Gadgetron reconstruction chain for peSpiral Sequence

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.

Gadgets

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                      |    |                            |   |                           |
+--------------------+     +----------------------------+    +----------------------------+   +---------------------------+

Dependencies

Gadgetron (build and runtime)
BART (in runtime for pics reco)
ismrmrdviewer (Optional)
siemens_to_ismrmrd (Optional)

Demo

Building

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.

Reconstruction

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 &

Results

Aliased image, GRE reference image from auto calibation data and CG-SENSE reconstruction can be seen. Reults from the above test

troubleshooting

Converting siemens data to MRD format

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

BART

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

Online reconstruction

Tunneling to your own Gadgetron

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 gadgetron@10.41.116.43

deploying in docker-conda environment for online reconstruction

The following steps are only valid for our gadgetron setup!

Mount the folder and start the docker container

scp -r <folder_path> username@192.168.0.1:~/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> gadgetron@10.41.xx.xx:/home/gadgetron/Documents/packages/gadgetron-gadgets/lib

Todo

[x] Accumulate data
[x] Add Trajectory information to Ismrmrd Reconbit
[x] Add nice NODE_PROPERTY for tunning gadgets with xml config.
[x] import and export functions for CFL files and h0NDArrays.
[x] Calculte coil maps from reference data using BART
[x] gridding reoconstruction
[x] coil combination with calculated sensitivity
[x] 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

Author

Praveen Iyyappan Valsala
Modified version of Spiral design package is from Philipp Ehses (philipp.ehses@dzne.de)

praveenivp / GenericSpiralReco

readme