General notes

So far only MR image reconstruction using raw data from Siemens Biograph mMR PET-MR scanners has been tested.

Both 2D (single or multi-slice) and 3D acquisitions are now supported.

• Supported trajectories (SIRF 3.1.1): cartesian, radial phase encoding.
• Soon supported (pull request 980): 2D radial (uniform and golden-angle), stack of stars.
• Not supported: EPI, 3D radial.

Caveat for 2D multi-slice acquisitions:

The computation of the geometrical information for 2D multi-slice data (i.e. location of reconstructed images in space) assumes that slice distance and slice thickness are identical, as well as all slices are oriented in the same direction. If this is not the case a warning is issued, but the data are still reconstructed. The image content is correct, however, their location in space is not captured correctly by the VoxelisedGeometricalInformation3D object.

Siemens mMR Biograph

MR raw data export

The MR raw data (i.e. k-space data) is automatically saved on a Siemens scanner and can be exported using the “Twix” tool. After the MR measurement is successfully completed go to “Start” and select “Twix.exe” or open a command window and type “twix” and select “open”.

This opens the “Twix” tool which lists all the currently available MR raw data. Select the appropriate file and then right click and select “Copy total raid file…”. Confirm and select folder where data shall be saved. For each scan one .dat file is exported which contains the MR raw data and the corresponding header information (i.e. scan and image reconstruction parameters).

MR raw data conversion to ISMRMRD format

SIRF uses the ISMRMRD data format (http://ismrmrd.github.io/) for MR raw and image data. In order to convert the MR raw data exported from MR scanners converters are available for different vendors: https://github.com/ismrmrd

In order to convert MR raw data from a Siemens PET-MR scanner, install siemens_to_ismrmrd (https://github.com/ismrmrd/siemens_to_ismrmrd) and then use the following command:

siemens_to_ismrmrd –f input_file.dat –o output_file.h5 

This will create one .h5 file which can then be used with SIRF for MR image reconstructions. For more details please see demo: fully_sampled_recon (.py) or (.m).

From software version VD onwards each .dat file can contain multiple acquisitions.
By default only the first acquisition is converted to ISMRMRD.h5 format. In order to access other acquisitions the option "-z" must be supplied:

siemens_to_ismrmrd –f input_file.dat –o output_file.h5 -z 2 

Hint: it is probable that the first acquisition contains data required for scan adjustments and thus a conversion seemingly fails. In this case, use option "-z 2" or higher to access the actual scan data. The program will issue a message in case you try an acquisition number higher than the ones contained in the file.

If SIRF is installed via the SIRF-SuperBuild, siemens_to_ismrmrd is an optional installation (enabled via BUILD_siemens_to_ismrmrd). Please refer the the relevant wiki pages on the SIRF-SuperBuild for details and additional dependencies.