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Thanks so much!

On Sat, Aug 1, 2009 at 5:33 AM, Mark Jenkinson <[log in to unmask]> wrote:

> Hi Nicole,
>
> This looks fine to me.
> Sometimes I would say that we get better results for step 1
> by using the skull-stripped image for T1High, but normally
> it doesn't matter much as long as you stick to 6 DOF.
>
> Everything else looks great, so should work fine.
>
> All the best,
>        Mark
>
>
>
> On 1 Aug 2009, at 02:16, Nicole Strang wrote:
>
>  Hi,
>> I've primarily used afni in the past, but want to take advantage of the
>> great non-linear registration in fsl. Because I've already run the
>> first-level stats is afni, I'd like to use fsl for registration alone, if
>> possible. I couldn't find an answer to my the question online, so I would
>> really appreciate it if someone could let me know if there are any
>> problems
>> with my approach. If there is a problem, alternative would be very much
>> appreciated.
>> Convert all relevant files to NIFTI
>> 1) Register run1 epi time series (there are 4 runs but all frames are
>> aligned to first frame of run1) to skull on T1High (with flirt)
>> 2) Register skull stripped T1High brain to MNI (with flirt)
>> 3) Register skull on T1High to MNI (with fnirt)
>> 4) Register output of glm which has been converted to percent signal
>> change
>> with output of (3) as warp and output of (1) as premat.
>>
>> Thanks!
>> Nicole
>>
>>


-- 
Nicole Strang
Child Emotion Research Lab
University of Wisconsin-Madison
1500 Highland Ave, Rm. 394
Madison, WI 53705
(608) 890-2525