamp: 2021/06/29-11:52:17-GMT BuildTime: Aug 11 2020 19:06:41
BuildStamp: freesurfer-darwin-macOS-7.1.1-20200811-8b40551 User: jurgenhanggi
Machine:
upddkp224.unibe.ch<http://secure-web.cisco.com/1SV0wPuNBydK7FxGu_z7xu1JTzd0pdxL_zr2NIs20D16nNkpJAQm-UZ_vY4A-rpC0RBPlOPiQq3Kw2qTFp5IR8m-fjDDOYMZOu5dp4LU-nRvZzN9e-23JKj3gUoqyqDXBQqYdS7XjnB7fC4QKUHKlvCNNZILcHUwSmKJR4qgoFJQwODsMyARCZ4GiikdLRxQOYXbbRTBcZzQ1stu8aG5R953WACkK1pyUOTOaYZEZ9XzLj9X_oSbmR1AsRxvatSbIrVYqPiM67JUIvHOkAtFfQA/http%3A%2F%2Fupddkp224.unibe.ch%2F>
Platform: Darwin PlatformVersion: 19.6.0 CompilerName: Clang
CompilerVersion: 10.0.1
ProgramName: dmri_train ProgramArguments:
/Applications/freesurfer/bin/dmri_train --all-info ProgramVersion: 7.1.1
TimeStamp: 2021/06/29-11:52:17-GMT BuildTime: Aug 11 2020 19:06:41
BuildStamp: freesurfer-darwin-macOS-7.1.1-20200811-8b40551 User: jurgenhanggi
Machine:
upddkp224.unibe.ch<http://secure-web.cisco.com/1SV0wPuNBydK7FxGu_z7xu1JTzd0pdxL_zr2NIs20D16nNkpJAQm-UZ_vY4A-rpC0RBPlOPiQq3Kw2qTFp5IR8m-fjDDOYMZOu5dp4LU-nRvZzN9e-23JKj3gUoqyqDXBQqYdS7XjnB7fC4QKUHKlvCNNZILcHUwSmKJR4qgoFJQwODsMyARCZ4GiikdLRxQOYXbbRTBcZzQ1stu8aG5R953WACkK1pyUOTOaYZEZ9XzLj9X_oSbmR1AsRxvatSbIrVYqPiM67JUIvHOkAtFfQA/http%3A%2F%2Fupddkp224.unibe.ch%2F>
Platform: Darwin PlatformVersion: 19.6.0 CompilerName: Clang
CompilerVersion: 10.0.1
ProgramName: dmri_paths ProgramArguments:
/Applications/freesurfer/bin/dmri_paths --all-info ProgramVersion: 7.1.1
TimeStamp: 2021/06/29-11:52:17-GMT BuildTime: Aug 11 2020 19:06:41
BuildStamp: freesurfer-darwin-macOS-7.1.1-20200811-8b40551 User: jurgenhanggi
Machine:
upddkp224.unibe.ch<http://secure-web.cisco.com/1SV0wPuNBydK7FxGu_z7xu1JTzd0pdxL_zr2NIs20D16nNkpJAQm-UZ_vY4A-rpC0RBPlOPiQq3Kw2qTFp5IR8m-fjDDOYMZOu5dp4LU-nRvZzN9e-23JKj3gUoqyqDXBQqYdS7XjnB7fC4QKUHKlvCNNZILcHUwSmKJR4qgoFJQwODsMyARCZ4GiikdLRxQOYXbbRTBcZzQ1stu8aG5R953WACkK1pyUOTOaYZEZ9XzLj9X_oSbmR1AsRxvatSbIrVYqPiM67JUIvHOkAtFfQA/http%3A%2F%2Fupddkp224.unibe.ch%2F>
Platform: Darwin PlatformVersion: 19.6.0 CompilerName: Clang
CompilerVersion: 10.0.1
ProgramName: dmri_pathstats ProgramArguments:
/Applications/freesurfer/bin/dmri_pathstats --all-info ProgramVersion: 7.1.1
TimeStamp: 2021/06/29-11:52:17-GMT BuildTime: Aug 11 2020 19:06:41
BuildStamp: freesurfer-darwin-macOS-7.1.1-20200811-8b40551 User: jurgenhanggi
Machine:
upddkp224.unibe.ch<http://secure-web.cisco.com/1SV0wPuNBydK7FxGu_z7xu1JTzd0pdxL_zr2NIs20D16nNkpJAQm-UZ_vY4A-rpC0RBPlOPiQq3Kw2qTFp5IR8m-fjDDOYMZOu5dp4LU-nRvZzN9e-23JKj3gUoqyqDXBQqYdS7XjnB7fC4QKUHKlvCNNZILcHUwSmKJR4qgoFJQwODsMyARCZ4GiikdLRxQOYXbbRTBcZzQ1stu8aG5R953WACkK1pyUOTOaYZEZ9XzLj9X_oSbmR1AsRxvatSbIrVYqPiM67JUIvHOkAtFfQA/http%3A%2F%2Fupddkp224.unibe.ch%2F>
