Hi Andreas,
> thanks. It does look reassuring. I will try it myself, I quite like the
> idea.
> One question: Your T2 was of the same dimensions like your B0 image ord
> did you downsample it to the B0 resolution? Often, the T2 will be of a
> higher res than the B0, at least when it come to in plane resolution.
topup expects all images to have the same matrix size, so you will typically need to downsample the T2. It is probably also a good idea to combine that with an RB registration to make sure they are not too far apart initially. There is a movement model inside topup but that is for small movements between the different scans and is unlikely to work with big position differences that you might get from different sequences/FOV.
Jesper
> Cheers,
> Andreas
>
> Am 22.03.13 17:02 schrieb "Mark Drakesmith" unter
> <[log in to unmask]>:
>
>> Hi Andreas
>>
>> I've attached images of the T2w, distorted and corrected B0 images.
>>
>> The topup call was:
>>
>> topup --imain=T2w_images_topup.nii.gz --datain=topup_dti_params.txt
>> --config=b02b0.cnf --out=my_topup_results --fout=my_field
>> --iout=my_unwarped_images -v
>>
>> The T2w_images_topup.nii.gz image contained the original B0 and the T2w
>> images. Note that the B0 image was rigidly transformed with flirt so it
>> is in the same voxel space a the T2w. the topup_dti_params.txt file
>> contained the following lines, corresponding to the B0 and T2w images
>> respectively. As per Jespers, suggestion the readout time for the T2w
>> was set close to zero:
>>
>> 0 1 0 0.0864
>> 0 1 0 0.00000001
>>
>> I've not yet applied this the full set of DWIs yet, but so far it looks
>> good.
>>
>> I hope this is of help.
>>
>> Mark
>>
>>
>> Dr. Mark Drakesmith
>> Research Associate
>>
>> Caridff University Brain Research Imaging Centre (CUBRIC)
>> School of Psychology
>> Cardiff University
>> Park Place
>> Cardiff
>> CF10 3AT
>>
>> Tel: +44 (0) 29 2087 0354
>> Fax: +44 (0) 29 2087 0339
>>
>> On 22/03/13 15:34, Andreas Bartsch wrote:
>>> Hi Mark,
>>>
>>> I have followed this with interest.
>>> Could you post an example (e.g. a slicer output) along with your topup
>>> call?
>>> You can also email me directly.
>>> Cheers,
>>> Andreas
>>>
>>> Am 22.03.13 15:53 schrieb "Mark Drakesmith" unter
>>> <[log in to unmask]>:
>>>
>>>> Hi Jesper
>>>>
>>>> I just tried it. It works beautifully! I didn't realise you could use
>>>> topup in that way (I had just followed the example in the FSL wiki).
>>>>
>>>> Thanks very much! :)
>>>>
>>>> Mark
>>>
>>
>
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