Hi:
I have some patient data with enlarged ventricles and atrophied parietal cortex(old and stroke), and I want to register the T1 to the MNI152 T1 1mm template.
I reviewed some comments, the 1mm template is not recommend with FNIRT, as it doesn't have a particular advantage given the current resolution of the warp(10*10*10), and the higher resolution of warp can cost much more execution time and memory. But when registering atrophied brains with a 10mm warp resolution,it is said that the resolution isn't quite enough and the widened sulci aren't "closed up" properly.
The execution time and memory won't be a problem for me, as I can use the High Performance Computing Cluster in my lab.
So I want to use a higher resolution of the warp and use the 1mm T1 as the reference image when estimate the warp. I read the user guide for FNIRT, but I can't work out the parameters in the config file by myself, can you help me with the more accurate config file?
the T1_2_MNI152_2mm.cnf containing:
--subsamp=4,4,2,2,1,1
--miter=5,5,5,5,5,10
--infwhm=8,6,5,4.5,3,2
--reffwhm=8,6,5,4,2,0
--lambda=300,150,100,50,40,30
--estint=1,1,1,1,1,0
--applyrefmask=1,1,1,1,1,1
--applyinmask=1
--warpres=10,10,10
--ssqlambda=1
--regmod=bending_energy
--intmod=global_non_linear_with_bias
--intorder=5
--biasres=50,50,50
--biaslambda=10000
--refderiv=0
Best wishes
Yijun
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