Hi all,
I noticed my FA map output from DTIFIT has white matter brain
voxels of 0 and >1. I ran the following procedures to get the FA
map.
i.eddycorrect on the original DTI
ii.bet the eddycorrected data.nii.gz (or the 1st B0) to derive the
nodif_brain_mask.
iii.feed the nodif_brain_mask, data.nii.gz,bvecs and bvals into DTIFIT.
If the original data is ok, could a problem with the bvecs file result
some brain voxels with 0 intensity (or intensity>1) in the FA map output
from the DTIFIT procedure?
Initially, I thought it may be a problem with the original DTI data,
however, it is a standard MGH 30 dir sequence, and the gradient file is
from the diffusion toolkit. I ran the data on another DTI software and
the FA map output doesnt seem to contain 0 intensity voxels, but it may be
a scaling issue??
The solution I tried with FSL is to do BET using the -F function (normally
used for 4D FMRI). The resulting FA map from DTIFIT only then will not
contain 0 intensity voxels, but still have voxels of intensity>1. I notice
this is not the standard way to process (BET) DTI data.
I am concern about this as I have significant positive results from the
tbss FA voxel analysis. I wonder if these results would be independent of
the fact that some voxels in the FA maps are >1. Also, I could not analyse
the tbss using the FA maps from the standard processing pipeline due to
some brain voxels having 0 intensity.
May I ask if using BET with -F is ok? Has anyone has come across this
problem before, and may explain why there may be voxel with 0 intensity or
intensity>1 in the FA maps output?
Many Thanks for some kind advice.
Siewmin
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