Hi Ravi,
Indeed, the FSL tools involved in the FSL-VBM protocol will not be able to identify the relevant structure in your noisy, subtraction images. I am a bit confused though, you mention having already normalised grey matter images, what do you mean by that exactly?
Regardless, the easiest is to run FSL-VBM on all your images (pre and post), and at the end, before smoothing the registered GM images, to do the subtraction in the standard space. This is a somewhat suboptimal, yet unbiased way of analysing longitudinal datasets. If you want a more optimised protocol, involving halfway space, please have a look at the FSL archives, doing a search on my name and longitudinal VBM.
Cheers,Gwenaëlle
Hello FSL Experts,
I am trying to run the FSLVBM protocol with subtraction images to look at differences from a pre-post condition. We have design our design and contrast matrices so we can look at correlations to behavioral variables. What we first did was subtract normalized grey matter images (pre-post), and used those as our files to select for “template_list” and“struc” files.
Since the brains are already extracted, we didn’t think it was necessary to run the BET protocol, so we went straight into fslvbm_2_template. Not surprisingly, we ran into errors.
It would be greatly appreciated if someone could please provide some guidance on how to do this type of analysis with FSLVBM. Thank you!
Ravi
________________________________
UCLA HEALTH SCIENCES IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.
