Am 20.11.2021 um 18:11 schrieb Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu>:

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):

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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-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, 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

 

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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.

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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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