You can't do directly from preproc-sess, but you can do it from register-sess if you have an additional whole brain acquisition in the same session. This can be any acquisition (BOLD, MPRAGE, low-b DTI, etc) as long as it is whole brain. If your anatomical was acquired in the same session, then it is even easier because you can run register-sess with the -init-header option (instead of using fsl or spm). This assumes that the subject did not move more than 5mm between EPI and MPRAGE (usually the case). Let me know if this works for you. doug
On 6/5/12 6:03 AM, Jörg Pfannmöller wrote:
Dear Doug,
I am having a partial field of view and a full brain scan. How can I integrate the results in the preproc-sess sequence in order to complete the preprocessing correctly?
Cheers pfannmoe
On Mon, 04 Jun 2012 11:42:32 -0400 Douglas N Grevegreve@nmr.mgh.harvard.edu wrote:
You can try running register-sess outside of preproc-sess, something like register-sess -s session -fsd bold -per-run -init-spm
before you do that, you need to have spm5 and matlab, and change your matlab/startup.m to add the spm5 path path(path,'/usr/pubsw/common/spm/spm5');
doug
ps. Is this whole brain coverage or are you chopping off some of the brain
On 06/04/2012 11:36 AM, Jörg Pfannmöller wrote:
Dear Doug,
indeed the initialization fails. I was able to initiate bbregister manually, giving a good registration result. Can you give me a hint how to modify the registration and keeping the preproc-sess stream intact?
Cheers
pfannmoe
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