This repo contains gadgetron gadgets to perform simple real-time gridding reconstrution for a custom 3D stack of spiral sequence. The gadgets are mainly adapted from the main gadgetron repo and gadgeton online course. It also has half-baked parallel imaging reconstruction with a help of BART reconstruciton package.
Please refer to piv_GadgetronSpiral.xml. The following four gadgets are mainly modified.
+--------------------+ +----------------------------+ +----------------------------+ +---------------------------+
| | | | | | | |
|RemoveRefOSGadget | |RefRecoGadget | | AddTrajInfoGadget | | SpiralGriddingGadget |
| | | | | | | |
|* removes readout +-----+* Calcultes Coil sensitivity+----+ * Parse spiral design para +---+ * perform gridding reco or|
| from GRE reference| | from reference scan by | | * Calculates trajectories | | pass data to pics of BART|
| scan | | calling BART ecalib | | and density compensation | | * do coil combination. |
| | |* Can also FFT reco the ref | | fucntion. | | |
| | | Data | | | | |
+--------------------+ +----------------------------+ +----------------------------+ +---------------------------+
- Gadgetron (build and runtime)
- BART (in runtime for pics reco)
- ismrmrdviewer (Optional)
- siemens_to_ismrmrd (Optional)
git clone https://github.com/praveenivp/GenericSpiralReco.git
cd GenericSpiralReco && mkdir build && cd build
cmake -DCMAKE_BUILD_TYPE=Debug -GNinja ..
ninja
Make sure the output dll is visible to gadgetron.
Start gadgetron and feed it with data. First, let us perform a simple reconstruction without BART.
gadgetron_ismrmrd_client -f testData/raw3D_R3.h5 -C config/SimpleReco.xml -o im_alias.h5
ismrmrdviewer im_alias.h5 &
If BART is on path, you can perform CG-SENSE reconstruction with ecalib and pics.
gadgetron_ismrmrd_client -f testData/raw3D_R3.h5 -C config/piv_GadgetronSpiral.xml -o im_sense.h5
ismrmrdviewer im_sense.h5 &
Aliased image, GRE reference image from auto calibation data and CG-SENSE reconstruction can be seen.
siemens raw data is already converted to MRD format using these commands!
siemens_to_ismrmrd -x parameter_maps/IsmrmrdParameterMap_peSpiral_VE11E.xsl -m parameter_maps/IsmrmrdParameterMap_peSpiral_VE11E.xml -f peSpiral.dat -z 1 -o data_z1.h5
ismrmrdviewer data_z1.h5
Make sure you enable calc_csm and do_pics flags to get all necessary files in the output folder for pics.
bart pics -i 10 -p DCF -t Traj coil_data sensCFL pics_reco
Turn off tunneling in gadgetron.ini file and make your own tunnel with ssh port forwarding.
ssh -L 192.168.2.1:9010:localhost:9002 [email protected]
The following steps are only valid for our gadgetron setup!
Mount the folder and start the docker container
scp -r <folder_path> [email protected]:~/code
docker run --rm -v <GenericSpiralReco_PATH>:/code <container_image_id>
docker exec -ti <container_id> bash
Inside the container shell, make sure the linker (ld) points to the ld inside conda by which ld. Otherwise, pthread library path was incorrect(ldconfig -p |grep pthread)
conda activate gadgetron
export PATH="${CONDA_PREFIX}/x86_64-conda-linux-gnu/bin":$PATH
install missing build dependencies and compile. If successful, commit the lib.so to gadgetron-gagets repo and restart gadgetron container via yacht.
apt update && apt install cmake libarmadillo-dev
cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=${CONDA_PREFIX} ..
make -j8
scp <libfile.so> [email protected]:/home/gadgetron/Documents/packages/gadgetron-gadgets/lib
- Accumulate data
- Add Trajectory information to Ismrmrd Reconbit
- Add nice NODE_PROPERTY for tunning gadgets with xml config.
- import and export functions for CFL files and h0NDArrays.
- Calculte coil maps from reference data using BART
- gridding reoconstruction
- coil combination with calculated sensitivity
- CG-SENSE reconstruction
- remove CFL_IO2.xx
- multi-slice reco fix
- GIRF correction
- coil maps calculation not starting immediately
- Mosiacing doesn't work with reference image
- Praveen Iyyappan Valsala
- Modified version of Spiral design package is from Philipp Ehses ([email protected])