Friday, 30 January 2015

GannetCoRegister and GannetSegment

Two additional functions that have been added to the Gannet for Philips SDAT data and GE data: GannetCoRegister and GannetSegment. 

GannetCoRegister registers the MRS voxel to the T1-weighted image (MPRage for Philips, FSPGR for GE) and creates a binary mask of the MRS voxel using the same geometry as the T1-weighted image. It uses a subroutine, GannetMask, which can also be used as a stand-alone function (for information on GannetMask, see posting from Dec 2014). GannetCoRegister is integrated into the Gannet workflow and to create voxel masks for each MRS file that have been processed with GannetLoad.

GannetSegment segments the T1-weighted image (using SPM) and then determines the tissue fractions (gray matter, white matter and CSF) for the voxel and provides a CSF-corrected GABA estimate (where the corrGABAconc = GABAconc/(1-fCSF) where GABAconc is the original concentration estimate of GABA and fCSF is the fraction of CSF in the voxel.  

For this to work you need to have SPM8 installed.

GE data
The folder containing the dicom images of the FSPGR (or other anatomical image) and the "rotator image" that is acquired parallel to the voxel plane and used to plan the MRS voxel are used in GannetCoRegister.

MRS = GannetLoad({‘Pfile.7'})

MRS = GannetFit(MRS)

MRS = GannetCoRegister(MRS, {‘FSPGR_dcm_directory'}, {‘rotator_directory’})

MRS = GannetSegment(MRS)

Philips SDAT data

MRS = GannetLoad({‘GABA.sdat'}, {‘waterref.sdat’})

MRS = GannetFit(MRS)

MRS = GannetCoRegister(MRS, {‘MPRAGE.nii’})

MRS = GannetSegment(MRS)

GannetCoRegister outputs one MRS_file1_mask.nii for each MRS dataset.  It also saves a pdf image of the voxel overlaid on a 3-plane view of the image at planes that transect the voxel. GannetSegment outputs segmented images for gray matter, white matter and CSF, adds the tissue fractions of the voxel to MRS_struct and saves a pdf image that includes the tissue fractions and a CSF-corrected GABA value. Note, GannetCoRegister can be run prior to GannetFit but GannetFit must be run prior to GannetSegment. 

For more details and more information, please refer to the updated manual. 

If you use these tools, please cite: Harris, Puts, Edden. 2015. Tissue correction for GABA-edited MRS: considerations of voxel composition, tissue segmentation and tissue relaxation. J Magn Reson Imaging. In Press.