Subject Example for FieldMap Toolbox
************************************
Copyright (C) 2012 Wellcome Trust Centre for Neuroimaging
Chloe Hutton

Overview
********
These data were acquired on a single subject comprising distorted EPI, fieldmap and 
(skull-stripped) anatomical image. 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 and if desired, the anatomical image can also be matched to the 
undistorted image.

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).

N.B. To apply the fieldmap correction (i.e. the resulting vdm file) to an EPI time series, 
one would typically use Realign&Unwarp. In cases when dynamic distortions are not (well) 
modelled by Realign & Unwarp (e.g. for fMRI data acquired with R->L phase-encoding 
direction, high field fMRI data or DTI data), the 'Apply VDM' option in the FieldMap 
Toolbox can be used (see the SPM Manual for details).

SubjectData
***********
1) fieldmap contains gradient fieldmap data acquired using Siemens FieldMap sequence: 

sMT0160-0012-00001-000001-01.nii - magnitude image with short echo time (10.00ms)
sMT0160-0012-00001-000001-02.nii - magnitude image with long echo time (12.46ms)
sMT0160-0013-00001-000001-02.nii - presubtracted phase image

2) epi_run1 and epi_run2 contain short epi time series (4 images each) (readout time=32.00ms, blip direction =-1):
fMT0160-0014-* and fMT0160-0015-*

3) anatomy contains skull-stripped anatomical image
stripped_sMT0160-0005-00001-000176-01.nii

4) pm_defaults_xxx file with parameters set for Subject Example data:
pm_defaults_SubjectExample.m	

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 SubjectExample_fieldmap_batch.m at MATLAB command line
or
use Batch->Load Batch to load SubjectExample_fieldmap_batch.mat and select run

Results
*******
Examples of graphical output from FieldMap toolbox are shown in fieldmap_results1.jpg and
fieldmap_results2.jpg. The impact of distortion correction can be seen at the crosshairs.
Processed results for comparison are in processed_data folder.