Hi there
I was wondering if someone could help me with some mask issues I am currently having.
So far I have created three masks for each of my subjects (i.e. hippocampus, parahippocampal cortex and perirhinal cortex) based on anatomical guidelines using their highres structural image. As such, all of these masks are in the respective subjects structural space.
Next I would like to combine these masks to create a group level image across subjects in standard (MNI) space for use in a group level analysis. So far I have tried to register each image to standard space using FLIRT:
e.g. flirt -in rightphc.nii.gz -ref standard.nii.gz -applyxfm -init highres2standard.mat -out standard
This, however, makes the masks much much bigger than the originals, and results in the hippocampus, parahippocampal cortex and perirhinal cortex overlapping in individual subjects. The plan was (if this had worked) to combine each subjects newly registered hippocampus (for example) using fslmaths in two different ways to create a mask that comprises: 1) a combination of all hippocampal voxels in all subjects and 2) a combination of the hippocampal voxels that overlapped in all of the subjects only.
Any help with this would greatly appreciated
Cheers
Hilary
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