fetal_cmr_4d

fetal whole-heart 4d reconstruction using motion-corrected multi-planar real-time MRI

Publications

Fetal whole-heart 4D imaging using motion-corrected multi-planar real-time MRI.
Joshua FP van Amerom, David FA Lloyd, Maria Deprez, Anthony N Price, Shaihan J Malik, Kuberan Pushparajah, Milou PM van Poppel, Mary A Rutherford, Reza Razavi, Joseph V Hajnal.
13 Apr 2019. Magnetic Resonance in Medicine. 2019. doi: 10.1002/mrm.27798 (accepted, peer-reviewed+revised)
05 Dec 2018. arXiv: 1812.02249 (preprint)

Directories

4drecon - preprocessing and 4D reconstruction scripts

cardsync - cardiac synchronisation

eval - summarise and evaluate results

irtk_cardiac4d - 4D reconstruction submodule linked to github.com/jfpva/irtk_cardiac4d, built on the Image Registration Toolkit (IRTK) v2.0.

ktrecon - k-t sense reconstruction submodule linked to github.com/jfpva/ktrecon

Installation

Build instructions for irtk can be found at sites.google.com/site/mariakuklisovamurgasova/software.

External Dependencies

ReconFrame - software platform providing the tools and the functionality to develop and execute a complete image reconstruction of Philips MR data (gyrotools.com/gt/index.php/products/reconframe)

Framework

Framework for 4D cine reconstruction, consists of:

1. acquisition and reconstruction of multi-planar dynamic2DMRI;
2. an initial motion correction stage to achieve rough spatial alignment of the fetal heart using temporal mean (i.e., static) images for stack-stack registration followed by slice-volume registration interleaved with static volume (3D) reconstruction;
3. cardiac synchronisation, including heart rate estimation and slice-slice cardiac cycle alignment; and
4. further motion-correction using dynamic image frames interleaved with 4D reconstruction; and
5. a final 4D cine reconstruction, including outlier rejection.

User-specified ROIs, and identification of a target stack for stack-stack registration are the only manual preparations required for reconstruction.

Steps

Setup
create working directories,
e.g., in shell:

RECONDIR=~/path/to/recon/directory
mkdir $RECONDIR
mkdir $RECONDIR/data
mkdir $RECONDIR/ktrecon
mkdir $RECONDIR/mask
mkdir $RECONDIR/cardsync

1. MRI
   • acquire 2D multi-planar real-time MRI data
   • reconstruct images using ktrecon,
     e.g., for each stack, in Matlab:

     reconDirPath        = '~/path/to/recon/directory';
     seriesNo            = 0;
     rawDataFilePath     = '~/path/to/rawdata.lab';
     senseRefFilePath    = '~/path/to/senserefscan.lab';
     coilSurveyFilePath  = '~/path/to/coilsurveyscan.lab';
     outputDirPath       = fullfile( reconDirPath, 'ktrecon' );
     outputStr           = sprintf( 's%02i', seriesNo );
     reconOpts           = { 'GeometryCorrection', 'Yes' };
     
     mrecon_kt(   rawDataFilePath, ...
                 'senseref', senseRefFilePath, ...
                 'coilsurvey', coilSurveyFilePath, ...
                 'outputdir', outputDirPath, ...
                 'outputname', outputStr, ...
                 'patchversion', patchVersion,...
                 'reconoptionpairs', reconOpts )

   • further processsing
     • copy/move all magnitude-valued DC (s*_dc_ab.nii.gz) and real-time (s*_rlt_ab.nii.gz) files from 'ktrecon' directory to 'data' directory
       e.g., in shell:

       cp ktrecon/s*_dc_ab.nii.gz data;
       cp ktrecon/s*_rlt_ab.nii.gz data;

     • manually draw fetal heart masks for each sXX_dc_ab.nii.gz file (e.g., using the Medical Imaging ToolKit (MITK) Workbench)
       • draw ROI containing fetal heart and great vessels for each slice
       • save segmentation as sXX_mask_heart.nii.gz segmentation in 'mask' directory
     • run preproc in Matlab,

       reconDir = '~/path/to/recon/directory';
       S = preproc( reconDir );
       save( fullfile( reconDir, 'data', 'results.mat' ), 'S', '-v7.3' );

