External Email - Use Caution        

Hi everyone,

I have used both T1 and (T2) Flair images as inputs to recon-all, and I have generated some coordinates (ROI) that I can transform to the original T1 images. Basically, I use the two matrixes obtained from the mri_info -- vox2ras commands:

        Sr = mri_info --vox2ras  $SUBJECTS_DIR/$subject/mri/orig/001.mgz
        Sc = mri_info --vox2ras  $SUBJECTS_DIR/$subject/mri/T1.mgz  

For a given point Coordinate=(x, y, z, 1) in the conformed space, I get the coordinates in the original T1 space using the formula:

        t1_Coordinate = inv(Sr) * Sc * Coordinate.

The above formula works fine. But I also want to get the transformed coordinates in the Flair image space. I have used a similar way:

        Srf = mri_info --vox2ras  $SUBJECTS_DIR/$subject/mri/orig/FLAIRraw.mgz
        Sc = mri_info --vox2ras  $SUBJECTS_DIR/$subject/mri/T1.mgz  
        flair_Coordinate = inv(Srf) * Sc * Coordinate.  

But the above calculation is not correct. Does anyone have an idea of how to get this flair coordinate?

Thank you!!!

Xiaojiang