Dear FSL mailing list,
I wanted to inquire to see if I am correctly extracting mean FA from each individual subject based on ROIs from the JHU white matter labels atlas. I currently seem to be getting some strange negative correlations between my behavioural measure and FA when I extract mean FA from the JHU labels. My TBSS results show only positive correlations.
Here are the steps I was using. I have data with 2mm voxels so I was not sure whether I should be using the 1mm template or 2mm one and which .cnf file to use. This script works, but I am just puzzled by the negative correlations from the ROIs. Please let me know if I am doing something wrong when warping the labels to native space and extracting mean FA from each region.
flirt -ref /usr/local/fsl/data/atlases/JHU/JHU-ICBM-FA-1mm.nii.gz -in subject1_FA.nii.gz -out flirted_JHU_ICBM_FA_1mm_subject1 -omat JHU_ICBM_FA_1mm_to_target_subject1.mat
fnirt --ref=/usr/local/fsl/data/atlases/JHU/JHU-ICBM-FA-1mm.nii.gz --in=subject1_FA.nii.gz --aff=JHU_ICBM_FA_1mm_to_target_subject1.mat --cout=coef_JHU_ICBM_FA_1mm_to_target_subject1 --iout=fnirted_JHU_ICBM_FA_1mm_subject1 --config=FA_2_FMRIB58_1mm.cnf
invwarp --warp=coef_JHU_ICBM_FA_1mm_to_target_subject1 --ref=subject1_FA.nii.gz --out=invwarp_subject1
applywarp -i /usr/local/fsl/data/atlases/JHU/JHU-ICBM-labels-1mm.nii.gz -o warpedlabels_subject1 -r subject1_FA.nii.gz -w invwarp_subject1.nii.gz --interp=nn
fslmaths warpedlabels_subject1.nii.gz -thr 1 -uthr 1 region1_subject1
fslmaths subject1_FA.nii.gz -mas region1_subject1 region1_subject1_masked
fslstats region1_subject1_masked -R -M -S
Best wishes,
Anna
|