I have a problem that looks a bit similar to the ongoing discussion here. I will quickly provide a summary of my work and what I have done so far. I work on a project that aims to validate a toolbox the goal of which is to generate a prediction about the white matter streamlines that will be affected following ischemic injury in a cohort of patients. The lesion volumes served as input for the toolbox and we have two DTI scanning sessions that we are comparing - session 1 and session 2. The output consisted of streamlines that will be affected by the stroke for each patient for each lesion volume (mostly comprising the ipsilesional CST). We also generated control output for this by swapping the simulated streamlines to the contralateral side (contralesional CST).
So far, I performed all the preprocessing using the MRTrix functionality, and generated maps of fa, md, ad and rd in order to compare these tensor parameters and their change from session 1 to session 2 post-stroke in both hemispheres.
I wanted to have a comparison between the affected hemisphere (affected CST) and control hemisphere (control CST) so I generated masks with mrcalc. In so doing, I generated two ROIs: the simulator output and its respective control.There were also some areas where the two outputs would overlap (cross) so I created a mask for the overlap containing the bilateral areas and the inverse mask of this overlap as these regions would not be perfect as lesion/control ROIs. When generating the masks and creating the overlap mask I used the following commands and everything worked fine. Then I generated the txt. files for the tensor-derived values and everything looked good.
mrcalc riwsub01ses2_lesion_simlesion_mean.nii 1.0 -gt riwsub01ses2_lesion_simlesion_mean_mask.nii
mrcalc sub01_lesion_roi.nii sub01_control_roi.nii -add sub01_overlapping_roi.nii
mrcalc sub01_overlapping_roi.nii 2. -lt sub01_invmask_roi.nii
Now I want to make the analysis along the predicted streamlines more focused along the CST (just like what one would do when manually drawing ROIs along the length of the CST to assess changes at various distances from the primary lesion). Thus, I want to threshold the simulation output files to focus on voxels with a distance larger than 0 until the threshold of 10mm, 20 mm, etc. (>1 and <10mm).
So I repeated the former steps that worked fine and thresholded the distance of 10 mm to begin with:
mrcalc riwsub01ses2_lesion_distance.nii 1.0 -gt 10.0 -lt riwsub01ses2_lesion_distance_mask.nii
However, this does not seem to work as the generated mask does not show a portion of the CST and the subsequently generated tensor txt. values (fa, md, ad and rd) are all 0. Do you have any advice on what could have gone wrong? Do I need to use tcksample and specify distances like that?
Thank you very much for your expert advice on this!