week 2 - image processing concepts Flashcards
What image distortions can be produced by the coil in the MRI scanner and the patient’s head?
What is this distortion called formally?
-non-uniformity: images tend to be incorrectly brighter/darker towards the centre of the scan
-intensity non-uniformity correction
What are some structural MRI analysis methods?
(processing images)
- brain extraction
- tissue segmentation & tissue volume
- Masks
- image registration
- pulling it all together?
What does brain extraction involve (aka skull stripping)?
removing/zeroing all voxels which are not the brain
What tissue does tissue segmentation distinguish?
differnt tissue types like grey and white matter
How do tissue probability maps (tpms) analyse MRI scanned images?
tpms remove all tissue which is not of interest (eg. grey matter tpm)
What does a TPM calculate?
percentage of each tissue type at a specific voxel - voxel values are now NOT arbitrary
eg.
0% CSF
43.53% white matter
56.47% grey matter
Can you calculate the overall volume of person’s grey matter/any tissue type from a single tissue segmentation image?
yes
for example answer would be 0.53 litres of grey matter
Why is it useful to know the total volume of white and grey matter in research?
What is the issue with using raw brain volume with many different patients?
-brain atrophy cause by neurodegenerative conditions (shrinkage of W or GM)
-people have naturally different sized brains
What is masking?
eg. setting a threshold of a certain percentage of a tissue type in all voxels AND make threshold them binary
Do two different people have the same ‘image space’?
Do two separate scans from the same person have the same image space? why?
- no, scans from different people will have different image spaces
- not usually: it’s safest to assume any two different scans are in their own unique space
-people can move around during scan etc
What is native space?
different image space unique to an individual
How does image registration affect ‘image space’?
image registration is a processing technique that moves, stretches and squishes one image to match the alignment of another
What is the ‘target image’?
the other image is registered to it, so to make both of them have the same image space as the target image
What does FLIRT stand for?
What is it used for?
What sort of transformations does it use?
What is the alternate use of FLIRT?
-FSL’s Linear Image Registration Tool
-Register images from the SAME person using linear transformations
-linear
-used as an initial step in a non-linear registration
What do we want to reduce when using FLIRT?
the number of manoeuvres/transformation used each one introduces more noise
What degrees of freedom can you use for each FLIRT manoeuvre/transformation?
up to 12
so you can have a 6DOF etc
What manoeuvre with 6 degrees of freedom with FLIRT?
What type of MRI images is it useful to do this manoeuvre with?
What is good about this manoeuvre?
rigid body registration
fMRI and DTI
it can shift the brain in many ways but WITHOUT deforming the actual shape (any stretching or squishing)
What is FNIRT used for?
What does it stand for?
register different people’s brain together
FSL NON-linear Image Registration Transformation
How is FNIRT classified as non-linear?
parts of the image can be differently warped in “uneven” ways
What mathematical function does registration require? What does this function do?
cost function -> calculates how similar/dissimilar images are to each other (real & desired outcome)
Are there multiples cost functions you can use to do an image registration with FLIRT?
How do you decide which cost function to use?
yes
depends on image modalities of the experiment - type of MRI eg T1, PET
What is a pipeline?
a combination of all these techniques (mentioned) which attempt to complete a more complex goal
What is a template?
What are the advantages of using a template?
-average brain scan of multiple people
-scanning many people and then registering their scans in same space and then taking the mathematical average
-use template as a target image in registration
What is an alternate use of templates?
used to help automate segmentation of different brain regions, by knowing where a structure is in MNI template space and then registering a person’s brain to the template.
How can you efficiently and quickly mark all the ROIs in each image scan in a data set from 100 different people?
(ROIs anatomical areas of brain)
1make a template from all images using NON-linear registration
2mark the ROIs on template
3do the opposite of registration so you can superimpose the ROIs on patient’s native image space (for each person)
Why do we perform brain extraction?
to make the scan easier to analyse in subsequent steps
What are the five MRI image analysis processing steps?
- Brain extraction
- Tissue segmentation/tissue volume
- Masks
- Image registration
- Pulling it all together
