Hi again Andreas,

> yes - that's why I was wondering, i.e. Mark must have downsampled / preregistered or recorded a T2 scan at low res.
> Given that such approach may work, would you invest scan time in full blip up / down recordings (of all diffusion directions) or prefer to double the dirs in one phase encoding dir?

what you can get from the b0-EPI<->T2 combo is an estimate of the field which you can then use to correct all your EPIs. You can achieve exactly the same thing with b0-EPI+<->b0-EPI- where the sign indicates the blip-direction. I.e. you don't need to acquire all your EPI images with both blip-directions.

Given that you would actually loose time by acquiring a T2 instead of a single EPI with reversed blips, which would only take you ~5sec. The potential problem with the T2 option is that the contrast might not be perfectly matched which might mean a somewhat poorer estimate of the field. So my vote would always be for reversed blips for at least a couple of b=0 images.

But it is nice to know that the T2 option works for when people forget.

Jesper

> Cheers,
> Andreas
> 
> 
> 
> Am 23.03.2013 um 08:34 schrieb Jesper Andersson <[log in to unmask]>:
> 
>> 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
>>>>> 
>>>> 
>>> 
>