I want to obtain a brain structure network through DTI with AAL template as ROI.
However, when I opened
/usr/local/fsl/data/standard/MNI152_T1_2mm.nii.gz supported by FSL and the
AAL3v1.nii.gz template downloaded from the official website using
fsleyes, I noticed a mismatch.
As shown in the picture, the upper left part is slightly out of the brain, and the lower left part does not have a label in the Gray Matter.
And it is definitely the right brain, but the label of the left about one or two voxels invades the right part.
Looking at this, I wonder if the structure network can be obtained accurately by using the AAL template, and I wonder if the volume of the ROI is accurate.
Can you confirm if it’s just me?
There is a typo in my post, I will correct it.
In the first picture, the label of the AAL template in the upper left (right brain) invades outside the brain,
In the lower right (left brain), the labels are lacking.
And in the second picture, the green line designates the right brain, but the label is the label of the left brain. (In the AAL template, the right brain is an even number, the left brain is an odd number, and the center is labeled as the left brain, but the corresponding part is labeled as the left brain even though it is the right brain)
In my view, a volume-based atlas based on the MNI space always has a ‘mismatch’, since the registeration between two images can not be that ‘accurate’. Maybe you can download the latest AAL atlas from their offical website AAL / AAL2 / AAL3 – Neurofunctional Imaging Group (GIN-IMN) (cnrs.fr), and check the issues you mentioned.