Thanks, will do. Is this written up anywhere that I missed?
On 08/01/18 09:02, Mark Jenkinson wrote:
> Hi Helen,
>
> Use the one without the "init" part - that is, eddy_correct_in_T1.mat
> as the "init" stands for initialisation and is just a first guess, which then gets improved.
>
> All the best,
> Mark
>
>
>> On 3 Jan 2018, at 15:56, Helen Beaumont <[log in to unmask]> wrote:
>>
>> Hi
>>
>> I am running epi-reg to register a b0 image to T1 using the command
>>
>> epi_reg --pedir=y --epi=eddy_correct_b0.nii.gz --t1=T1.nii.gz --t1brain=T1_betf0_3robust.nii.gz --out=eddy_correct_in_T1.nii
>>
>> I get two transformation matrices: eddy_correct_in_T1.mat and eddy_correct_in_T1_init.mat.
>>
>> I want to apply the transform to register other images in b0 space to T1 space, but I am not certain which of these matrices I should use, or the command to use. Please can someone help.
>>
>> Helen Beaumont PhD
>>
>> University of Manchester
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