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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of juergen.haenggi@upd.unibe.ch juergen.haenggi@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

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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.chhttp://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 <AYENDIKI@MGH.HARVARD.EDUmailto:AYENDIKI@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of juergen.haenggi@upd.unibe.chmailto:juergen.haenggi@upd.unibe.ch <juergen.haenggi@upd.unibe.chmailto:juergen.haenggi@upd.unibe.ch> Sent: Tuesday, June 29, 2021 8:27 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto: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.chhttp://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.chhttp://secure-web.cisco.com/1SV0wPuNBydK7FxGu_z7xu1JTzd0pdxL_zr2NIs20D16nNkpJAQm-UZ_vY4A-rpC0RBPlOPiQq3Kw2qTFp5IR8m-fjDDOYMZOu5dp4LU-nRvZzN9e-23JKj3gUoqyqDXBQqYdS7XjnB7fC4QKUHKlvCNNZILcHUwSmKJR4qgoFJQwODsMyARCZ4GiikdLRxQOYXbbRTBcZzQ1stu8aG5R953WACkK1pyUOTOaYZEZ9XzLj9X_oSbmR1AsRxvatSbIrVYqPiM67JUIvHOkAtFfQA/http%3A%2F%2Fupddkp224.unibe.ch%2F Darwin upddkp224.unibe.chhttp://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.chhttp://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.chhttp://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.chhttp://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.chhttp://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.chhttp://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.chhttp://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.chhttp://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.chhttp://secure-web.cisco.com/1SV0wPuNBydK7FxGu_z7xu1JTzd0pdxL_zr2NIs20D16nNkpJAQm-UZ_vY4A-rpC0RBPlOPiQq3Kw2qTFp5IR8m-fjDDOYMZOu5dp4LU-nRvZzN9e-23JKj3gUoqyqDXBQqYdS7XjnB7fC4QKUHKlvCNNZILcHUwSmKJR4qgoFJQwODsMyARCZ4GiikdLRxQOYXbbRTBcZzQ1stu8aG5R953WACkK1pyUOTOaYZEZ9XzLj9X_oSbmR1AsRxvatSbIrVYqPiM67JUIvHOkAtFfQA/http%3A%2F%2Fupddkp224.unibe.ch%2F Darwin upddkp224.unibe.chhttp://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 /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0000 processing 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/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0109 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0110 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0111 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0112 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0113 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0114 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0115 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0116 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0117 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0118 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0119 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0120 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.chhttp://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

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1uSGg1rtKAhCeinnzMni66E3f7QWK2WoRk3Donj0Ch3P3PghZO257gynA_jp-px0e5nuzNKteK_hVHLYXFD6Wjluea_HACL6db_VekmUlJGxKxlDpto7PCWCYOk4dOKV897kdPQZ1GkGeW1Pi02kqzmxpn-pxD4ZHgJ2ZFWQg94ODfc-pUbdQgo-5tVCDOXpcCcVbPmp0ty4y-6x255F61UMVwNKvL6TQwauJbtYNtNjU1DxRFI0-aJA4PGQjX1Z_okGeHMSbmAiDREeLa4tLzw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1uSGg1rtKAhCeinnzMni66E3f7QWK2WoRk3Donj0Ch3P3PghZO257gynA_jp-px0e5nuzNKteK_hVHLYXFD6Wjluea_HACL6db_VekmUlJGxKxlDpto7PCWCYOk4dOKV897kdPQZ1GkGeW1Pi02kqzmxpn-pxD4ZHgJ2ZFWQg94ODfc-pUbdQgo-5tVCDOXpcCcVbPmp0ty4y-6x255F61UMVwNKvL6TQwauJbtYNtNjU1DxRFI0-aJA4PGQjX1Z_okGeHMSbmAiDREeLa4tLzw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.massgeneralbrigham.org/compliancelinehttp://secure-web.cisco.com/17HqZtB72KPD9UkUsYZqlnzBiXETlg0uMVzkmJODyasSHV0-PzO1zqhn3BiXTrLBxxuHmKanMmfa8h7bVc62UJKFV8Vb-3null6PdFiSQFu7rz71M9adJNzVrfopjfUW0gDnNJ0ZsOkZXrOpue-gbLEH5dfj53uS_WZS1awC3f7G4kREgNbSb_sqvueZp1nVRBRv-jAW2gQwf3wSksJP9-4eHpHoHLS6yNQ6C6nHQde9JkLpKd96F766PqYMaZJD0_EeCmrsSOVZdEqfA3DS0eQ/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

Hi Jürgen - In the 7.2 beta version (which will also be the official version any day now), you should be able to set the variable "dTE" (the TE difference) directly in the config file, so you don't need to provide the fieldmap scan as a dicom.

