Hi,
I hope to get some advice on the following (Sorry if this is a very basic question, but I couldn't find the answer in previous posts).
I am trying to transform the coordinates of an ROI from MNI space (1mm) to the original non-transformed T1 space. I have tried both img2img and std2img (vox and mm), however, both options give different coordinates when I tried it. After visually inspecting, both coordinates do not correspond to the anatomical region of the ROI in MNI space (quite often even outside the brain).
I used the following code (coordinate is just a random example):
echo 73 156 78 | img2imgcoord -dest T1_subject1_brain.nii -src MNI152_T1_1mm_brain.nii -vox -
echo 73 156 78 | std2imgcoord -std MNI152_T1_1mm_brain.nii -img T1_subject1_brain.nii -vox -
Also, I have tried including '-xfm inversed_matrix_subject1_to_std_sub.mat' (.mat file created with FIRST hippocampus segmentation and inverted with convert_xfm), but this didn't work either. I must be doing something wrong..
I would really appreciate your suggestions.
Thank you.
Kind regards,
Liza
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