Possible Alignment Problems

We are running a lot of subjects using the standard proc.py process and we have identified patterns/abnormalities among the subjects. We are not sure if these patterns are acceptable as is or if we need to run additional functions to get a better alignment. We’ve categorized the patterns into 6 types of groups:

  • Chunk missing from OFC
  • OFC shifted up
  • Halo/Ghosting
  • Parietal Bump
  • Shrinking
  • Whole brain shift
    I’ll attach images to show examples of each group. I’ve attached the first 4 of 6 images to this post. I’ll attached the remaining two as a separate reply


Remaining 2 images


It’s a bit difficult to tell what’s going on from these images. If you’re amenable, I will PM (private message) you with instructions on uploading data, and I will take a look.

Hi Daniel,

Thank you for your response. Yes please, can you send me instructions on a better way to upload data?
Also, is there anything in particular you’d like me to send you?


I sent a PM to you earlier with upload instructions. Look for the “Private Messages” text on the upper right. You should send the minimal amount of data to reproduce this problem. An EPI dataset and anatomical dataset, for instance. Also some text showing what you tried.

The new upload server is now password protected, so I’ve PM’ed you with updated instructions.