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
 

        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 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.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.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of juergen.haenggi@upd.unibe.ch <juergen.haenggi@upd.unibe.ch>
Sent: Tuesday, June 29, 2021 8:27 AM
To: freesurfer@nmr.mgh.harvard.edu <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 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
Darwin upddkp224.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
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  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  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  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  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  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  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  Platform: Darwin  PlatformVersion: 19.6.0  CompilerName: Clang  CompilerVersion: 10.0.1


New invocation of trac-preproc


jurgenhanggi
upddkp224.unibe.ch
Darwin upddkp224.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
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 /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0010
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0011
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0012
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0013
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0014
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0015
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0016
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0017
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0018
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0019
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0020
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0021
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0022
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0023
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0024
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0025
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0026
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0027
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0028
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0029
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0030
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0031
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0032
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0033
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0034
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0035
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0036
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0037
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0038
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0039
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0040
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0041
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0042
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0043
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0044
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0045
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0046
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0047
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0048
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0049
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0050
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0051
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0052
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0053
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0054
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0055
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0056
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0057
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0058
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0059
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0060
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0061
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0062
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0063
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0064
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0065
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0066
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0067
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0068
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0069
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0070
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0071
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0072
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0073
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0074
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0075
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0076
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0077
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0078
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0079
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0080
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0081
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0082
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0083
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0084
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0085
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0086
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0087
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0088
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0089
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0090
processing /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 /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0100
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0101
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0102
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0103
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0104
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0105
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0106
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0107
processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0108
processing /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.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 Tue Jun 29 13:55:16 CEST 2021


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