Dear Jesper,
I am sorry that I missed to correct the file names of the last 2 commands and I confused you with their inconsistency. Here is the correct set of commands I've used.
1) flirt -in IBSR_brain -ref /usr/share/fsl/4.1/data/standard/MNI152_T1_2mm_brain -out IBSR_brain_reg2MNIbrain_2mm.nii.gz -omat IBSR_brain_reg2MNIbrain_2mm.mat -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12 -interp trilinear
2) fnirt --in=IBSR --aff=IBSR_brain_reg2MNIbrain_2mm.mat --config=T1_2_MNI152_2mm.cnf --cout=coef_IBSR --iout=fnirted_IBSR
3) invwarp --ref=IBSR --warp=coef_IBSR --out=rev_coef_IBSR
4) applywarp --ref=IBSR --in=$FSLDIR/data/standard/MNI152_T1_2mm_brain --warp=rev_coef_IBSR --out=MNI152_T1_2mm_brain_reg2_IBSR
Thank you
Antonios Konstantinos
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