Fdt diffusion analysis
For CBU data.
These are just notes of work in progress by MatthewBrett.
FDT documentation: http://www.fmrib.ox.ac.uk/fsl/fdt/index.html
FDT FAQ entries: http://www.fmrib.ox.ac.uk/fslfaq/#title_fdt
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