Hello HCP community, We have just GE data, as opposed to SIEMENS data, and we'd like to use this for the HCP pipeline code. The GE data we have is in NIFTI (.nii) format. The files are named as imaginary, real, and magnitude. In the HCP code's global/scripts/GeneralElectricFieldMapPreprocessingAll.sh script (run during the PreFreeSurfer step) it initializes a variable called GEB0InputName, which is defined in the code as "GEB0InputName should be a General Electric style B0 fieldmap with two volumes". The script takes that variable as the only input option (-fmap).
We'd like help being able to run the HCP pipeline using this GE data. Note that we've already looked at http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FUGUE/Guide, and we believe we already have what is needed to run the pipeline in terms of starting input. The way we understand it, all we need is the magnitude and real NIFTI files, and we can disregard the imaginary NIFTI files. Also, based on our understanding, the complex NIFTI files that this site is referring to is a combination of the imaginary and real files. But we'd really appreciate any clarification and correction on our understanding of this. Any help would be appreciated! Thanks, Jesse Chiem Research Assistant II Developmental Brain Imaging Lab Oregon Health & Sciences University ch...@ohsu.edu<mailto:ch...@ohsu.edu> _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
