Protocols¶
This section addresses some frequently asked questions regarding acquisition protocols and how to set them in qMRLab.
mp2rage¶
You can visit our MP2RAGE blog post to find out about
the basics of the MP2RAGE
method.
NumberOfShots
¶
This section of the Protocol
panel expects two NumberOfShots
values: Pre
and Post
.
In the original implementation, the
NumberOfShots
is referred as nZSlices
, and before/after
designates the number of segments
before and after the center of k-space.
To calculate these values, you need to know the values of Slices Per Slab
(NSlices) and Slice Partial Fourier
(PF) parameters. To calculate Pre
and Post
:
- Pre
Formula:
Pre = NSlices(PF - 0.5)
- Post
Formula:
Post = NSlices/2
Repetition Times
¶
- Inversion (Inv)
RepetitionTime
(inDICOM
) between two inversion pulses in seconds. In the (Siemens)PDF
it is described asTR
under the Contrast - Common section. In BIDS, this corresponds to theRepetitionTimePreparation
metadata field. Typically between 3 - 6 seconds.- Excitation (Inv)
- The repetition time between two excitation pulses in each GRE readout block. In the (Siemens)
PDF
it is described asEcho spacing
(usually) under the Sequence - Part 1 section. In BIDS, this corresponds to theRepetitionTimeExcitation
metadata field. Typically around 0.006 - 0.008 seconds.
Warning
Some parameters are not included in the DICOM
header by Siemens, such as the
RepetitionTimeExcitation
. Nonetheless, can be accessed in the protocols exported as PDF
.
Inversion Times
¶
Inversion times belonging to each GRE readout block. In the (Siemens) protocol PDF
, these
values can be found under the Contrast - Common section with the names of TI 1
and TI 2
.
Flip Angles
¶
Excitation flip angles in each GRE readout block. In the (Siemens) protocol PDF
, these
values can be found under the Contrast - Common section with the names of Flip angle 1
and Flip angle 2
.