Hi Jürgen - You have diagnosed the problem correctly. It's specific to the case
when you have 1 DWI run only. I committed a bug fix for this. For now you can
get it from here (and it should get merged into the dev version in a couple of
days):
https://raw.githubusercontent.com/ayendiki/freesurfer/trcdev/scripts/trac-preproc
Can you please save this version of trac-preproc to your $FREESURFER_HOME/bin/
and tell us if it fixes the problem? Thank you for bringing this to our
attention.
Best,
Anastasia.
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
juergen.haen...@upd.unibe.ch <juergen.haen...@upd.unibe.ch>
Sent: Wednesday, October 27, 2021 8:19 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file
External Email - Use Caution
Dear TRACULA experts
I try to run TRACULA FS7.2 on a Linux machine and get the following error (see
below). A similar problem has already been reported in the archives, but I
found no solution.
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com"
claiming to be
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg71032.html<https://secure-web.cisco.com/15ekCi1WQB-CkH0WPGgECXGvPn99_mRmsow_C5M9nEA423BRbW-FKtNsZUbezZE_QDLB9tTrAhEngv6e3pZzRpvDIkIm6KXSCKMpikqqr8I7UzDhYNp9r4WMD_cNPQ1H9iJM_mZEjcL74q2XaK_BJMKcDCUR2IEVhTB14V-0-KDoDCIvf8avZH8sAQdlpf1AtWVaBOzP_a_q2ytmsXQq_z-VTqwl4kZhDQUh3pe3qM0Xq2I8WgvFw4OeT6omPBozJ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg71032.html>
Because the file "dwi_orig_las.1.bvals“ was renamed to „dwi_orig_las.bvals“
earlier in the run
mv -f
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.1.bvals
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.bvals
it cannot be found by awk and as a result, I guess, the index.txt file is empty
and therefore eddy_openmp terminated.
How can I fix this problem?
The terminal output, log and config files are attached.
Thank you for any advise in advance
Regards
Jürgen
—————— error ————
awk: fatal: cannot open file
`/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.1.bvals'
for reading (No such file or directory)
eddy_openmp
--imain=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.nii.gz
--mask=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/lowb_orig_las_brain_mask.nii.gz
--bvecs=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.bvecs
--bvals=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.bvals
--acqp=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/acqp.txt
--index=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/index.txt
--data_is_shelled
--out=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi
EddyInputError: Error when attempting to read --index file
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/index.txt
Terminating program
Linux upd-159253 4.15.0-147-lowlatency #151-Ubuntu SMP PREEMPT Fri Jun 18
20:06:19 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Wed Oct 27 13:41:49 CEST 2021
upd-159253:/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test>
——————
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