Hello all,
I am trying to find the best way to align native FA maps to MNI space in order to use the JHU atlases provided by Mori's group to extract out FA values for each DTI ROI. I have come up with one method that seems to work, but I want to make sure it is the best way to do this.
So currently I take my processed FA maps that are in native space for each individual and I run the following command:
fsl_reg ${subj}.DWI2DT_FA.nii /usr/local/fsl/data/standard/FMRIB58_FA_1mm.nii.gz ${subj}.DWI2DT_FA.MNI-fsl-reg.nii -FA
To my knowledge this is essentially the same command used by TBSS when registering each subject to the predefined standard target. That is, this essentially uses nonlinear registration (FNIRT) to align the FA map of each subject to the FA template FMRIB58_FA_1mm.nii.gz. Can you confirm that this interpretation is correct (or feel free to correct me)?
This gives decent results for most subjects (in terms of aligning the subject to MNI space and having the JHU ROIs overlay on the correct white matter structure... i.e. the genu of the CC), and is far more superior than trying to use FLIRT or FNIRT to align the FA map to the T1 weighted MNI standard brain. So I guess my question is, is this the best method to try to align individual FA maps to standard space to extract FA values for each of the JHU ROIs? Is there another method that would be more appropriate? And lastly, our DTI data is in 2x2x2 mm voxels prior to this alignment, and then of course it is resampled down to 1x1x1 mm. I prefer not to resample the data more than need be, so is there a way to use the following fsl_reg command listed above, or another command that may nicely warp the FA data into MNI space that doesn't require the data to be sampled into 1x1x1 space?
Any suggestions or tips would be very much appreciated! Thank you for your time and help!
Megan
