Hi Ameen - diffusion_recons/elmo.2005 should have the freesurfer recon of the T1 data and diffusion_tutorial/elmo.2005 should have the diffusion data. Can you confirm if this was in what you downloaded?

Thanks!

a.y

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From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Al Qadi, Ameen <ameen.alqadi@icahn.mssm.edu>
Sent: Tuesday, January 28, 2020 5:38 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] TRACULA Preprocessing Error

 

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Hi Freesurfer Developers,

I downloaded the Freesurfer tutorial data to run the TRACULA tutorial, and encountered a number of issues: 

1. When running trac-all, I get the following error:

trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial
INFO: SUBJECTS_DIR is /zstore/data/aalqadi/aalqadi/tutorial_data/diffusion_recons
INFO: Diffusion root is /zstore/data/aalqadi/aalqadi/tutorial_data/diffusion_tutorial
Actual FREESURFER_HOME /usr/local/freesurfer

ERROR: cannot find /zstore/data/aalqadi/aalqadi/tutorial_data/diffusion_recons/elmo.2005

I found the elmo.2005 directory in diffusion_tutorial, and not diffusion_recons. Unsure why this happened, I copied all the data from diffusion_tutorial to diffusion_recons.

2. After re-running trac-all, the following error appeared:

mri_convert --bvec-voxel /zstore/data/aalqadi/aalqadi/tutorial_data/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm /zstore/data/aalqadi/aalqadi/tutorial_data/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel /zstore/data/aalqadi/aalqadi/tutorial_data/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm /zstore/data/aalqadi/aalqadi/tutorial_data/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz
ERROR: file /zstore/data/aalqadi/aalqadi/tutorial_data/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm does not exist
trac-preproc exited with ERRORS at Tue 28 Jan 2020 10:21:41 PM UTC

The issues with mri_convert stemmed from the failure to locate the dwi_orig.nii.gz file in diffusion_tutorial/elmo.2005/dmri/. The dmri subdirectory did not have the .gz file, so I was wondering if there was an issue with the tutorial data? (Couldn't find the .gz file anywhere else, re-downloaded the data and the same error showed up).

Any guidance would be much appreciated. The log file for error #2 is attached.

Best,

Ameen

--

Ameen Al Qadi

MSBS Candidate

Icahn School Of Medicine at Mount Sinai '20

+1-646-500-1521

ameen.alqadi@icahn.mssm.edu

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