Example data set to demonstrate FieldMap toolbox from i)Subject and ii)Phantom

i) Overview of Subject data:

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).

Files:

Gradient fieldmap data comprises two magnitude and one subtracted phase image. There are two short EPI time series each comprising four distorted images and a skull-stripped anatomical image.

Description of FieldMap Toolbox usage:

Readme file: SubjectExample_readme.txt
SPM12: manual.pdf
SPM8: manual.pdf
SPM5: manual.pdf

NIfTI format fieldmap, functional and structural data:

ZIP archive: FieldMap_SubjectExampleData.zip (33Mb)

Batch:

SPM batch script:

SubjectExample_fieldmap_batch.m

ii) Overview of Phantom data:

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).

Files:

Gradient fieldmap data comprises two magnitude and one subtracted phase image. EPI data comprises a single distorted image.

Description of FieldMap Toolbox usage:

Readme file: PhantomExample_readme.txt
SPM12: manual.pdf
SPM8: manual.pdf
SPM5: manual.pdf

NIfTI format fieldmap and functional data:

ZIP archive: FieldMap_PhantomExampleData.zip (33Mb)

Batch:

SPM batch script:

PhantomExample_fieldmap_batch.m