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If the number of measurements or averages is greater than one, dummy scans are used. The numbers of dummy
scans (used for stabilizing the signal) depend on the TR selected. The sequence takes the TR that is selected by
the user, and then calculates how many repeats (so-called "dummy scans" or prep scans) to run based on a FIXED
TIME of 3 seconds. No matter what the TR is, at least 1 dummy scan will always be performed. Then, based on the
TR as it compares to 3 seconds, any additional dummy scans are determined. Finally, if iPAT is selected, there are
one or more additional scans before data acquisition for acquiring the reference lines.
# of dummy scans
e.g.
Example:
If TR is 1500 ms, 2 more dummy scans will be performed (total of 3 dummy scans).
If TR is 2500 ms, 1 more dummy scan will be performed (total of 2 dummy scans).
If TR is 3000 ms, 1 more dummy scan will be performed (total of 2 dummy scans).
If TR is 3001 ms, no more dummy scans will be performed (total of 1 dummy scan).
If TR is 3500 ms, no more dummy scans will be performed (total of 1 dummy scan).
After the dummy scans, there are 1 or more scans (TRs) to acquire iPAT reference lines, depending on what iPAT
factor is selected. In the EPI sequence, the iPAT reference lines are acquired separate from the imaging scans.
These are acquired after the dummy scans and before the imaging scans.
3.2.9 Slice timing
Typically, a multislice protocol (multiple slices per measurement) is used for BOLD EPI scans. Since each slice
is acquired at a different time, a "slice timing correction" must be applied to account for these differences in
acquisition time in relation to the stimulus. In the MOSAIC display format though, the timing of each slice is not
available, and only one time point is displayed for the entire volume. The acquisition time for each slice can be
extracted from the image header in syngo® software version VB15A. For VB13A and earlier software versions, this
time is not available in the header. The slices can be assumed to be distributed evenly in TR (Delay in TR).
Note: Take interleaved reordering when calculating slice timing, as described in Section 3.2.3.
3.2.10 Slice Time Correction
This means to account for slice timing differences relative to the stimulus. This is possible with syngo software
versions VB13A and later. See the BOLD Imaging Application Brochure, page 14, Covariates of no interest, column
5: Derivation of the activation pattern. It is necessary to model the offset in time while measuring the individual
slices. Prerequisites: Parameter "Ignore after transition = 0", and "Model transition states" active.
= 1 + quotient[ 3/TR(in seconds) ]
= 1 + quotient[ 3/TR(in seconds) ] + 1
= 1 + quotient[ 3/TR(in seconds) ] + 3
= 1 + quotient[ 3/TR(in seconds) ] + 4
fMRI User Guide
if no iPAT
if iPAT = 2
if iPAT = 3
if iPAT = 4
9
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