Phantom Example for FieldMap Toolbox ************************************ Copyright (C) 2012 Wellcome Trust Centre for Neuroimaging Chloe Hutton Overview ******** These data were acquired on a gel phantom scanned with manually disrupted shim in anterior posterior (phase-encoding) direction to give rise to distorted (squashed) epi data. The FieldMap toolbox can be used to process the fieldmap data to create a 'vdm' file (voxel displacement map) and undistort a single epi image. The undistorted image (prefix='u') can be used as a visual check of the fieldmap correction. Note that the resulting undistorted image (prefix='u') will have the same geometry as the fieldmap magnitude data (which is not distorted). Data were acquired on a 3 T whole-body MRI scanner (Magnetom TIM Trio, Siemens Healthcare, Erlangen, Germany) operated with a 12-channel RF head receive coil and RF body transmit coil. FieldMap data were acquired using a Siemens FieldMap sequence with short TE=10.0ms and long TE=12.36ms. EPI data were acquired with matrix size=64x64, readout time=32.0ms, blip direction=-1. (Other image acquisition parameters can be viewed using the Check Reg button). PhantomData *********** 1) fieldmap contains Nifti format gradient fieldmap data acquired using Siemens FieldMap sequence: sPhantom-0006-00001-000001-01.nii - magnitude image with short echo time (10.00ms) sPhantom-0006-00001-000001-02.nii - magnitude image with long echo time (12.46ms) sPhantom-0007-00001-000001-02.nii - presubtracted phase image 2) epi contains Nifti format single 'squashed' epi image (readout time=32.00ms, blip direction =-1): fPhantom-0005-00001-000001-01.nii 3) pm_defaults_xxx file with parameters set for Phantom Example data: pm_defaults_PhantomExample.m (NB -for phantom data, brain masking=0 (pm_def.MASKBRAIN = 0, should=1 for Subject data); Execution ********* To process this example data set follow steps in manual.pdf to set up a batch job using Batch->SPM->Tools->FieldMap->Presubtracted Phase and Magnitude Data or run the example batch script PhantomExample_fieldmap_batch.m at Matlab command line or use Batch->Load Batch to load PhantomExample_fieldmap_batch.mat and select run Results ******* Example of graphical output from FieldMap toolbox is shown in fieldmap_results.jpg and processed results for comparison are in processed_data folder.