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ismrmrd_to_nifti

New beta version of ismrmrd_to_nifti

Data used for test :

The dataset we worked on is available here : https://zenodo.org/record/3674622#.Xk031Y7Pw5k

Usage

Two version are available : one for the conversion in Matlab (matlab_version) and one in Python (python_version). In the Matlab folder you will find :

  • "main_conversion.m" : main code to run conversion from ".dat"/".h5" to Nifti ".nii"
  • "load_ismrmrd_ifft3d_reconstruction.m" : function to load ".h5" file and reconstruct images
  • "load_reconstructed_data.m" : function to load ".mat" file of ismrmrd images
  • "extract_ismrmrd_parameters_from_headers.m" : function to compute and stock parameters from ismrmrd format needed by "set_nii_hdr.m"
  • "set_nii_hdr.m" : function to compute and create nifti structure from computed parameters in *"extract_ismrmrd_parameters_from_headers.m" *
  • "flip_image.m" : function to flip the reconstructed image and fit with the true Nifti one.
  • "crop_image.m" : function to crop the reconstructed image and fit with the reconstructed data size.
  • "comparison_test.m" : main code to compare two nifti files (usefull to compare true and converted nifti files)

Equivalent files are available in the Python folder.

To convert data (Matlab Version):

  1. Open "main_conversion.m" :

  2. In "%% Add path to needed librairies", change paths for your computer

addpath('/usr/local/share/ismrmrd/matlab/')
addpath('/home/path_to_ismrmrd_to_nifti')
addpath('/home/path_to_ismrmrd_to_nifti/xiangruili-dicm2nii-b76a158')

  1. Change the "ouput_path" to save in a different name or path (by default : data_path/filename+_ismrmrd_to_nifti_version_matlab.nii).

  2. Run the code and select your data file in ISMRMRD format (.h5 extension).

To compare real Nifti format and the converted one :

  1. Open "comparison_test.m"
  2. Set the true_filename to the true Nifti dataset
  3. Set the converted_filename to the converted Nifti dataset
  4. Run and compare

To convert data (Python Version):

  1. In a terminal go to the folder .../ismrmrd_to_nifti/python_version.

  2. Set the file main_conversion.py a executable file by running the following command :

chmod +x main_conversion.py
  1. Run the command :
./main_conversion.py -i <input> -o <output>

Be carreful : must be a ".h5" file and a ".nii" file.

Description

This new version includes :

  • a Matlab code to convert ISMRMRD data files into Nifti format from ".h5" or ".mat" files (available in matlab_version folder);
  • a Python code to convert ISMRMRD data files into Nifti format from ".h5" or ".mat" files (available in python_version folder);
  • this version allows conversion for ismrmrd data converted after the addition of the table_position_offset parameter to the patient position (siemens_to_ismrmrd, commit on the May 15th 2019)
  • little changes in the conversion formula : we hilighted issues on transformation matrix concerning the position of the image. Those little differences between the true Nifti image and the converted one were due to a bad way to deal with matrices dimensions. Indeed, it's necessary to substract 1 voxel dimension on x and y coordinates AND 1/2 slice dimension on z coordinate to center the image. This part is a bit more dark and real explanations are missing, so if you know why it's necessary, don't hesitate to share your ideas and change the formula !

Thoses changes have been tested on SIEMENS AREA system, with Sagittal, Coronal and Transversal views, for all read directions and rotations (positives and negatives but not for all cases) in HFS.

If you need our dataset to test the code, tell us !