Thanks Mark,


With regards to my registration woes, this is an old dataset from an  
old scanner. It turns out we have about 1/2 brain coverage for both the  
functionals and the Hi Res. We have full brain coverage T1 weighted 3D  
only. I have tried registering the HiRes to the 3D with 3DOF  and with  
6DOF, but either way my registration is terrible.

Also, my functional to HiRes are problematic. I used 3DOF and 6DOF and  
its clear the slices do not match up properly.

I could send you images if you would like. I am really at a loss at  
this point.

As for checking on BET, I don't see any prefiltered_func_data files  
that I can view. I see these files in the mc directory:
prefiltered_func_data_mcf.mat
prefiltered_func_data_mcf.par
prefiltered_func_data_mcf_abs.rms
prefiltered_func_data_mcf_abs_mean.rms
prefiltered_func_data_mcf_rel.rms
prefiltered_func_data_mcf_rel_mean.rms

As far as I can tell, none of these are images. I would like to check  
that BET is in fact working properly.

On Sep 25, 2006, at 4:20 AM, Mark Jenkinson wrote:

> Dear Jen,
>
> If your registrations are bad then I'd check the registration options
> in the registration tab.  If you look at your prefiltered_func_data
> then you can see if bet is doing a bad job or not, although I think
> it is more likely that your registration is failing due to small FOV
> or similar.  If you do have a small FOV then we recommend using
> an initial_highres image with a 3DOF transformation to align
> it with the functionals.  This image should, ideally have full FOV
> and the same contrast and distortions as the functional (i.e. an
> EPI with the same parameters but more slices).
>
> If you can't figure out what is wrong or how to fix it then let us
> know some more details and hopefully we can help.
>
> All the best,
> 	Mark
>
>
> On 23 Sep 2006, at 19:24, Bramen, Jennifer E. wrote:
>
>>
>> Actually, I am getting horrible registration. How can I check that  
>> the BET
>> options are appropriate?
>>
>>
>> -----Original Message-----
>> From: FSL - FMRIB's Software Library
>> To: [log in to unmask]
>> Sent: 9/22/06 11:26 PM
>> Subject: Re: [FSL] Error
>>
>> If you have only a few slices FEAT may change the default BET
>> preprocessing option and/or registration DoF to be more appropriate
>> to the FoV - you just need to check that what it has changed these
>> settings to is what you want.
>>
>> Cheers.
>>
>>
>> On 22 Sep 2006, at 19:52, Jennifer Bramen wrote:
>>
>>> Hi Guys,
>>>
>>> I am getting the following error:
>>>
>>> Warning-have auto-set BET preprocessing option and/or registration
>>> DoF on the basis of image
>>> fields-of-view; check settings.
>>>
>>> What does this mean?
>>>
>>> Thanks,
>>>
>>> Jen Bramen
>>
>>
>> ---------------------------------------------------------------------- 
>> --
>>
>> ---
>> Stephen M. Smith, Professor of Biomedical Engineering
>> Associate Director,  Oxford University FMRIB Centre
>>
>> FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
>> +44 (0) 1865 222726  (fax 222717)
>> [log in to unmask]    http://www.fmrib.ox.ac.uk/~steve
>> ---------------------------------------------------------------------- 
>> --
>>
>> ---
>>
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>
>
Jennifer Bramen
UCLA Brain Mapping Center
660 Charles Young Dr. So
Los Angeles, CA 90095


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