DiffusionFdtNotes - MRC CBU Imaging Wiki

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Fdt diffusion analysis

For CBU data.

These are just notes of work in progress by MatthewBrett.

Extracting the bvals, bvecs values from Siemens data

See: http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI

Note that the B gradient=0 has no direction information.

So, for the example dataset I have been playing with, you can fetch the diffusion directions from the DICOM headers, by getting the DICOM file names from a diffusion dataset into the matlab string matrix input_files, and doing something like: 

hdr = spm_dicom_headers(input_files);
n = length(hdr);
bvals = zeros(n, 1);
bvecs = zeros(n, 3);

for i = 1:n
  H = hdr{i};
  bvals(i) = str2num(H.CSAImageHeaderInfo(7).item(1).val);
  if bvals(i) == 0 % no gradient
    continue
  end
  d_info = H.CSAImageHeaderInfo(22).item;
  for D = 1:3
    bvecs(i,D)= str2num(d_info(D).val);
  end
end

I've implemented this as cbu_diffusion_params.m in the SPM common directory at the CBU.

We then have to write out the gradient values and directions in a format that FDT understands - see dtifit documentation in the FDT pages: http://www.fmrib.ox.ac.uk/fsl/fdt/index.html.

bvals

All one one line, one value per DWI acquisition, appears to be exponential format separated by 3 spaces per value, and needs new line at end of file. For example: 

   0.0000000e+00   0.0000000e+00   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03  1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   0.0000000e+00   0.0000000e+00   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   1.0000000e+03   0.0000000e+00l

(Note new line at end of file).

bvecs

One line per direction (one line for X direction, one line for Y direction, one line for Z direction). New line at end of each. Need to include zeros for no diffusion gradient acquisitions. E.G: 

0  0.0000000e+00   7.6937618e-01   9.9999924e-01   4.0214920e-02   1.9526217e-01   5.1096926e-01   6.4449110e-01   1.1639260e-01  4.1472436e-01   6.8663556e-01   3.8949705e-01   5.0524772e-01   1.1717751e-01   7.6094012e-01   7.8334360e-01   4.4028061e-01   2.0589133e-01   1.3436626e-01   2.7000378e-01   4.4543086e-01   2.1816264e-01   3.6644717e-01   1.9651463e-01   5.6797954e-01   4.2364378e-01   4.8425159e-01   4.8837442e-01   7.1876309e-01   9.3607570e-02   1.7722160e-01 0 0.0000000e+00   5.1711309e-01   7.5808487e-01   8.0234240e-01   1.9735010e-02   3.3516758e-01   6.3448454e-01   8.1168960e-02   1.0445113e-01   2.6766319e-01   6.7016636e-01   1.5391958e-01   4.1367573e-01   8.8398617e-01   2.1753901e-01   9.3271228e-01   6.9488384e-01   8.8211118e-01   6.9509295e-01   8.7347998e-01   7.5283496e-01   8.8371946e-01   8.8840244e-01   5.5232725e-01   9.3679074e-01   9.4961311e-01   6.4277964e-01   3.4381087e-01   9.9971116e-01   9.9821503e-01   4.6606173e-01   1.3874523e-01 0
0  0.0000000e+00   6.6306062e-01   1.6707810e-02  -9.9903292e-01   7.6591725e-01   7.7929365e-01  -7.8747432e-01  -9.9961185e-01 -8.8677651e-01   3.4283814e-01  -4.8693386e-01   8.8074278e-01  -8.8352002e-01  -7.8999910e-02   2.6876947e-01   2.5290552e-01   9.3262713e-01  -3.3491810e-01   3.2593888e-01   7.5894353e-01  -2.6638000e-03  -9.4866592e-01   9.9998147e-01  -7.8726452e-01  -7.2459950e-01  -6.4709189e-01  -1.7825689e-01   5.5582022e-01   8.8285078e-01   4.8544349e-01 0  0.0000000e+00   4.7983043e-01  -4.9330514e-01  -6.0886478e-01  -4.8934133e-01   9.3013284e-01  -3.1901719e-01  -1.8293329e-01  -6.6242333e-01  -8.8671109e-01  -4.2004243e-01  -7.2580995e-01  -9.4553600e-02   4.6713278e-01   6.6282962e-01   3.7641775e-01  -6.4060372e-01  -4.9143385e-01   1.4877920e-02  -1.6054820e-01   5.4879866e-01  -2.8861432e-01   1.8916095e-01   1.5049253e-01   6.7304890e-02  -3.1584415e-01   7.6457665e-01  -4.3058758e-01  -1.6450303e-01   1.8210187e-01   5.8200226e-01   1.4422617e-01 0
0 -0.0000000e+00  -9.1990930e-02  -1.9943366e-01  -2.0091641e-01  -6.4443377e-01  -4.1432263e-01   6.7578430e-02   1.6516763e-01  2.8580159e-01  -6.7159887e-01   8.0699374e-01  -9.5227750e-02   4.9569470e-01   6.7437421e-01   5.9513629e-01  -8.8444514e-01  -3.5758470e-01   9.5384852e-01   9.2785410e-01   5.1541002e-01   9.9621754e-01  -7.6163460e-02  -3.8346860e-02  -3.1251438e-01   5.7925205e-01  -6.2195169e-01   8.7736329e-01   4.6313598e-01   5.0186008e-01  -8.7919767e-01 0  -0.0000000e+00   7.3648370e-01  -4.7117809e-01  -1.5994303e-01  -8.9454291e-01   2.5013402e-01  -7.3192133e-01  -9.9999922e-01   7.6833373e-01  -4.2679184e-01   6.4381118e-01  -6.9968571e-01  -9.2735292e-01   2.0101452e-01   7.4389858e-01  -1.6854941e-01   3.8316412e-01   1.4291280e-01  -7.4610714e-01  -5.0130672e-01  -4.1486259e-01   4.1927689e-01  -4.6369242e-01   8.4400121e-01   3.9742244e-01  -1.9628767e-01   2.0568982e-01  -8.5816073e-01   1.1648077e-01   1.0225989e-01  -6.9578104e-01  -1.0000000e+00 0