Thanks, Helmut!

For the Atlas & Probabilistic Masks, a Registration Form need to be filled and sent to [log in to unmask]. Then the agreement is required by the current contact person -- maybe they changed their policy.

Dr. Nie (2013, Human Brain Mapping) kindly sent me their template (tissue priors are still under working).

Also, Dr. Schwarz (2006, Neuroimage) kindly sent me his templates as well. He also provides probability maps for brain parenchyma, CSF, and muscle. I am not sure if these "parenchyma, CSF, and muscle" files can be feed into New Segment and DARTEL. Basically, I am trying:

1. Lineally Coregister each rat to the template.

2. Test which of the following strategy can work.

2.1. Feed "parenchyma, CSF, and muscle" files to New Segment and do DARTEL.

2.2. Apply brain mask and feed into FSL's FAST->create tissue priors->Feed into New Segment+DARTEL.

2.3. If the above doesn't work, simply normalize (nonlinear) each rat to the template.

Thanks a lot for your inputs!

Best,

Chao-Gan

On Thu, Oct 31, 2013 at 8:32 AM, H. Nebl <[log in to unmask]> wrote:

This is interesting to know. Our lab had received a copy of the Kawashima templates one and a half or maybe two years ago, at that time they didn't require co-authorship. As we didn't continue with animal fMRI I don't know when they changed their politics, maybe it was a consequence of people quitting the lab. But it is strange that they don't state anything related on their website http://www.idac.tohoku.ac.jp/bir/en/db/rb/ and it seems the T2 template can still be obtained without coauthorships.

What about the other workgroup, Nie et al. (2013, Human Brain Mapping)? Did you have any success?

Leaving this aside, do you really need priors for GM and WM? If you just want to use segmentation to normalise fMRI or PET data onto a template, then priors for CSF and brain tissue (or standard normalisation with a simple T2 template) might be sufficient. Rat brains are much less variable compared to e. g. human brains.

Chao-Gan YAN, Ph.D.

Research Scientist

The Nathan Kline Institute for Psychiatric Research, 140 Old Orangeburg Road, Orangeburg, NY 10962

Center for the Developing Brain, Child Mind Institute, 445 Park Avenue, New York, NY 10022

The Phyllis Green and Randolph Cowen Institute for Pediatric Neuroscience, New York University Child Study Center, New York, NY 10016

Initiating + Service Node

The R-fMRI Network (RFMRI.ORG)

http://rfmri.org/yan

http://scholar.google.com/citations?user=lJQ9B58AAAAJ&hl=en