Hello SPM community,
I am trying to warp MNI ROIs into subject space using the _sn.mat file generated during T1 normalization, but am running into trouble because of an atypical acquisition sequence. The normalized T1 (SPM8), looks good in SPM display and in MriCron, however, application of the _sn.mat file during the warp back to subject space using the Deformations utility produces really badly registered ROIs. Seeing this, I used FSL's fslhd command to read the header information and found that the qform (scanner read-in orientation) and sform (transform to atlas space) matrices are oriented in the following way:
xorient: ant.-to-post.
yorient: inf.-to-sup.
zorient: left-to-right
Given that these seem to be swapped (well, at least not RAS), if I change the order of the transformation matrix in the _sn.mat file to match the acquisition orientations, will the back-registration be accurate? Alternatively, is there a good way to alter the image to match a typical RAS acquisition? I did use a right-side fiducial so I can play around with the images a bit and check for flips.
Any help is greatly appreciated...I have yet to find anyone who has run into this.
Best,
Jennifer
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