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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 >>>>> >>>> >>> >