Processing high resolution data with an isotropic resolution other than 1mm³ with Freesurfer (Version 5.1+)

NOTE- AS OF DEV AUG. 2015 and stable6, THESE MANUAL MODIFICATIONS ARE NO LONGER NECESSARY. THERE IS NOW A -hires FLAG FOR RECON-ALL. SEE SubmillimeterRecon

Notes from Falk Lüsebrink on the modifications to the default recon-all stream necessary to process high-resolution data (< 1mm), used in his paper: Cortical thickness determination of the human brain using high resolution 3T and 7T MRI data.


For best results I advise to do an inhomogeneity correction by division before processing the data. See T1 weighted Brain Images at 7 Tesla Unbiased for Proton Density, T2* contrast and RF Coil Receive B1 Sensitivity with Simultaneous Vessel Visualization. The "corrected by division" image can be generated in SPM by first to aligning the MP-RAGE and the GE by co-registration. Afterwards use the image calculator to do the division using the formula: (i1./i2 .* (i2>20)) .* 100. The value of 20 depends on the image intensity and 100 is simply a scaling facotr (i1= MP-RAGE, i2= GE)

First: downsample high resolution data to 1mm and process completely

Second: process high resolution data and use downsampled data whenever needed

HiResRecon (last edited 2016-08-16 17:00:02 by AllisonMoreau)