Hi! I’m working through a multi-tissue FBA analysis. So far so good, but I’m unclear on how to handle tensor metrics (FA, RD, etc) I’m also interested in. Apologies in advance for the newbie questions.
My plan is detailed below, but I’m not sure if a) I should even be converting the tensor metrics to fixels (vs running mrclusterstats), and b) if I should, then do I have the correct steps below (e.g, not sure if I need to reorient and assign these fixels).
- Calculate tensors (dwi2tensor)
- Calculate tensor metrics (tensor2metric)
- Register metrics to population template:
mrtransform \
-reorient_fod no \
./tensor_metrics/${sub}_${ses}-${metric}.mif \
-warp ./template/FODs_in_template_space/${sub}_${ses}-to-template_warp.mif \
./tensor_metrics/${sub}_${ses}-${metric}_in_template_space.mif
- Continue with conversion to fixels or just run mrclusterstats on the registered output from step 3?
voxel2fixel \
./tensor_metrics/${sub}_${ses}-${metric}_in_template_space.mif \
./template/fixels/${sub}_${ses}-fixel_in_template_space \
./template/tensor_metrics_fixels/${metric}/${sub}_${ses}-${metric}-fixel \
${sub}_${ses}-${metric}-fixel.mif
- Reorient:
fixelreorient \
./template/tensor_metrics_fixels/${metric}/${sub}_${ses}-${metric}-fixel \
./template/FODs_in_template_space/${sub}_${ses}-to-template_warp.mif \
./template/tensor_metrics_fixels/${sub}_${ses}-${metric}-reoriented
- Assign:
fixelcorrespondence \
./template/tensor_metrics_fixels/${sub}_${ses}-${metric}-reoriented/${sub}_${ses}-${metric}-fixel.mif \
./template/fixels/fixel_mask \
./template/tensor_metrics_fixels/${metric}-reoriented-assigned \
${sub}_${ses}-${metric}.mif
- Run fixelcfestats.
Thanks!
Mark