Hi Mahshid,

If the MB factor information is saved in the header file of your dicom images, then using the newer version of dcm2niix you will have a json file that stores some of the header information.

You may feed that json file to the attached m-file (that I got from the FSL forum or wiki) and it creates a slspec.txt for you that you may use it for eddy.

Hope this helps.

Mahmoud

On Mon, Dec 31, 2018 at 4:06 AM Mahshid Fouladivanda <[log in to unmask]> wrote:

Dear Experts,

I want to apply eddy correction including Correcting slice-to-volume movement on dMRI data. So I need to create slspec.txt file, in order to use the command:
eddy --imain=data --mask=my_hifi_b0_brain_mask --acqp=acqparams.txt --index=index.txt --bvecs=bvecs --bvals=bvals --topup=my_topup_results --niter=8 --fwhm=10,8,4,2,0,0,0,0 --repol --out=eddy_corrected_data --mporder=6 --slspec=my_slspec.txt --s2v_niter=5 --s2v_lambda=1 --s2v_interp=trilinear
But I don know how I can calculate the multiband (MB) factor? and what is the number of slices? is it (MB factor) the value of the z dimension of the images???

Regards,

Mahshid
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