Thanks, Ameen. We'll look into this and let you know.
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Al Qadi, Ameen
<ameen.alq...@icahn.mssm.edu>
Sent: Wednesday, January 29, 2020 11:04:46 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] TRACULA Preprocessing Error
External Email - Use Caution
Hi Anastasia,
There wasn't a directory called "elmo.2005" in diffusion_recons, only a
directory called "Diff001". I had to copy the elmo.2005 directory from
diffusion_tutorial to diffusion_recons to get tract-all to run.
Best,
Ameen
On Tue, Jan 28, 2020 at 8:48 PM Yendiki, Anastasia
<ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>> wrote:
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
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Al Qadi, Ameen
<ameen.alq...@icahn.mssm.edu<mailto:ameen.alq...@icahn.mssm.edu>>
Sent: Tuesday, January 28, 2020 5:38 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] TRACULA Preprocessing Error
External Email - Use Caution
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.alq...@icahn.mssm.edu<mailto:ameen.alq...@icahn.mssm.edu>
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--
Ameen Al Qadi
MSBS Candidate
Icahn School Of Medicine at Mount Sinai '20
+1-646-500-1521
ameen.alq...@icahn.mssm.edu<mailto:ameen.alq...@icahn.mssm.edu>
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