Re: [Freesurfer] b0dc flag for Freesurfer7

It is expecting a voxel shift map, which won't work with topup. One thing you can do is to do the preprocessing (motion correction, slice timing correction, topup) outside of fsfast, save the output as something like f.mypreproc.nii.gz, then specify -funcstem f.mypreproc when running mkanalysis-sess

On 3/31/2021 6:13 AM, Manenti, Giorgio wrote:

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Dear Experts,

I am wondering if there is additional documentation about the -b0dc flag for mkanalysis-sess. This flag is applying field distortion correction. Is it possible to use my topup information in order to correct it or it s a different field correction?

Many thanks,

Best Giorgio

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