External Email - Use Caution
Hello,
I am still having the same issue as in my previous post. I have
successfully run dt_recon and upon looking at the images there seems to be
no issue with the registrations of outputs including the FA, lowb and other
images.
I wanted to mask my FA images using the wmparc.mgz image from recon-all
using
mri_vol2vol --mov $subj_dir/dtrecon/${subj}.${cond}./lowb.nii.gz --targ
$subj_dir/diffusion_recons/${subj}.${cond}/mri/wmparc.mgz --inv --interp
nearest --o
/Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/mri/wmparc2diff.mgz
--reg $subj_dir/dtrecon/${subj}.${cond}./register.dat --no-save-reg
This works perfectly for all of my subjects except 2 of them. These
subjects seem to have normal lowb, wmparc, and FA images compared to the
other 58 subjects. However, the wmparc2diff that is created from
mri_vol2vol has significantly shifted away from the lowb and fa so that
when I try to mask the fa with
mri_mask $subj_dir/dtrecon/${subj}.${cond}./fa.nii.gz
/Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/mri/wmparc2diff.mgz
$subj_dir/dtrecon/${subj}.${cond}./fa-masked.nii.gz
It cuts a large part of the brain off and masks incorrectly.
Is there a way to troubleshoot the registration of wmparc to wmparc2diff? I
am not sure why the registration is so off?
Any troubleshooting help for why the registration of the segmentation to
diffusion space is so poor (or if the issue is registration from diffusion
space to anatomical space) would be greatly appreciated.
Best,
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com <ddcc2...@gmail.com>*
443-254-6298
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