MPRAGEised uniform image + INV2 stripmask misalignment

[ndrewvo]

Hi! I'm using presurfer to prepare some MP2RAGE images for FreeSurfer. The code itself runs without issue and provides the expected outputs. When I open the images (i.e., *_UNI_MPRAGEised.nii and *_INV2_stripmask.nii) in ITK-SNAP, they are significantly aligned, however. It seems like Step 0 (MPRAGEise UNI) shifts the image because stripmask does align with the raw *_UNI.nii image. Am I loading the wrong files, or might there be an issue in my input files (although they look normal from visual inspection)? Thanks in advance for any help!

[srikash]

Hi Andrew. That's quite odd behaviour. All four MP2RAGE images are (by design) in register. Do you by chance have data from multiple sessions? Feel free to share a screenshot of what the problem exactly is!

[ndrewvo]

Hi Sriranga, I don't have multiple session data, just a single acquisition per subject. I've included two screenshots in which I've overlaid the INV2_stripmask (green) and the UNI_brainmask (blue) over either the raw UNI image or the MPRAGEised image. You can see that the stripmask aligns with the raw UNI but not MPRAGEised image, whereas the brainmask aligns with the MPRAGEised but not raw UNI image.

[srikash]

I haven't had this happen to with any of my data before. I would have to hazard a guess that some part of SPM alignment could be failing here.
Short of sharing the data for me to take a closer look, I can suggest one thing to try first: you could download try running this script first. Then, try presurf_MPRAGEise on the output files.