Hi Matthew,
Thanks for the ongoing help and sorry for my delayed response. As I wrote, I analyze the data of a single run, and therefore, I had to register the native ttest map to MNI :
/usr/local/fsl/bin/flirt -in tstat1 -ref /usr/local/fsl/data/standard/MNI152_T1_2mm_brain -out tstat1_MNI -applyxfm -init featfolder/reg/example_func2standard.mat -interp trilinear
The tstat1_MNI is the output of this registration
Warm wishes,
Erez
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