Hi
I have some partial FoV functional scans that I'm trying to register to standard space. I don't have any functional images of the entire head. However, I do have T1 scans that were taken at the same time as the functional scans.
I've looked on the FSL wiki and done some experimenting. I've found that epi_reg seems to be fairly robust against partial FoV effects, so I've been taking the following steps:
1. I use epi_reg to to register the functional images to T1 space.
2. I use flirt to register the t1 scan to the MNI standard space image.
3. I concatenate the functional-to-T1 transformation matrix with the T1-to-standard transformation matrix.
4. I apply the concatenated matrix to the original functional scan, registering it to standard space.
Is that how I am supposed to do that? Or is there a better way?
However, I've run into a strange problem. I've compared the image output by epi_reg to the image being used as a reference volume, and the output image always looks like it's been shifted a few pixels upwards (in the superior direction).
I don't know what could be causing this. Do any of you have ideas?
Also, I have a few other questions about epi_reg
Am I supposed to input skull-stripped functional images or whole head functional images to epi_reg?
If I am supposed to submit whole head functional images, can I skull-strip the scans after they've been registered to standard space?
Thank you for your time,
Kyle
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