CEST_Data_Bruker

[MinhVo89]

Hi Vsevans,

Thanks for your contribution to the MRI community! I would like to ask a question related to the data structure. How can I convert the Bruker format file to the data structure you used in your code: CESTToFitNorm, PPMToFit, RefDataRaw?

Thanks and best regards,

Minh Vo

[vsevans]

Hi MinhVo89,

I'm not familiar with Bruker file format, but as mentioned in the comments at the top of the script itself, each object must be a MATLAB matrix with the following dimensions:

---

% (1) CESTToFitNorm
% Description: Normlized and B0-corrected CEST images from 1 or more files,
% with 1 or more offsets (typically tens of offsets) in ascending order
% (-ve to +ve), 1 or more slices, and 1 or more rows/columns
% Dimensions: [row, col, slice, offsets, files]

% (2) PPMToFit
% Description: A single-dimension vector containing the list of saturation
% offset frequencies expressed in ppm ordered from -ve to +ve
% Dimensions: [Noffsets,1]

% (3) RefDataRaw
% Description: A set of unsaturated reference images.
% Dimensions: The same as CESTToFitNorm but with a size of only 1 in the
% 'offsets' dimension.

---

So:

CESTToFitNorm is a matrix with dimensions: [row, col, slice, offsets, files]

• Note: the ordering of 'offsets' must by the CEST offsets in ascending order (from -ve to +ve)

PPMToFit is a single-dimension vector specifying the CEST offsets (in ppm) [which must correspond to the 'offsets' dimension in 'CESTToFitNorm']

RefDataRaw is the reference (unsaturated) image for each CEST file, therefore this has the same dimensions as 'CESTToFitNorm' but has a size of only 1 in the 'offsets' dimension (assuming a single unsaturated reference image for each file).

I hope this helps. Without more knowledge of the Bruker file format I am unable to provide specific instructions for how to convert it into the relevant format but if you can read your Bruker files into MATLAB it should be possible to then pre-process them to get them into the suitable format of the three objects mentioned above.

Good luck and please let me know how things go!