Hi,
I'm using FLIRT to register the FSL-FIRST segmentation to MNI space:
flirt -in ${subj_id_nosuffix}_first12_all_fast_firstseg.nii.gz -ref $FSLDIR/data/standard/MNI152_T1_1mm_brain -out ${subj_id_nosuffix}_first12_all_fast_firstseg_std.nii.gz -init ${subj_id_nosuffix}_to_std_sub.mat -applyxfm
In my output file I observe a lot of scattered points with values that suggest that they belong to the subcortical structures. These scattered point are not in the original file that I get from FIRST.
FSL version 4.1.9, but I don't know how to find out the version of FLIRT.
I would be very greatful for any hint.
Thank you very much!
Best wishes,
Katharina
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