Dear Abhinet,
this is a tricky case, especially since the FOV of your “fieldmap” is smaller than that of the scan that you want to correct. The “general” steps that you need to follow are
1. Use the reference scan and topup to calculate a fieldmap (in Hz) in the reference space. You do that by specifying the read-out time 0.0268 in the fourth column of the acqpar file “as usual”. Make sure that you specify the --fout parameter as you will need the field rather than the coef file.
2. Register the fieldmap to the space of your DKI data. Ideally you have a valid s/qform in all your files, in which case you can use flirt and -applxfm -usesqform. If not, or if the subject has moved a lot between acquisitions, you will need to achieve a reasonably good registration (using flirt) between the reference scan (as -in) and the DKI data (as -ref), specify the -omat parameter and then apply the resulting transform to the fieldmap.
3. Make a new acqpar file with the fourth column given by 0.0401 and use that in eddy (using the --field) or applytopup depending on exactly what you want to do.
The problem you will likely encounter is that because of the smaller FOV of the fieldmap and the resampling into a new space, parts of your fieldmap will be set to zero (field is unknown and unknowable) and that will cause problems for eddy when attempting to invert it. If you are a dab hand at image processing you might attempt to take your resampled fieldmap and fill out the zero areas with “reasonable” values. What you primarily want to avoid are sharp edges as you go along the PE-direction.
For future reference, you will make your life a whole lot easier if you acquire your “reference data” such that one of the volume is the first b0 volume of your DKI data, and the other volume is a b0 acquisition with opposing PE (and all other parameters identical) acquired immediately before your DKI data set.
If, for some reason, you have to acquire your “reference data” with different parameters you should make sure you acquire it with a larger FOV than the DKI data. Such that you have enough margin that even after resampling into another space you don’t end up with any zeros.
Jesper
> On 13 Jan 2020, at 09:34, Abhineet Ojha <[log in to unmask]> wrote:
>
> Hi everyone,
> I need your suggestion on running the topup tool for a few subjects, for whom I have different acquisition parameters (mentioned below) for reference scan(in PA and AP direction) and DKI data.
> Can you guys provide suggestions on how to run distortion correction on this data?
>
>
> Reference scan
> Voxel_size 2x2x2
> Field of view 240x240x140
> EPI_Total_read_out_time 0.0268
>
> DKI data
> Voxel_size 2.5x2.5x2.5
> Field of view 256x256x160
> EPI_Total_read_out_time 0.0401
>
>
> Thanks in advance.
>
> With regards
>
> Abhineet Ojha
> Senior Research Fellow,
> NIMHANS, Bengaluru,
> Karnataka, India.
>
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