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Francis Loayza
Functional Neuroimaging Laboratory
Center for Applied Medical Research
University of Navarra
So
Reconstructed me
fMRI Data S tep Pre
Slice Timing s pro
AdjustmentRealignment ce
ssi
Motion ng
Correction
Coregistration
Table of
Local Max
Tools for preprocessing
SPM (fMRI, VBM)
FSL (fMRI, VBM)
Brain Voyager (fMRI, VBM)
VoxBo (fMRI, VBM)
AFNI (fMRI, VBM)
ANTs (for Deep Learning)
SITK libraries (for Deep Learning)
Basic terminology for different scales
a period of time during which the subject is
session in the scanner, motionless (~1-2 hours)
volume
slice
voxel
Functional MRI (fMRI)
Uses echo planar imaging (EPI) for fast
acquisition of T2*-weighted images.
Spatial resolution:
3 mm (standard 1.5 T scanner)
< 200 μm (high-field systems)
Sampling speed:
1 slice: 50-100 ms
Requires spatial pre-processing and statistical
analysis.
Quality control
• It is essential that you perform QC checks at
multiple points in your data analysis stream
You MUST know how to look at raw data!
You can’t trust your analysis package to do everything
for you.
Things to look for
Data acquisition artifacts
Subject-related artifacts
Analysis-related artifacts
Quality control
MRI data artifact:
Things to look for:
Spikes
Ghosting
Geometric distortions
Signal dropout
Tools:
ForSPM: art_repair
(matlab toolbox)
Quality control
Spikes Ghosting
Quality control
Geometric distortions Susceptibility dropout
M Cohen.
Ojemann et al.
Quality control
Movement artifact
The traditional preprocessing
1. Slice Timing
2. Realignment
3. Coregistration
4. Normalisation
5. Smoothing
Slice Timing
Some researches don't
recommend to perform this steep
exposed last
exposed first
Slice Timing
exposed last
exposed first
Slice Timing
Correction shifts each voxel's time series so
that all voxels in a given volume "appear" to
have been captured at exactly the same time
TR RAW
TA
0 3 6
time in seconds
Slice Timing
Slices of an EPI image acquired separately
Therefore, information from different slices come
from varying points in time after task events
Different orders of slice acquisition:
ascending vs. descending
sequential vs. interleaved
Slice Timing
Only needed if:
Temporal dynamics of evoked responses are
important and if
TR is sufficiently small to permit interpolation
( <3 seconds )
afilename.nii
afilename.mat
FSL Slice timing
Included in FEAT module
Realignment (motion correction)
hemodynamic response is small compared to signal from
movement
increase sensitivity of T-Test (movement contributes to
variance)
When to do it
Must be before Normalization
Can be either before or after slice time correction
(disadvantages to both options)
For interleaved acquisitions it’s recommended to slice time
correct first
For sequential acquisitions it’s recommended to realign first
May introduce errors due to interpolation and interaction
with motion
Applying rigid-body transformations: 3 translation and 3
rotation
Métodos: análisis de imagen preprocesado
Activation
Imágenes RMf:
Realineación
Detección de artefactos
Realignment (3D motion correction)
Subjects move, like it or not
EPI image also moves from B0 shift
Along phase encode
(L->R or A->P)
Shift X, Y, Z (in mm)
Rotate X, Y, Z (pitch, roll, yaw)
If voxel at high-contrast
edge, then time series
will show changes
just from motion
Realignment
Movements could be due to stimulation
Realignment
Gadgets for prevent artifacts movements
A B
C D
Realignment
In extreme cases, up to 90% of the variance in
fMRI time-series can be accounted for by effects
of movement AFTER realignment:
subject movement between slice acquisition
interpolation artefacts
nonlinear distortion due to magnetic field
inhomogeneities (EPI distortion)
Realignment and Unwarp
EPI images are distorted relative to the structural scans
Bigger magnet = more distortion
Different tissues have different magnetic susceptibilities
Magnetic field warps at tissue boundaries
Realignment and Unwarp
Either anatomical scan or functional data is used to estimate
warping parameters, using one of the following models:
12 parameter affine transformation
Low frequency basis spatial functions
Vector field specifying the mapping for each voxel SPM
FSL (FLIRT)
in function of degrees of freedom
Realign: 6 DF
Unwarp: 6 DF
Total 12 DF
Realignment
SPM adds a prefix r to each
file
rafilename.nii
Coregistration
Align different modalities (eg PET & MRI)
Align functional (EPI) with structural (T1)
and different runs between each other
Optimize parameters describing rigid body
transformation to match functional with
structural
Coregistration
Advantages
Aids in normalization
Allows display of activation on anatomical images
Allows comparison across modalities
Necessary if no coplanar anatomical images
Disadvantages
May severely distort functional data
May reduce correspondence between functional and
anatomical images
Normalization
Normalization
Advantages
Allows generalization of results to larger population
Improves comparison with other studies
Provides coordinate space for reporting results
Enables averaging across subjects
Disadvantages
Reduces spatial resolution
May reduce activation strength by subject averaging
Time consuming, potentially problematic
Doing bad normalization is much worse than not normalizing
Normalization
Template
152 MNI; Voxel size: 2x2x2
SPM: Prefix w warfilename.nii
Normalization Template Normalized Data
fMRI to structural
Matching the functional image
to the structural image
– Overlaying activation on
individual anatomy
– Better spatial image for
normalisation
Two significant differences
between co-registering to
structural scans and motion
correction
– When co-registering to
structural, the images do not
have the same signal intensity
in the same areas; they
cannot be subtracted
– They may not be the same
shape
Problem: Images are different
Differences in signal intensity between the
images
Brain
visualisation:
Source Template
Deformation
field
Warped
image
Smoothing
Application of
Gaussian kernel
Usually expressed in
#mm FWHM
“Full Width – Half
Maximum”
Typically ~2 times
voxel size
Smooth 5 to 8 mm.
Smoothing
Corregistro
Normalización
Filtrado espacial
Smoothing FSL:
SPM:
Smoothing
Advantages
Increases Signal to Noise Ratio (SNR)
Matched Filter Theorem: Maximum increase in SNR by filter with
same shape/size as signal
Reduces number of comparisons
Allows application of Gaussian Field Theory
May improve comparisons across subjects
Signal may be spread widely across cortex, due to intersubject
variability
Disadvantages
Reduces spatial resolution
Challenging to smooth accurately if size/shape of signal is not
known
Smoothing effects
SPM:
Adds prefix s
swarfilename.nii
Smoothing
Unsmoothed Data
IRTK
SPM-Dartel steps
Important..! process all subjects
Realign
New segment (split off the differents brain tissues: gray,
white, CSF, bone, etc)