FMRI Data

FMRI Data
Image File formats, conversion, reading,
visualization tools, MRI data artifacts
Akila Rajagopal, MS
What happens after
scan?
Scanner
Users
Console
Server
Image data formats
• Philips
• PAR REC
• DICOM
• NIFTI
• Siemens
• DICOM
• Mosaic DICOM
• Raw Data
DICOM
• Digital Imaging and Communications in Medicine
• Enables integration of scanners, servers, workstations,
printers and network hardware from multiple
manufactures into a Picture Archiving
Communication System (PACS)
• Widely used in hospitals
• Subject ID -> Study Date -> Scan Series
DICOM - HEADER
MOSAIC DICOM
PAR REC
IRC04H_03M030_P_1_WIP_T1W_3D_IRCstandard32_SENSE_4_1.PAR
Analyze and NIFTI
• Analyze: Developed by Biomedical Imaging
Resource (BIR) at Mayo Clinic
• Example_Data.img and Example_Data.hdr
• Popular format for several packages for processing
MRI data
• Analyze Data format has less header information,
but not well-defined patient orientation info.
• Neuroimaging Informatics Technology Initiative
Tools to view
• Raw data, ANALYZE, DICOM and NIFTI
•
Any software image processing packages: IDL, MATLAB, PYTHON, ETC
• DICOM
•
•
•
Neurolens (MAC)
Osirix (MAC)
MRICro (Windows)
• NIFTI and ANALYZE
•
FSLView (MAC and LINUX)
• DICOM, NIFTI and ANALYZE
•
•
•
3D Slicer (Win, Mac, Linux)
MRICRON (Win, Mac, Linux)
Mango (Win, Mac)
Many other viewers exist
Conversion Tools
• DICOM to NIFTI
• MRICRON
• 3D SLICER
• PARREC TO NIFTI
• Programs in IDL
• Programs in MATLAB
• Programs to run in FSL
T1 and T2 – Anatomical
images
Axial
T1 - 3D
Sagittal
T1 - 3D
Axial
T2 - 3D
Sagittal
T2 - 3D
Motion in Anatomical
Images
Axial
T1 - 3D
(With some motion)
Sagittal
T1 - 3D
(With some motion)
Axial
T1 - 3D
(With lots of motion)
Sagittal
T1 - 3D
(With lots of motion)
HUSH Stories Data
Vol 0
Vol 1
Vol 2
Baseline CBF Images
CBF – Cerebral Blood Flow
No Motion
Some Motion
Lots of Motion
Functional Images
Motion in
Functional Images
MRI Artifacts
• Numerous kinds of artifacts can occur in MRI.
• Some of them affects the quality of the MRI exam.
• Some artifacts are resolved in data processing while
others might require an engineer
• Sources:
•
•
•
•
Hardware Issues
Software Issues
Physiological Phenomena
Physics Limitations
Types of Artifacts
• Aliasing
• Gibbs Ringing or Truncation Artifact
• Spike Artifact
• Susceptibility Artifact
• Inhomogeneity
• Ghosting
• Slice-Overlap Artifact
• Zipper Artifact etc..
Aliasing or Wraparound
• Occurs when the field of view (FOV) is smaller than
the body part being imaged causing the region beyond
to project on the other side of the image.
• Caused by undersampling in the phase or frequency
(rarely) direction.
Aliasing
Correction:
Increase the FOV.
Oversampling the data in the frequency direction and increasing the phase
steps in the phase-encoded direction.
Swapping phase and frequency direction so phase is in the narrower direction
Use surface coil so no signal detected outside of FOV.
Gibbs Ringing /
Truncation Artifact
Spike Artifact
• Bad data points
in K-space.
• The intensity of
the spike
determines the
severity of the
artifact.
Susceptibility
Artifact
• Variations in magnetic
field strength that
occurs near the
interfaces of substances
of different magnetic
susceptibility such as
ferromagnetic foreign
bodies.
• In this case metallic
dental filling.
Inhomogeneity
B0
Mitigation: Shimming, Coil use volume vs surface coil
Dielectric
Mitigation: use phased array
coils, software compensation
Artifacts - Ghosting
• Most common problem with EPI sequence is Nyquist (N/2)
Ghosting.
• Odd and even echoes are acquired under opposite read gradients.
• Inaccurate timing of the sampling relative to the gradient cause a
modulation of alternate lines in k-space.
• This leads to ghost image shifted by N/2 in the phase encode
direction.