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DWI & tractography preprocessing output check
After you have finished preprocessing each of your subjects and before you move on with your analysis you will want to visually inspect your outputs.
Open NoMachine and navigate to your project. You will use mrview to visualise the outputs so first module load mrtrix3. Then enter “mrview” to open the program.
The first thing you want to check are the boundaries drawn between the grey and white matter. If this is not delineated correctly, streamlines will not terminate reliably at the GM or may be missing from areas of the WM.
You will want to open the T1brain_Registered file (Use File > Open… from the top of the window), overlayed with the 5TThsvs file (select the overlay tool from the Tool menu). You can press the arrow on the right under the overlay selection window to move through the volumes. Volume 0 is the GM and volume 2 the WM. Move through the brain either with the cursor or up and down arrow keys.
The next thing you will check is the streamlines. Hide the HSVS file in the overlay by unchecking it and then open the 200k .tck file (select tractography from the Tool menu). Move through the brain and check the streamlines do not go beyond or are missing from the white matter in places. Also check that the streamline directions seem to be anatomically correct by looking for clusters of streamlines you expect to go in a certain direction. The following three should be easy to locate.
Corticospinal tract in blue (top to bottom):
Longitudinal fasciculi in green (front to back):
Corpus collosum in red (left to right):
Instead of opening each file manually, you can use the lines of code below to open all the relevant files for a subject.
sub='FTDXXXX'
mrview Preprocessing/${sub}/${sub}_T1brain_Registered.mif.gz -overlay.load Preprocessing/${sub}/${sub}_5TThsvs.mif.gz -overlay.threshold_min 0.1 -tractography.load Preprocessing/${sub}/${sub}_tracks_200k_iFOD2.tck -mode 2
Depending on the type of analysis you will carry out, it can be helpful to also quickly check over your processed DWI. You can use the command below rather than the one above to open the DWI along with the other files you will check. You can check the DWI-T1 co-registration by decreasing and increasing the opacity of the DWI over the T1. Also look for bright spots outside of the brain or any other abnormalities in the DWI. This may affect your group template later on.
mrview Preprocessing/${sub}/${sub}_T1brain_Registered.mif.gz -overlay.load Preprocessing/${sub}/tmp/${sub}_DWI_Denoised_Unringed_PreProc_BiasCorr.mif.gz -overlay.load Preprocessing/${sub}/${sub}_5TThsvs.mif.gz -overlay.threshold_min 0.1 -tractography.load Preprocessing/${sub}/${sub}_tracks_200k_iFOD2.tck -mode 2