Thanks a lot for the answer!
Premise: my objective is to put the T1 (of different people) into the standard MNI152_T1mm and so I compare different ROIs.
What do you recommend is this? (I write specifically for security)
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 preceding FNIRT) –iout=(any name) –fout=(any name)
• In the folder I find these files: pz1_to_MNI152_T1_1mm.log; pz1_warpcoef.nii.gz.
The _warpcoef file contains the non-linear warp that can be used to transform your image to the target (--ref) using applywarp. I am not sure why you don’t also get the --iout (warped --in image) or the --fout output, but I strongly suspect it has to do with the . in the filenames.
For this I try to rename files without points .
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