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
trac-all.log
Description: Binary data
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