Sorry, to be clear, I'm trying to register DWI data with a T1/T2. I
only have fieldMap data to use in this process. I have a nice fieldMap
to T1 string, I can get a shiftmap out of fugue for the b0, I just can't
figure out how to string the shiftmap and fieldmap_to_T1.mat file I have.
I tried using epi_reg, with the b0 in place of EPI, T2, in place of the
typical T1, but the results weren't very good. The distortion
correction from fugue looked much better than the output of epi_reg
(even with a good WM segmentation on the T2), the problem is that I
can't figure out how to use the shiftmap like I would a .warp or .mat
file. Is there a file I can spit out from fugue that I can sum/string
together with a flirt or fnirt output so that I can have a b0 to T1 (or
MNI)?
On 11/27/2014 09:36 AM, Mark Jenkinson wrote:
> Hi,
>
> I would advise you to use epi_reg to achieve this.
> Start by getting a white matter segmentation from your T2, and then use this along with your EPI images and fieldmaps. There is no need to do any registration before using epi_reg, as it will do all the necessary registrations internally.
>
> All the best,
> Mark
>
>
>> On 25 Nov 2014, at 17:57, Joel Bruss <[log in to unmask]> wrote:
>>
>> Jesper-
>>
>> Thank you for your response. I played around with FUGUE and was able to save out my corrected b0 and a bo_correction shift file.
>>
>> I have a series of registrations (T1_to_T2, fieldmap_to_T2), to which I can invert, sum and save as fieldmap_to_T1.mat (affine). How do I go about summing the bo_correction shiftmap and fieldmap_to_T1.mat? I don't see a way with convert_xfm to take a shiftmap and no matter what I do with convertwarp, anything I warp via that output (b0_to_T1_warp.nii.gz) is badly misplaced from the T1.
>>
>> -Joel
>>
>> On 11/25/2014 07:24 AM, Jesper Andersson wrote:
>>> Dear Joel,
>>>
>>>
>>>> I have DWI data collected but only one b0 image, with the same phase encoding direction. It's my understanding that I need two b0's with opposite phase encoding in order to use and apply topup. I do have a phase and magnitude fieldmap collected with the same orientation, direction and dimensions. Is there a way to apply this fieldmap to correct for distortion to the b0 and DWI data?
>>> yes, but then you need to use different tools than applytopup. You can for example use fugue, or you can feed a 1D displacement field (shiftmap) into convertwarp if you want to combine it with registration into standard space.
>>>
>>>> Along these lines, could I use this fieldmap with BBR to help in alignment to a 3D T2 that was also collected?
>>> I don’t think there should be any problems to use BBR with a T2 image. As long as your segmentation (of the T2) works well you should be fine.
>>>
>>> Jesper
>>>
>>>
>>>> I can create the prepped fieldmap with fsl_prepare_fieldmap but I don't know what to use to apply this to the b0. epi_reg and the tools in that script look to be optimized for epi to T1 registration only. Is there a way to insert a prepped fieldmap into apply topup or use the current scans that I have to correct for distortion? Thanks for any and all responses.
|