TL;DR: white matter template mask created through dwiintensitynorm has different dimensions compared to input DWI/mask files. Why is this the case?
Hello all,
My lab has recently completed the AFD workthrough, which means we have an FOD template of 15 subjects in specific dimensions (93x112x88).
I’ve created a white matter template based off of these 15 subjects, and the DWI and mask images used as input were all transformed into the FOD template space.
What’s peculiar is that although the input DWI and mask images shared the same dimensions, the output FA and WM template files had changed dimensions. Rather than being like the DWI/mask inputs of 93x112x88, the FA and WM template files were in the dimensions of 86x108x84.
The specific commands I used are as follows:
Transforming DWI images to FOD template space:
for i in sub*; do mrtransform ${i}/cbed${i}_dwi.nii.gz -warp ${i}/subject2template_warp.nii.gz dwi_in_template_space_dir/dwi_${i}.nii.gz -fslgrad ${i}/e${i}_dwi.bvec ${i}/e${i}_dwi.bval; done
Converting DWI images to .mif format to retain bvec/bval information (the directories were changed from the one referenced above):
for i in sub*; do mrconvert template_dwi_2/PRE_${i}.nii.gz template_dwi_3_mif/PRE_${i}.mif -fslgrad ${i}/e${i}_dwi.bvec ${i}/e${i}_dwi.bval; done
dwiintensitynorm:
dwiintensitynorm template_dwi_3_mif/ template_mask_2/ dwiintensitynorm_dir_2/ new_population_FA_template.nii.gz new_population_WM_mask_template.nii.gz -force
I then warped the WM mask template into FOD template space as follows:
I used only one subject’s subject2template_warp file - please let me know if this is an error & if it’s necessary to somehow use all subjects’ subject2template_warp files.
Was there an error in the way I created the WM template file which caused the dimension mismatch?
Thank you very much,
A