Newbie to SPM here using SPM8 to analyze some resting state data. Data comes to me as one MPRAGE and one rs per subject, already in NIFTI. My issue is that during initial "manual" reorientation
before realignment, while I can get the structural to align nicely with the EPI template, about half of the resting state images are horribly off. Here is what I am doing:
1. Recentering structural scan on AC, with y axis crosshair flat to AC-PC line
2. Reorienting both the structural and resting state to these coordinates
3. Use check reg to assess fit with EPI template
Should I not be reorienting the rs but only the structural? Am I missing some step specific to rs?
Other questions:
1. Does the "origin" specified in the uncorrected images in the right hand box in Display (which I assume is what the scanner thinks is the origin of the image) give me any clues? In almost every
case these are quite different between the structural and rs. If this means the subject moved significantly between structural and rs should I attempt to reorient the rs itself separately from the structural?
2. Should I set the crosshair flat to the AC-PC line? Have seen some guidelines saying the head should be tilted much further forward in SPM -- if so what posterior landmark should I look for?
Any help very much appreciated. Please be very basic and concrete! Thanks, Nina
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