ejcanalesr / parametric-t2-spiral Goto Github PK

- numpy
- nibabel
- matplotlib
- scipy
- skimage
- joblib
- multiprocessing
- progressbar2
- joypy
- pandas
- tabulate

$ python call_estimation_script.py -h

usage: call_estimation_script.py [-h] --path_to_folder PATH_TO_FOLDER --input INPUT --mask MASK --denoise {TV2D,TV3D,None} [--reg_param REG_PARAM] --savefig {yes,no} --savefig_slice SAVEFIG_SLICE
                                 [--numcores NUMCORES]

Myelin Water Imaging

optional arguments:
  -h, --help            show this help message and exit
  --path_to_folder PATH_TO_FOLDER
                        Path to the folder where the data is located, e.g., /home/Datasets/T2spiral/
  --input INPUT         Input data, e.g., Data.nii.gz
  --mask MASK           Brain mask, e.g., Mask.nii.gz
  --denoise {TV2D,TV3D,None}
                        Denoising method
  --reg_param REG_PARAM
                        Regularization parameter for TV denoising
  --savefig {yes,no}    Save reconstructed maps in .png
  --savefig_slice SAVEFIG_SLICE
                        Axial slice to save reconstructed maps, e.g., --Slice=90
  --numcores NUMCORES   Number of cores used in the computation: -1 = all cores

- Brain extraction for obtaining the brain mask (i.e., bet, FSL)
- Bias-field correction of the estimated proton density map, and segmentation to obtain WM, GM, and CSF probabilistic tissue-maps (i.e., fast, FSL)

- MWF.nii.gz: Myelin Water Fraction
- IEWF.nii.gz: Intra- and Extra-cellular Water Fraction
- FWF.nii.gz: Free and quasi-free Water Fraction (i.e., T2 > 200ms) 
- T2_M.nii.gz: T2 of the myelin water.
- T2_IE.nii.gz: T2 of the intra- and extra-cellular water
- K_global.nii.gz: It is proportional to the Proton density (i.e., total water content)
- Predicted_Data4D.nii.gz: Predicted signal