Thanks a lot for the answer!
Premise: my aim is putting the T1 (of different people) into the standard MNI152_T1mm and so I compare different ROIs.
Is this what you recommend? (I only ask to be sure)
STEP1: Create the –aff file for FNIRT.
--aff file is created with FLIRT. Then in terminal: flirt –in=myT1.nii –ref=MNI152_T1_1mm –omat=(I don’t know what to write)
The result of this command of FLIRT is xxx.mat file and this should be entered in FNIRT.
STEP2: use FNIRT twice. In terminal:
1. fnirt –ref= MNI152_T1_2mm.nii (or put it T1_2_MNI152_2mm.cnf?) –in=mybrain.nii aff=file.mat
2. and then: fnirt –ref= MNI152_T1_1mm.nii.gz –in=(output of the previous FNIRT) –iout=(any name) –fout=(any name)
• In the folder I find these files: pz1_to_MNI152_T1_1mm.log; pz1_warpcoef.nii.gz.
If the dots in the file names are the problem I can try to rename them all without any dot.
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