Dear FSL community,
I wonder if it's feasible to run FNIRT to coregister using a high-res MNI template (e.g. the 2009b nlin series in 0.5x0.5x0.5mm resolution). My anatomical file is of 0.7x0.7x0.7 resolution.
If I try using a modified T1_2_MNI152_2mm.cnf, the command runs >12 hours and is not really feasible on a laptop.
Any ideas how I could make this work or whether I'm doing something wrong?
The full command I use is the following:
[' --ref=mni_hires.nii.gz --in=anat.nii.gz --aff=aff_anat2mni.mat --inmask=anat_mask.nii.gz --refmask=bmni_hires.nii.gz --iout=anat_2mni.nii.gz --cout=warp_struct2mni.nii --verbose --subsamp=4,4,2,2,1,1 --warpres=8,8,8 --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 --ssqlambda=1 --regmod=bending_energy --intmod=global_non_linear_with_bias --intorder=5 --biasres=50,50,50 --biaslambda=10000 --refderiv=0 --applyrefmask=1,1,1,1,1,1 --applyinmask=1']
Since this is for DBS imaging, I need a high resolution overall. Also tried with the standard --warpres=10,10,10 which still takes >12 hrs.
Thanks so much for any hint/suggestion!
Best, Andy
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