Friday, 13 February 2015

TRACULA - if reconstruction of tract fails

After all processing steps you will need to check the reconstruction of the white matter tracts either by viewing each tract individually:

freeview -v $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dmri/dtifit_FA.nii.gz \
            $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/rh.ilf_AS_avg33_mni_bbr/path.pd.nii.gz:colormap=jet:isosurface=0,0:color='Red':name=rh.ilf \
            $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr/path.pd.nii.gz:colormap=jet:isosurface=0,0:color='Red':name=lh.ilf

Or by viewing the tracts simultaneously:

freeview -tv $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/merged_avg33_mni_bbr.mgz \
         -v $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dmri/dtifit_FA.nii.gz &


If you notice that any of the tracts look wrong, or do not appear in 3D at all, this may mean that the intialisation of the tract failed and will need to be corrected.

To re-run this, you will need to add in a command to the config.file that you have set up. Just before specifying which tracts to reconstruct add the command ' set reinit = 1'.

You will then also need to specify below, which tract/tracts need to be reinitialised. Remember to also change the number of controls points. ( Any number greater than 2 is a valid choice but, as a rule of thumb, a fairly straight pathway can be modeled using only a few control points, whereas a highly curved pathway may require more control points. The default, as shown above, is to use 7 for the forceps major, 6 for the corticospinal tract, 4 for the angular bundle, and 5 for all other pathways.)

Then also specify which subject this needs to corrected for.

You can then run two commands:

trac-all -prior -c /home/config.file

trac-all -path -c /home/config.file

Re-check the paths.

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