Hi Mark,
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.
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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