There are many more and (more exciting!) reasons than just this to use TRACULA in 7.2 instead of the old version ??

Best, Anastasia.

PS: Please excuse any latency in responses over the summer as I'll be on and off vacation.

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of juergen.haenggi@upd.unibe.ch juergen.haenggi@upd.unibe.ch Sent: Friday, July 9, 2021 1:37 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA: No b0info.dat file / error epidewarp.fsl

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Dear Anastasia

Thanks for the information. I do not want to start with the DICOMs and therefore the difference in TE cannot be extracted. Is there an easy work around to provide —tediff or the file b0info.dat to trac-all -prep? I tried to define —tediff in the config file, but it does not work.

Thanks for any advise Best, Jürgen

Am 02.07.2021 um 19:09 schrieb Yendiki, Anastasia <AYENDIKI@MGH.HARVARD.EDUmailto:AYENDIKI@MGH.HARVARD.EDU>:

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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of juergen.haenggi@upd.unibe.chmailto:juergen.haenggi@upd.unibe.ch<juergen.haenggi@upd.unibe.chmailto:juergen.haenggi@upd.unibe.ch> Sent: Wednesday, June 30, 2021 4:44 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] TRACULA: No b0info.dat file / error epidewarp.fsl

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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.chhttp://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 <AYENDIKI@MGH.HARVARD.EDUmailto:AYENDIKI@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of juergen.haenggi@upd.unibe.chmailto:juergen.haenggi@upd.unibe.ch <juergen.haenggi@upd.unibe.chmailto:juergen.haenggi@upd.unibe.ch> Sent: Tuesday, June 29, 2021 8:27 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] trac-all -prep problem (error: corRead(): can't open file PATH/TO/DCMROOT/COR-.info)

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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.chhttp://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.chhttp://secure-web.cisco.com/1SV0wPuNBydK7FxGu_z7xu1JTzd0pdxL_zr2NIs20D16nNkpJAQm-UZ_vY4A-rpC0RBPlOPiQq3Kw2qTFp5IR8m-fjDDOYMZOu5dp4LU-nRvZzN9e-23JKj3gUoqyqDXBQqYdS7XjnB7fC4QKUHKlvCNNZILcHUwSmKJR4qgoFJQwODsMyARCZ4GiikdLRxQOYXbbRTBcZzQ1stu8aG5R953WACkK1pyUOTOaYZEZ9XzLj9X_oSbmR1AsRxvatSbIrVYqPiM67JUIvHOkAtFfQA/http%3A%2F%2Fupddkp224.unibe.ch%2F Darwin upddkp224.unibe.chhttp://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.chhttp://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.chhttp://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.chhttp://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.chhttp://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.chhttp://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.chhttp://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.chhttp://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.chhttp://secure-web.cisco.com/1SV0wPuNBydK7FxGu_z7xu1JTzd0pdxL_zr2NIs20D16nNkpJAQm-UZ_vY4A-rpC0RBPlOPiQq3Kw2qTFp5IR8m-fjDDOYMZOu5dp4LU-nRvZzN9e-23JKj3gUoqyqDXBQqYdS7XjnB7fC4QKUHKlvCNNZILcHUwSmKJR4qgoFJQwODsMyARCZ4GiikdLRxQOYXbbRTBcZzQ1stu8aG5R953WACkK1pyUOTOaYZEZ9XzLj9X_oSbmR1AsRxvatSbIrVYqPiM67JUIvHOkAtFfQA/http%3A%2F%2Fupddkp224.unibe.ch%2F Darwin upddkp224.unibe.chhttp://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 /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0000 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 /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0004 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0005 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0006 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0007 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0008 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0009 processing 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/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0091 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0092 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0093 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0094 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0095 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0096 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0097 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0098 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0099 processing 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/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0109 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0110 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0111 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0112 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0113 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0114 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0115 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0116 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0117 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0118 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0119 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0120 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.chhttp://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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I'll let @Greve, Douglas N.,Ph.D.mailto:DGREVE@mgh.harvard.edu reply that 🙂

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of juergen.haenggi@upd.unibe.ch juergen.haenggi@upd.unibe.ch Sent: Thursday, July 15, 2021 2:28 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA: No b0info.dat file / error epidewarp.fsl

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Dear Anastasia

thanks for your information. I will try TRACULA in the FS 7.2 beta or wait for the FS 7.2 official release. do you know when about the official FS 7.2 release is?

