Basic Processing for Structural Images Flashcards

Question

What happens when you multply the original scan by the mask?

Answer 1

Leaves behind an image of just grey matter with its original values This is a way of identifying and defining voxels of particular interest for further analysis- useful approach for getting rid of information we arent interested in

Answer 2

Making decisions about which voxels should be considered grey matter vs which ones should be considered white matter Usually grey matter tends to be higher than 0.5 Sometimes researchers may only want pure grey matter voxels, e.g. value 1 only

Answer 3

Images are in the same space when they are in alignment. This means that the same co-ordinates in each image refer to the same bit of brain anatomy. Overlaid images from one person share the same space e.g. scans layed over with white matter TPMs and grey mapper TPMs Scans from different people do not share the same space

Answer 4

It is the raw image, unadjusted and how it came out of the scanner each person has their own native space

Answer 5

Via image registration

Answer 6

Image registration is a processing technique that moves, stretches and squishes one image to match the alignment of another. It always involves a target image, and the image you are wanting to register to the target.

Answer 7

Linear Non-linear

Answer 8

Used to register images from the same person It will shift the brain around in the space of the image up/down, left/right, forward/back, roll it, spin it and re-angle it but without deforming its actual shape

Answer 9

linear =With 6 DOF – “Rigid body” registration - this is simply moving the objects around in space without changing the data too much -e.g. to align the many images that form the basis of an fMRI or DTI dataset before modelling non-linear= With 12 DOF it's more extreme - the number of ways the program can move, stretch and squish the image- this may result in a scan being upscaled or downscaled in resolution

Answer 10

It introduces noise into the data and into the results Image registration can blur the image or things don't end up quite where they should be But its the best approximation and the experimental benefits it allows outweights the cost of the noise

Answer 11

Most extreme Differentially warps section of the brain to make two or more different brains share the same space where the core anatomy is different

Answer 12

To compare a before and after pf the same person's brain if its had a lot of atrophy over 20 years If someone's had a stroke or a tumour and a chunk is now removed and other brain areas have morphed around that Essentially when the brains have different anatomy to a significant degree then its non-linear we use

Answer 13

Cost function

Answer 14

A mathematical approach to determine how similar or dissimilar the images being registered are, and therefore when a good registration has been achieved e.g. when the two images are aligned sufficiently

Answer 15

A method in interpolation- having to change the data, modifying it- the way you go about this is the interpolation

Answer 16

This method simply determines the “nearest” neighboring pixel and assumes its intensity value -not changing any values, just assigning them to the closest pixel in the new image space

Answer 17

Whilst you preserve the data values in their entirety, its not neatly lined up anymore so the shape gets fairly distorted

Answer 18

Modify the pixel values, they become like a weighted average of the pixels that they are now closest too

Answer 19

Whilst it does preserve the shape, it is at the expense of modifying the data

Answer 20

Save it as a set of instructions on FSL so it can recreate the transformation whenever It also lets us reverse the transformation too

Answer 21

Takes significant training to know where the hippocampus is Human error in the drawings meaning it is not very repeatable Many MRIs have hundreds of thousands of scans Blinding- could be bias in the data if we know who is healthy vs disease

Answer 22

A template is not a brain scan of a single person, but the average brain scan of multiple people It can be created by scanning many people, registering their T1 scans into the same space, and then taking a mathematical average

Answer 23

Can be used as a "target" image to register everyone's scans in the same space Can be used to pre-draw ROIs

Answer 24

Can take your scan from your participants, do a non-linear registration into the template space where we know where things are Because we know how to move between the two spaces, we can reverse transform this atlas back into the participants native space to see where these structures are in their brain and how big they are