CS MoCo LAB: An MR acquisition and reconstruction system

mex CS_FOCUSS.cpp -Iinclude\gadgetron -Iinclude\cuda -Isrc\FOCUSS -Iinclude\fftw -Iinclude -Llib\boost -Llib\ace -lACE -Llib\CS_LAB -lCS_LAB

g++ -std=c++0x -fopenmp Approx.cpp LinkedList.cpp Point.cpp SomeFunctions.cpp SubsampleMain.cpp VDSamplingUpper.cpp VariableDensity.cpp -o Subsample

>> Subsampling -h

============================================================================================================

--- Subsampling Mask Generation ---

============================================================================================================

 input parameters in ascending order (just numbers) with [default value] if left blank:

 no input parameters allows them to be entered in the command window

 parameter [defVal]            description                                                     possible values

------------------------------------------------------------------------------------------------------------

 nX [256]:                     width of subsampling mask                                       [16:1024]

 nY [128]:                     height of subsampling mask                                      [1:1024]

 accel [3]:                    desired acceleration factor                                     [2:15]

 subsampling type [1]:         Poisson-Disc {1}, Gaussian {2}                                  {1,2}

 fully sampled [0.065]:        percentage of fully sampled region                              [0:1]

 elliptical scanning [0]:      sample in elliptical scan region                                {0,1}

 ESPReSSo factor [1]:          ESPReSSo/Partial Fourier compactification factor                [0.5:1]

 ESPReSSo direction [0]:       ESPReSSo/Partial Fourier direction along width {0}, height {1}  {0,1}

 variable-density [4]:         variable-density options                                        {1,2,3,4,5}

                                  none {1}

                                  central point {2}

                                  central block {3}

                                  central ellipse {4}

                                  local adaptive variable-density (needs external fraction.txt file) {5}

 Poisson Sampling [1]:         Poisson-Disc sampling options                                    {0,1,2}

                                  2D Poisson-Disc {0} (chosen automatically if nY=1)

                                  3D Poisson-Disc {1} (strictly obeying neighbourhood criterion)

                                  3D pseudo Poisson-Disc {2} (approximately obeying neighbourhood criterion)

 power [2]:                    power of variable-density scaling                                [1:5]

 root [2]:                     root of variable-density scaling                                 [1:5]

long lLines = 256;             // ky size

long lPartitions = 64;         // kz size

double dAccel = 4;             // desired subsampling acceleration

float fully_sampled = 0.065;   // percentage fully sampled center region

float ESPReSSoVal = 1;         // ESPReSSo compactification factor

bool ESPReSSoDir = false;      // ESPReSSo direction (ky = false, kz = true)

long lMeasurements = 1;        // temporally changing subsampling mask

short int varDensity = 4;      // variable-density type

short int smpl_type = 1;       // Poisson-Disc subsampling algorithm

bool ellipScanning = false;    // elliptical scanning

long lLine, lPartition, lMeasurement;

// Poisson-Disc subsampling

int*** subsamplingMask = SubsampleMain::startPD(lLines, lPartitions, dAccel, fully_sampled, ESPReSSoVal, ESPReSSoDir, lMeasurements, varDensity, smpl_type, ellipScanning);

// Gaussian subsampling

//int*** subsamplingMask = SubsampleMain::startGaussian(lLines, lPartitions, dAccel, fully_sampled, ESPReSSoVal, ESPReSSoDir, lMeasurements);

for(lMeasurement = 0; lMeasurement < lMeasurements; lMeasurement++)

{

    for(lLine = 0; lLine < lLines; lLine++)

    {

        for(lPartition = 0; lPartition < lPartitions; lPartition++)

        {

            if(subsamplingMask[lLine,lPartition,lMeasurement] > 0)

                // run sequence kernel

        }

    }

}

Subsample[.exe] lLines lPartitions dAccel subSampleDistribution fully_sampled ellipScanning ESPReSSoFac ESPReSSoDir varDensity

CS_LAB *pCS = new CS_LAB();

pCS->process_config(XML_FILE);

int iRet = pCS->opCS_->fRecon(hoArray, hoArray); // hoArray in ISMRMD format

<gadget>

<name>FOCUSS</name>

<dll>CS_LAB</dll>

<classname>CS_LAB</classname>

<property>

    <name>PARAMETER_NAME</name>

    <value>PARAMETER_VALUE</value>

</property>

...

</gadget>

CS_LAB_Interface.m

kSpace (subsampled or fully sampled)

    cell array: nSlices x nChannels x nRepetitions x nAverages

    each cell: 2D: nYPhase x nXFreq x    -    x (nTime) (single/double array)

               3D: nYPhase x nXFreq x nZPhase           (single/double array)

               4D: nYPhase x nXFreq x nZPhase x nTime   (single/double array)

// if subsampled kSpace

mask (subsampling mask)

    double/logical array: nSparseDim1 x nSparseDim2 (1D pattern: nSparseDim2 = 1, 2D pattern: nSparseDim2 > 1)

sparseDim (sparse dimensions)

    double array: [Dim1, Dim2] (Dim-i: matrix dimension along which subsampling occurs, e.g. for 3D kSpace: [1 3] := [yPhase, zPhase])

// data: - subsampled k-space: ISMRMD format

//                             or following structure:

//                             cell array: nSlices x nChannels x nRepetitions x nAverages

//                             each cell: 2D: nYPhase x nXFreq x (nTime) (single/double array)

//                                        3D: nYPhase x nXFreq x nZPhase (single/double array)

//                                        4D: nYPhase x nXFreq x nZPhase x nTime (single/double array)

//       - path to raw Siemens measurement file (*.dat)

// para: - path to parameter file (e.g. parameters.m)

//       - parameter struct

[imageSOS, imageCha] = CS_reconstruction(data, para);