Hi FSL-users
I want to do an ROI analysis on DTI maps(FA,MD, RD) using the JHU white matter label template. I was able to use the JHU template for ROI analysis of white matter skeleton generated by TBSS. I did this by back projecting the JHU template to the skeleton native space using the deproject JHU template 2 and I used the -n option. The result from this process was a good transformation of "JHU ROI template" to native space. But to do a full ROI analysis I want to register the JHU template to native DTI maps(FA,MD,RD). So, I was wondering if any one has tried to warp the JHU White matter label template to native space. I tried doing this by Flirt and the results were not good. In the transformed template the ROI labels did not contain the same index number, I am guessing this is caused by the interpolation. I also tried the following set of commands that I found on the listserv. They resulted in the same outcome. Any suggestions or help is appreciated.
fsl_reg ${subj}.DWI2DT_FA.nii /usr/local/fsl/data/standard/FMRIB58_FA_1mm.nii.gz ${subj}.DWI2DT_FA.MNI-fsl-reg.nii -FA
convert_xfm -omat ${subj}.FMRIB58_to_FA_Native-fsl-reg.nii.mat -inverse ${subj}.DWI2DT_FA.MNI-fsl-reg.nii.mat
invwarp -w ${subj}.DWI2DT_FA.MNI-fsl-reg.nii_warp.nii.gz -o ${subj}.FMRIB58_to_FA_Native-fsl-reg.nii_warp.nii.gz -r ${subj}.DWI2DT_FA.nii
applywarp -i /usr/local/fsl/data/atlases/JHU/JHU-WhiteMatter-labels-2mm.nii.gz -o ${subj}.JHU_to_FA_Native -r ${subj}.DWI2DT_FA.nii -w ${subj}.FMRIB58_to_FA_Native-fsl-reg.nii_warp.nii.gz -d float -s --superlevel=a --interp=nn
Ish
