Tyger - MRIlab

In this repository we have a first version of the use of Tyger for reconstruction and post-processing of magnetic resonance images acquired in systems controlled by MaRCoS and MaRGE.

RawDatas to test

In the following link you can download rawDatas generated by one of our low-field scanners.

RARE rawData

Knee and Brain rawDatas

Testing - RARE

Python codes to execute.

• Tyger recon: RARE_recon/run_files/runTyger.py

• Local recon: RARE_recon/run_files/runPythonFit.py

Among the inputs for these codes, you must indicate the path to a yml file containing the reconstruction information. There are several examples in the path: RARE_recon/yml_files/.

Testing - PETRA

Python codes to execute.

• Tyger recon: PETRA_recon/run_files/runTyger.py

• Local recon: PETRA_recon/run_files/runPythonscripts_PETRA.py

Among the inputs for these codes, you must indicate the path to a yml file containing the reconstruction information. There are several examples in the path: PETRA_recon/yml_files/.

Testing - Brain

Here are some examples of use.

1. FFT:

   python3 recon_xyz/scripts/fromMATtoMRD3D_RARE.py -i 'brainIR.mat' | tyger run exec -f recon_xyz/scripts/stream_recon_FFT_gpu.yml | python3 recon_xyz/scripts/fromMRDtoMAT3D.py -o 'brainIR.mat'
   

2. ART:

   python3 recon_xyz/scripts/fromMATtoMRD3D_RARE.py -i 'brainIR.mat' | tyger run exec -f recon_xyz/scripts/stream_recon_ART_gpu.yml | python3 recon_xyz/scripts/fromMRDtoMAT3D.py -o 'brainIR.mat'

3. ART PK Bo:

   python3 recon_xyz/scripts/fromMATtoMRD3D_RARE.py -i 'brainIR.mat' | tyger run exec -f recon_xyz/scripts/stream_recon_ARTPK_gpu.yml | python3 recon_xyz/scripts/fromMRDtoMAT3D.py -o 'brainIR.mat'

4. Conjugate Phase:

   python3 recon_xyz/scripts/fromMATtoMRD3D_RARE.py -i 'brainIR.mat' | tyger run exec -f recon_xyz/scripts/stream_recon_CP_gpu.yml | python3 recon_xyz/scripts/fromMRDtoMAT3D.py -o 'brainIR.mat'

Testing - knee

Here are more examples of use.

1. FFT:

   python3 scripts/fromMATtoMRD2D.py -i 'knee.mat' -s 10 | tyger run exec -f scripts/stream_recon.yml | python3 scripts/fromMRDtoMAT2D.py -o 'knee.mat'

2. ART:

   python3 scripts/fromMATtoMRD2D.py -i 'knee.mat' -s 10 | tyger run exec -f scripts/stream_recon_art.yml | python3 scripts/fromMRDtoMAT2D.py -o 'knee.mat'

3. ART PK Grad:

   python3 scripts/fromMATtoMRD2D.py -i 'knee.mat' -s 10 | tyger run exec -f scripts/stream_recon_artPK.yml | python3 scripts/fromMRDtoMAT2D.py -o 'knee.mat'

4. BART FFT:

   python3 scripts/fromMATtoMRD2D.py -i 'knee.mat' -s 10 | tyger run exec -f scripts/stream_recon_bart_fft.yml | python3 scripts/fromMRDtoMAT2D.py -o 'knee.mat'

5. BART FFT undersampled:

   python3 scripts/fromMATtoMRD2D.py -i 'knee.mat' -s 10 | tyger run exec -f scripts/stream_recon_bart_fftus.yml | python3 scripts/fromMRDtoMAT2D.py -o 'knee.mat'

6. BART Compressed Sensing:

   python3 scripts/fromMATtoMRD2D.py -i 'knee.mat' -s 10 | tyger run exec -f scripts/stream_recon_bart_cs.yml | python3 scripts/fromMRDtoMAT2D.py -o 'knee.mat'

7. Pix2Pix knee model:

   python3 Pix2Pix_Tyger/scripts/fromMATtoMRD2D.py -i 'knee.mat' -s 17 | tyger run exec -f Pix2Pix_Tyger/scripts/stream_recon_pix2pix.yml | python3 Pix2Pix_Tyger/scripts/fromMRDtoMAT2D.py -o 'knee.mat'

Docker images

Docker images with code from this repository can be found here:

Docker Images

These images are the ones that run on tyger.

References

1. Tyger
   https://microsoft.github.io/tyger/
2. MRD
   https://ismrmrd.github.io/mrd/