From: Mahmoud <[log in to unmask]>
To: [log in to unmask]
Date: Mon, 31 Dec 2018 09:44:32 -0500
Subject: Re: [FSL] How to create slspec.txt file for eddy correction
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.MahmoudOn 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=trilinearBut 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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