Platform: Darwin PlatformVersion: 19.6.0 CompilerName: Clang
CompilerVersion: 10.0.1
ProgramName: dmri_mergepaths ProgramArguments:
/Applications/freesurfer/bin/dmri_mergepaths --all-info ProgramVersion: 7.1.1
TimeStamp: 2021/06/29-11:52:17-GMT BuildTime: Aug 11 2020 19:06:41
BuildStamp: freesurfer-darwin-macOS-7.1.1-20200811-8b40551 User: jurgenhanggi
Machine:
upddkp224.unibe.ch<http://secure-web.cisco.com/1SV0wPuNBydK7FxGu_z7xu1JTzd0pdxL_zr2NIs20D16nNkpJAQm-UZ_vY4A-rpC0RBPlOPiQq3Kw2qTFp5IR8m-fjDDOYMZOu5dp4LU-nRvZzN9e-23JKj3gUoqyqDXBQqYdS7XjnB7fC4QKUHKlvCNNZILcHUwSmKJR4qgoFJQwODsMyARCZ4GiikdLRxQOYXbbRTBcZzQ1stu8aG5R953WACkK1pyUOTOaYZEZ9XzLj9X_oSbmR1AsRxvatSbIrVYqPiM67JUIvHOkAtFfQA/http%3A%2F%2Fupddkp224.unibe.ch%2F>
Platform: Darwin PlatformVersion: 19.6.0 CompilerName: Clang
CompilerVersion: 10.0.1
ProgramName: dmri_group ProgramArguments:
/Applications/freesurfer/bin/dmri_group --all-info ProgramVersion: 7.1.1
TimeStamp: 2021/06/29-11:52:17-GMT BuildTime: Aug 11 2020 19:06:41
BuildStamp: freesurfer-darwin-macOS-7.1.1-20200811-8b40551 User: jurgenhanggi
Machine:
upddkp224.unibe.ch<http://secure-web.cisco.com/1SV0wPuNBydK7FxGu_z7xu1JTzd0pdxL_zr2NIs20D16nNkpJAQm-UZ_vY4A-rpC0RBPlOPiQq3Kw2qTFp5IR8m-fjDDOYMZOu5dp4LU-nRvZzN9e-23JKj3gUoqyqDXBQqYdS7XjnB7fC4QKUHKlvCNNZILcHUwSmKJR4qgoFJQwODsMyARCZ4GiikdLRxQOYXbbRTBcZzQ1stu8aG5R953WACkK1pyUOTOaYZEZ9XzLj9X_oSbmR1AsRxvatSbIrVYqPiM67JUIvHOkAtFfQA/http%3A%2F%2Fupddkp224.unibe.ch%2F>
Platform: Darwin PlatformVersion: 19.6.0 CompilerName: Clang
CompilerVersion: 10.0.1
New invocation of trac-preproc
jurgenhanggi
upddkp224.unibe.ch<http://secure-web.cisco.com/1SV0wPuNBydK7FxGu_z7xu1JTzd0pdxL_zr2NIs20D16nNkpJAQm-UZ_vY4A-rpC0RBPlOPiQq3Kw2qTFp5IR8m-fjDDOYMZOu5dp4LU-nRvZzN9e-23JKj3gUoqyqDXBQqYdS7XjnB7fC4QKUHKlvCNNZILcHUwSmKJR4qgoFJQwODsMyARCZ4GiikdLRxQOYXbbRTBcZzQ1stu8aG5R953WACkK1pyUOTOaYZEZ9XzLj9X_oSbmR1AsRxvatSbIrVYqPiM67JUIvHOkAtFfQA/http%3A%2F%2Fupddkp224.unibe.ch%2F>
Darwin
upddkp224.unibe.ch<http://secure-web.cisco.com/1SV0wPuNBydK7FxGu_z7xu1JTzd0pdxL_zr2NIs20D16nNkpJAQm-UZ_vY4A-rpC0RBPlOPiQq3Kw2qTFp5IR8m-fjDDOYMZOu5dp4LU-nRvZzN9e-23JKj3gUoqyqDXBQqYdS7XjnB7fC4QKUHKlvCNNZILcHUwSmKJR4qgoFJQwODsMyARCZ4GiikdLRxQOYXbbRTBcZzQ1stu8aG5R953WACkK1pyUOTOaYZEZ9XzLj9X_oSbmR1AsRxvatSbIrVYqPiM67JUIvHOkAtFfQA/http%3A%2F%2Fupddkp224.unibe.ch%2F>
19.6.0 Darwin Kernel Version 19.6.0: Thu May 6 00:48:39 PDT 2021;
root:xnu-6153.141.33~1/RELEASE_X86_64 x86_64
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 8192 kbytes
coredumpsize 0 kbytes
memoryuse unlimited
descriptors 256
memorylocked unlimited
maxproc 11136
PhysMem: 64G used (5024M wired), 7906M unused.
