Dear Ashwati - Check out the instructions in the example config file: https://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc
... # Diffusion gradient tables (file names can be relative to dcmroot) ... # Diffusion b-value tables (file names can be relative to dcmroot) ...
Because you defined dcmroot, these filenames should be relative paths (which you did correctly for the DWI nifti file). The error occurs because it prepends dcmroot to the filenames you provided, so there's a replication (check what the error says and you'll see that).
Best, Anastasia.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Ashwati Vipin (Dr) ashwati.vipin@ntu.edu.sg Sent: Tuesday, August 16, 2022 9:50 PM 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.
[cid2203429043*image001.png@01D8B09D.94718010]
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
[signature_3677307404]
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.
[cid:image001.png@01D8B09D.94718010]
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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