Running recon-all on data collected at 7T

Bias correction prior to recon-all

Compared to 3T MPRAGE and MEMPRAGE scans collected at 7T have stronger intensity inhomogenity, which won't be fully corrected in the default recon-all. Therefore, to process 7T data we recommend the following steps:

1) Bias-correct your input images using SPM12's unified segmentation algorithm (Ashburner and Friston, 2005)

2) Run recon-all as usuall with your bias-corrected image as input. (If your 7T voxel size is less than 1mm3 and you would like to process it at native resolution, see SubmillimeterRecon page on how to run recon-all)

Recommended bias-correction parameters:

Bias FWHM = 18

Sampling distance = 2

For Martinos Center MEMPRAGE with FOCI pulses

If the gray matter of the temporal lobes apears particularly dark, your pial surfaces may be misplaced in those regios as illustrated in the example below.