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> 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 < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Al Qadi, Ameen < > ameen.alq...@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 > > > 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 > _______________________________________________ > Freesurfer mailing list > 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.alq...@icahn.mssm.edu
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