Dear experts
I am created spherical ROIs and registered in functional space, with the intention of extract timeseries and use them as seed regions for PPI analysis.
I didn't have any problem creating the mask, but the registration of the mask is completely off in many subjects (mask appears flipped A-P, L-R, or without any systematic offset in some cases), therefore I would like to check that I haven't done any mistake
in my analysis. Specifically:
1. I created a spherical roi (looks OK in fslview):
fslmaths $FSLDIR/data/standard/MNI152_T1_2mm_brain -mul 0 -add 1 -roi 57 1 15 1 36 1 0 1 Lmidocc -odt float
fslmaths Lmidocc -kernel sphere 5 -fmean LmidoccSph -odt float
2. In my first (non ppi) FEAT analysis I used nonlinear registration to standard space (12 DOF).
Since the inv warp was taking to long I first created a 2mm highres warp:
flirt -in highres -applyisoxfm 2 -ref highres -out highres_2mm
I then created the inverse of highres2standard_warp with:
invwarp
--force --ref==highres_2mm --warp=highres2standard_warp --out=highres2standard_warp_inv
(I had to force the command for the alarm message of too large ROI)
3. Finally I registered my mask in functional space:
applywarp --ref=example_func --in=LmidoccSph.nii.gz --warp=highres2standard_warp_inv --postmat=highres2example_func.mat
--out=LmidoccSphFS
Many thanks,
best wishes
Flavia
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Flavia Mancini, PhD
Research Associate
Institute of Cognitive Neuroscience
University College London