Dear Freesurfer developers,
I am running the trac-all -prep for my DWI data on Freesurfer version 7.2.0. The configuration file seems to be alright but when I start running the -prep step it gives me the error:
writing to /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.nii.gz...
/Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula//Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/bvecs.txt:
No such file or directory.
Darwin DRCSs-iMac.local 21.5.0 Darwin Kernel Version 21.5.0: Tue Apr 26 21:08:22 PDT 2022; root:xnu-8020.121.3~4/RELEASE_X86_64 x86_64
trac-preproc exited with ERRORS at Mon Aug 15 11:32:11 +08 2022
I have attached the log file, error file, bvals and bvecs and the configuration file and as the screenshot below shows: the directory does have the bvals.txt and bvecs.txt files, so I’m not sure
why it’s giving me this error? I thought the error was because the bvals and bvecs were given in rows, so I transposed them so they are now in columns but it still doesn’t work.
I have run tracula before with no issues so I’m really lost here. Could you please help?
Thank you so much!
Best,
Ashwati
--
Ashwati Vipin (PhD)
Research Fellow - Dementia Research Centre (Singapore)
Lee Kong Chian School of Medicine
Nanyang Technological University, Singapore
www.drcs.sg
From:
freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Ashwati Vipin (Dr) <ashwati.vipin@ntu.edu.sg>
Date: Monday, 15 August 2022 at 11:59 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Unable to run trac-all -prep : cannot file bvals bvecs file
External Email - Use Caution
Dear Freesurfer developers,
I am running the trac-all -prep for my DWI data on Freesurfer version 7.2.0. The configuration file seems to be alright but when I start running the -prep step it gives me the error:
writing to /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.nii.gz...
/Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula//Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/bvecs.txt: No such file or directory.
Darwin DRCSs-iMac.local 21.5.0 Darwin Kernel Version 21.5.0: Tue Apr 26 21:08:22 PDT 2022; root:xnu-8020.121.3~4/RELEASE_X86_64 x86_64
trac-preproc exited with ERRORS at Mon Aug 15 11:32:11 +08 2022
I have attached the log file, error file, bvals and bvecs and the configuration file and as the screenshot below shows: the directory does have the bvals.txt and bvecs.txt files,
so I’m not sure why it’s giving me this error? I thought the error was because the bvals and bvecs were given in rows, so I transposed them so they are now in columns but it still doesn’t work.
I have run tracula before with no issues so I’m really lost here. Could you please help?
Thank you so much!
Best,
Ashwati
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