#-------------------------------------
/Applications/freesurfer/bin/trac-preproc
#-------------------------------------
#@# Image corrections Tue Jun 29 13:52:17 CEST 2021
mri_convert --bvec-voxel
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Prepared/IPS_CO_007/DTI/dti4D.nii
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_orig.nii.gz
mri_convert --bvec-voxel
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Prepared/IPS_CO_007/DTI/dti4D.nii
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_orig.nii.gz
reading from
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Prepared/IPS_CO_007/DTI/dti4D.nii...
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)
writing to
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_orig.nii.gz...
mv -f
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/bvecs.tmp
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_orig.bvecs
mv -f
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/bvals.tmp
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_orig.bvals
orientLAS
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_orig.nii.gz
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_orig_las.nii.gz
INFO: input image orientation is LAS
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 3.04031
28.5933 61.3756 -rt nearest
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_orig.nii.gz
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_orig_las.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 3.04031
28.5933 61.3756 -rt nearest
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_orig.nii.gz
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_orig_las.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
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_orig.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
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_orig_las.nii.gz...
INFO: found
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_orig.bvals,
copying
INFO: found
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_orig.bvecs,
converting to LAS
mv -f
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_orig_las.bvecs
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/bvecs
mv -f
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_orig_las.bvals
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/bvals
eddy_correct
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_orig_las.nii.gz
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi.nii.gz
0
processing
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processing
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0001
processing
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0002
processing
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0003
processing
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processing
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0005
processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0052
processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
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processing
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0121
processing
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0122
mv -f
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/bvecs
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/bvecs.norot
xfmrot
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi.ecclog
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/bvecs.norot
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/bvecs
mv -f
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi.nii.gz
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_eddy.nii.gz
mri_convert /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Prepared/
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/b0mag.nii.gz
mri_convert /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Prepared/
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/b0mag.nii.gz
reading from /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Prepared/...
error: corRead(): can't open file
/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Prepared/COR-.info
Darwin
upddkp224.unibe.ch<http://secure-web.cisco.com/1SV0wPuNBydK7FxGu_z7xu1JTzd0pdxL_zr2NIs20D16nNkpJAQm-UZ_vY4A-rpC0RBPlOPiQq3Kw2qTFp5IR8m-fjDDOYMZOu5dp4LU-nRvZzN9e-23JKj3gUoqyqDXBQqYdS7XjnB7fC4QKUHKlvCNNZILcHUwSmKJR4qgoFJQwODsMyARCZ4GiikdLRxQOYXbbRTBcZzQ1stu8aG5R953WACkK1pyUOTOaYZEZ9XzLj9X_oSbmR1AsRxvatSbIrVYqPiM67JUIvHOkAtFfQA/http%3A%2F%2Fupddkp224.unibe.ch%2F>
19.6.0 Darwin Kernel Version 19.6.0: Thu May 6 00:48:39 PDT 2021;
root:xnu-6153.141.33~1/RELEASE_X86_64 x86_64
trac-preproc exited with ERRORS at Tue Jun 29 13:55:16 CEST 2021
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