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 (in DICOM) between two inversion pulses in seconds. In the (Siemens) PDF it is described as TR under the Contrast - Common section. In BIDS, this corresponds to the RepetitionTimePreparation 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 as Echo spacing (usually) under the Sequence - Part 1 section. In BIDS, this corresponds to the RepetitionTimeExcitation 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.