A lot of this may depend on the stability of your scanner. I hope that
a MR physicist out there can comment more on the effects of shimming etc.
Realignment is not a panacea for all movement artifacts within the scanner.
Some of the artifacts it does not correct are:
Interpolation error from the resampling algorithm used to
transform the images can be one of the main sources of motion
related artifacts. When the image series is resampled, it is
important to use a very accurate interpolation method such as
sinc or Fourier interpolation.
When MR images are reconstructed, the final images are usually
the modulus of the initially complex data, resulting in any
voxels that should be negative being rendered positive. This has
implications when the images are resampled, because it leads to
errors at the edge of the brain that can not be corrected however
good the interpolation method is. Possible ways to circumvent
this problem are to work with complex data, or possibly to apply
a low pass filter to the complex data before taking the modulus.
The sensitivity (slice selection) profile of each slice also
plays a role in introducing artifacts.
fMRI images are spatially distorted, and the amount of distortion
depends partly upon the position of the subject's head within the
magnetic field. Relatively large subject movements result in the
brain images changing shape, and these shape changes can not be
corrected by a rigid body transformation.
Each fMRI volume of a series is currently acquired a plane at a
time over a period of a few seconds. Subject movement between
acquiring the first and last plane of any volume leads to another
reason why the images may not strictly obey the rules of rigid
body motion.
After a slice is magnetised, the excited tissue takes time to
recover to its original state, and the amount of recovery that
has taken place will influence the intensity of the tissue in the
image. Out of plane movement will result in a slightly different
part of the brain being excited during each repeat. This means
that the spin excitation will vary in a way that is related to
head motion, and so leads to more movement related artifacts.
Ghost artifacts in the images do not obey the same rigid body
rules as the head, so a rigid rotation to align the head will not
mean that the ghosts are aligned.
The accuracy of the estimated registration parameters is normally
in the region of tens of micro m. This is dependent upon many
factors, including the effects just mentioned. Even the signal
changes elicited by the experiment can have a slight effect on
the estimated parameters.
Best regards,
-John
| We have a design consisting of four sessions. Sessions A and B are aquired
| together in one examination, whereas sessions A' and B' are also aquired
| together a week later. In order to compare sessions A/A' and B/B', I put all
| four sessions in one model. My understanding was that the realignment
algorithm
| would account for the differences in position and orientation and realigns all
| images to the first image of the first session. I believed that this should
| work regardless of whether the sessions were acquired all at once or whether
| several delayed examinations were involved.
|
| It is quite certain, that the position of the subject's head in the scanner
| differs considerably between examination 1 (sessions A an B) and examination 2
| (session A' and B'), conducted several days later.
|
|
| Now, are my assumptions correct or should I be concerned about the adequacy of
| the image coregistration between sessions ?
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