Best Jürgen

Am 13.07.2021 um 02:15 schrieb Yendiki, Anastasia <AYENDIKI@MGH.HARVARD.EDUmailto:AYENDIKI@MGH.HARVARD.EDU>:

Hi Jürgen - In the 7.2 beta version (which will also be the official version any day now), you should be able to set the variable "dTE" (the TE difference) directly in the config file, so you don't need to provide the fieldmap scan as a dicom.

There are many more and (more exciting!) reasons than just this to use TRACULA in 7.2 instead of the old version ��

Best, Anastasia.

PS: Please excuse any latency in responses over the summer as I'll be on and off vacation.

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of juergen.haenggi@upd.unibe.chmailto:juergen.haenggi@upd.unibe.ch <juergen.haenggi@upd.unibe.chmailto:juergen.haenggi@upd.unibe.ch> Sent: Friday, July 9, 2021 1:37 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] TRACULA: No b0info.dat file / error epidewarp.fsl

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Dear Anastasia

Thanks for the information. I do not want to start with the DICOMs and therefore the difference in TE cannot be extracted. Is there an easy work around to provide —tediff or the file b0info.dat to trac-all -prep? I tried to define —tediff in the config file, but it does not work.

Thanks for any advise Best, Jürgen

Am 02.07.2021 um 19:09 schrieb Yendiki, Anastasia <AYENDIKI@MGH.HARVARD.EDUmailto:AYENDIKI@MGH.HARVARD.EDU>:

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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of juergen.haenggi@upd.unibe.chmailto:juergen.haenggi@upd.unibe.ch<juergen.haenggi@upd.unibe.chmailto:juergen.haenggi@upd.unibe.ch> Sent: Wednesday, June 30, 2021 4:44 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] TRACULA: No b0info.dat file / error epidewarp.fsl

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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.chhttp://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 <AYENDIKI@MGH.HARVARD.EDUmailto:AYENDIKI@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of juergen.haenggi@upd.unibe.chmailto:juergen.haenggi@upd.unibe.ch <juergen.haenggi@upd.unibe.chmailto:juergen.haenggi@upd.unibe.ch> Sent: Tuesday, June 29, 2021 8:27 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto: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.chhttp://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.chhttp://secure-web.cisco.com/1SV0wPuNBydK7FxGu_z7xu1JTzd0pdxL_zr2NIs20D16nNkpJAQm-UZ_vY4A-rpC0RBPlOPiQq3Kw2qTFp5IR8m-fjDDOYMZOu5dp4LU-nRvZzN9e-23JKj3gUoqyqDXBQqYdS7XjnB7fC4QKUHKlvCNNZILcHUwSmKJR4qgoFJQwODsMyARCZ4GiikdLRxQOYXbbRTBcZzQ1stu8aG5R953WACkK1pyUOTOaYZEZ9XzLj9X_oSbmR1AsRxvatSbIrVYqPiM67JUIvHOkAtFfQA/http%3A%2F%2Fupddkp224.unibe.ch%2F Darwin upddkp224.unibe.chhttp://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.chhttp://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.chhttp://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.chhttp://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.chhttp://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.chhttp://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.chhttp://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.chhttp://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.chhttp://secure-web.cisco.com/1SV0wPuNBydK7FxGu_z7xu1JTzd0pdxL_zr2NIs20D16nNkpJAQm-UZ_vY4A-rpC0RBPlOPiQq3Kw2qTFp5IR8m-fjDDOYMZOu5dp4LU-nRvZzN9e-23JKj3gUoqyqDXBQqYdS7XjnB7fC4QKUHKlvCNNZILcHUwSmKJR4qgoFJQwODsMyARCZ4GiikdLRxQOYXbbRTBcZzQ1stu8aG5R953WACkK1pyUOTOaYZEZ9XzLj9X_oSbmR1AsRxvatSbIrVYqPiM67JUIvHOkAtFfQA/http%3A%2F%2Fupddkp224.unibe.ch%2F Darwin upddkp224.unibe.chhttp://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 /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0000 processing 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/Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0109 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0110 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0111 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0112 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0113 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0114 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0115 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0116 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0117 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0118 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0119 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0120 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.chhttp://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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