Thanks, Ameen. We'll look into this and let you know. ________________________________ 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: Wednesday, January 29, 2020 11:04:46 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA Preprocessing Error

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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 <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Al Qadi, Ameen <ameen.alqadi@icahn.mssm.edumailto:ameen.alqadi@icahn.mssm.edu> Sent: Tuesday, January 28, 2020 5:38 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:ameen.alqadi@icahn.mssm.edu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Ameen Al Qadi MSBS Candidate Icahn School Of Medicine at Mount Sinai '20 +1-646-500-1521 ameen.alqadi@icahn.mssm.edumailto:ameen.alqadi@icahn.mssm.edu