     • optionally, manually specify
       • target stack by changing value in 'data/tgt_stack_no.txt' (stacks are index 1,2,...)
       • excluded stacks/slices/frames by specifying in 'data/force_exclude_*.txt' (stacks/slices/frames are zero-indexed)
2. Motion-Correction (static)
   • create 3D mask of fetal chest
     • recon reference volume,
       e.g., in shell:

     RECONDIR=~/path/to/recon/directory
     ./recon_ref_vol.bash $RECONDIR ref_vol

     • draw fetal chest ROI using 'ref_vol.nii.gz' as a reference (e.g., using MITK)
     • save segmentation to 'mask' directory as 'mask_chest.nii.gz'
       • note: the orientation of all later 3D/4D reconstructions is determined by this mask file; the orientation can be changed by applying a transformation to 'mask_chest.nii.gz' prior to further reconstructions
   • static (slice-wise) motion-correction,
     e.g., in shell:

     RECONDIR=~/path/to/recon/directory˜
     ./recon_dc_vol.bash $RECONDIR dc_vol

3. Cardiac Synchronisation
   • heart-rate estimation
     • run cardsync_intraslice, in Matlab:

       reconDir    = '~/path/to/recon/directory';
       dataDir     = fullfile( reconDir, 'data' );
       cardsyncDir = fullfile( reconDir, 'cardsync' );
       M = matfile( fullfile( dataDir, 'results.mat' ) );
       S = cardsync_intraslice( M.S, 'resultsDir', cardsyncDir, 'verbose', true );

   • slice-slice synchronisation
     • recon cine volume for each slice,
       e.g., in shell:

       RECONDIR=~/path/to/recon/directory
       ./recon_slice_cine.bash $RECONDIR

     • optionally, specify target slice by creating file 'data/tgt_slice_no.txt' containing target slice number (indexed starting at 1)
     • run cardsync_interslice, in Matlab:

       % setup
       reconDir    = '~/path/to/recon/directory';
       dataDir     = fullfile( reconDir, 'data' );
       cardsyncDir = fullfile( reconDir, 'cardsync' );
       cineDir     = fullfile( reconDir, 'slice_cine_vol' );    
       M = matfile( fullfile( cardsyncDir, 'results_cardsync_intraslice.mat' ) );
       
       % target slice
       tgtLoc = NaN;
       tgtLocFile = fullfile( dataDir, 'tgt_slice_no.txt' );
       if exist( tgtLocFile , 'file' )
         fid = fopen( tgtLocFile, 'r' );
         tgtLoc = fscanf( fid, '%f' );
         fclose( fid );
       end
       
       % excluded slices
       excludeSlice = [];
       excludeSliceFile = fullfile( dataDir, 'force_exclude_slice.txt' );
       if exist( excludeSliceFile , 'file' )
         fid = fopen( excludeSliceFile, 'r' );
         excludeSlice = fscanf( fid, '%f' ) + 1;  % NOTE: slice locations in input file are zero-indexed
         fclose( fid );
       end
       
       % slice-slice cardiac synchronisation
       S = cardsync_interslice( M.S, 'recondir', cineDir, 'resultsdir', cardsyncDir, 'tgtloc', tgtLoc, 'excludeloc', excludeSlice );

4. Motion-Correction (dynamic)
   • performed interleaved with 4D Reconstruction
5. 4D Volumetric Reconstruction
   • recon 4D (cine) volume,
     e.g., in shell:

   RECONDIR=~/path/to/recon/directory
   ./recon_cine_vol.bash $RECONDIR cine_vol

Summarise
e.g., in Matlab:

S = summarise_recon( '~/path/to/recon/directory/cine_vol', '~/path/to/recon/directory/cardsync', 'verbose', true );
I = plot_info( '~/path/to/recon/directory/cine_vol/info.tsv');