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Dear Anastasia

when I type $FSLDIR in the terminal, I get /usr/local/fsl: permission denied.

this is the right path where fsl is installed.

however, I can start FSL GUI and also other FSL commands.

Best Jürgen

Am 24.11.2021 um 01:20 schrieb Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu>:

Hi Jürgen - What's your $FSLDIR set to?

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, November 23, 2021 9:36 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file

        External Email - Use Caution

Dear Anastasia

thank you for the new option. It works. Now we were able to finish trac-all -prep without any further problem.

However, when we try to run trac-all -bedp, the following error occurred:

----------

trac-all -bedp -c /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/tracula_config_IPS_all_example_DICOM_NIFTI_ANTs.txt

INFO: SUBJECTS_DIR is /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_FS_subjects

INFO: Diffusion root is /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720

Actual FREESURFER_HOME /usr/local/freesurfer

ln -sf ../dlabel/diff/aparc+aseg_mask.bbr.nii.gz /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720/IPS_CO_007_ANTs/dmri/nodif_brain_mask.nii.gz

WARN: Running bedbostx locally - this might take a while

WARN: It is recommended to run this step on a cluster

bedpostx_mgh -n 2 -model 1 /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720/IPS_CO_007_ANTs/dmri

/usr/local/freesurfer/bin/bedpostx_mgh: 128: /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected

——————

we have found this message from 2014

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is it meanwhile possible to run bedpostx_mgh also locally or do we have to run bedpostx directly as suggested in the link?

Best

Jürgen

Am 23.11.2021 um 01:14 schrieb Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu>:

Ah yes, I did say that this would be feasible in 7.2, before 7.2 came out �� One more bug fix, in the same place (and then in the dev version):

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>From now on the dTE from the config file will supersede the one from the DICOM header. Thanks for finding this and let us know if there are any other issues.

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: Monday, November 22, 2021 4:47 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file

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Dear Anastasia

thank you for providing the bug fix. It works and solved our problem.

However, another (old) problem occurred wrt the field map for which we did not find any solution yet:

---------------------------------------------------------

writing to /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/b0pha.nii.gz...

mri_probedicom --i /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Prepared_DICOMs_FS720/IPS_CO_007/Phase/33163229.dcm > /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/b0info.dat

ERROR: Need dTE for field map /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Prepared_DICOMs_FS720/IPS_CO_007/Phase/33163229.dcm

Linux upd-159253 4.15.0-162-lowlatency #170-Ubuntu SMP PREEMPT Mon Oct 18 13:19:21 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Mon Nov 22 09:18:01 CET 2021

-----------------------------------------------------------

For some reasons, dTE cannot be extracted from the b0info.dat file (see attachment). Indeed, there is only one echo time entry (EchoTime 7.38) in the b0info.dat file maybe due to the fact that there is also only one echo time entry (EchoTime 7.38) in the DICOM header.

Specifying dTE = 2.46 in the config file does not solve the problem, neither with NIFTI nor DICOM file format for the field map.

In a former email, you mentioned that this should be possible.

The log and config file are also attached.

Is there any work around for this problem?

Thanks in advance

Best,

Jürgen

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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