I’m currently trying to pull FA and MD metrics from a DWI image I ran through 5ttgen. Since I added a pathology image, I am unsure how to account for that. I registered my 5tt output to DWI space.
Before I added the pathology scan, I was able to do this by pulling the 5tt wm mask and converting to a tensor with
mrconvert -coord 3 2 5tt.mif wm_mask.nii.gz dwi2mask dwi_denoised_unringed_preproc_unbiased.mif dwimask.nii.gz dwi2tensor dwi_denoised_unringed_preproc_unbiased.mif tensor.nii.gz -mask dwimask.nii.gz
And then I pulled the metrics and wrote out to files via
tensor2metric tensor.nii.gz -fa wm_FA.nii.gz tensor2metric tensor.nii.gz -adc wm_MD.nii.gz mrgrid wm_mask.nii.gz regrid -template wm_FA.nii.gz wm_mask_regrid.nii.gz mrstats -ignorezero -output mean -mask wm_mask_regrid.nii.gz wm_FA.nii.gz >> FA.txt mrstats -ignorezero -output mean -mask wm_mask_regrid.nii.gz wm_MD.nii.gz >> MD.txt
Would I have to do a subtraction of sorts from the wm mask by the path image before generating the tensor? Can I skip regridding since I have already registered to DWI space?
Thanks so much, please excuse my novice knowledge on the topic- I’m more used to working with fMRI!