Dear Zhewei,
I think that the problem you report is caused by the fact, that .mat file from FLIRT codes vox2vox transformation, so that cannot be applied to another dataset (in your case fMRI) unless it has the same geometry as the original image the .mat file was generated on.
Antonin
Can you send your freeview command line and pictures of the mismatch? On 2/9/17 5:58 PM, Zhewei Wang wrote: Hi all,
I have a problem maybe relevant to the orientation of images in freeview. I have two images, one is fMRI and one is MRI. They are produced from the same machine at the same time. I loaded both of them in freeview and it showed they are matched very well, even they have different resolutions, different orientation (fMRI is LAS and MRI is PSR), different sform and qform. I registrated MRI to MNI152, and a transformation matrix is generated. I apply this matrix on fMRI, then I got the wrong result: I loaded the fMRI after transformation and MNI152 in freeview, they are not matched. I use /flirt/ for registration. Can anyone explain to me why it happened? At beginning they are shown matched in freeview, even they have different orientation. After apply same transformation, they are shown not matched in freeview even they have same orientation now (both are LAS). Thank you so much.
Zhewei