Added the feature to read DICOM images into a 4D Nifti image utilizing dicom2niix

updated Dockerfile, README, and nifti_wrapper.py

Author: jph6366

Docker/Dockerfile

@@ -5,6 +5,13 @@ WORKDIR /usr/src/app
 RUN apt-get update && apt-get install -y --no-install-recommends \
     build-essential \
     libssl-dev \
+    wget \
+    pigz \
+    && wget https://github.com/rordenlab/dcm2niix/archive/refs/tags/v1.0.20241211.tar.gz \
+    && tar -xzf v1.0.20241211.tar.gz -C /usr/local/bin \
+    && rm v1.0.20241211.tar.gz \
+    && apt-get remove -y wget \
+    && apt-get autoremove -y \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/*
 

Docker/README.md

@@ -24,7 +24,7 @@ This project is designed to run the `nifti_wrapper` script using a Docker contai
 
 Before running the Docker container, here are the available options for the `Docker image` script:
 
-- `input_file`: Path to the input 4D NIfTI file.
+- `input_file`: Path to the input 4D NIfTI file or dicom files 4D images like fMRI and DTI/DKI are supported.
 - `bvec_file`: Path to the b-vector file.
 - `bval_file`: Path to the b-value file.
 - `--affine`: Affine matrix for NIfTI image (optional).
@@ -58,4 +58,23 @@ Before running the Docker container, here are the available options for the `Doc
 
     Replace `brain.nii.gz`, `brain.bvec`, and `brain.bval` with the actual file names you want to use.
 
+### Reading in DICOM images
+
+1. you can run the same Docker container using the `docker run` command. This command runs the Docker image with the specified input files:
+
+    ```sh
+    sudo docker run -it --rm --name TF2.4_IVIM-MRI_CodeCollection \
+        -v ~/TF2.4_IVIM-MRI_CodeCollection:/usr/src/app \
+        -v ~/TF2.4_IVIM-MRI_CodeCollection:/usr/app/output \ 
+        tf2.4_ivim-mri_codecollection Downloads/dicom_folder
+    ```
+
+    Replace `dicom_folder` with the actual directory (containing DICOM Images) you want to use.
+
+[Note that NIfTI and DICOM encode space differently](https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#Spatial_Coordinates)
+
+
+##### The goal of dcm2niix is to create FSL format bvec/bval files for processing. A crucial concern is ensuring that the gradient directions are reported in the frame of reference expected by the software you use to fit your tractography. [dicom2niix should generate a ".bvec" file that reports the tensors as expected](https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#Diffusion_Tensor_Imaging) by FSL's dtifit, where vectors are reported relative to image frame of reference (rather than relative to the scanner bore). 
+
+#### It is strongly recommend that users check validate the b-vector directions for their hardware and sequence as [described in a dedicated document](https://www.nitrc.org/docman/?group_id=880)
 ---

WrapImage/nifti_wrapper.py

@@ -1,11 +1,51 @@
 import argparse
 import json
 import os
+from pathlib import Path
+import subprocess
 import nibabel as nib
 from src.wrappers.OsipiBase import OsipiBase
 import numpy as np
 from tqdm import tqdm
 
+def dicom_to_niix(vol_dir: Path):
+    """
+    For converting DICOM images to a (compresssed) 4d nifti image
+    """
+
+    try:
+        res = subprocess.run(
+            [
+                "dcm2niix",
+                "-f", "%s_%p", # dcm2niix attempts to provide a sensible file naming scheme
+                "-o", vol_dir,
+                "-z", "y", #specifying compressed nii.gz file
+                # https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage
+                # for further configuration for general usage see page above
+                vol_dir         
+            ],
+            capture_output=True,
+            text=True,
+            check=True
+        )
+        
+        nifti_files = list(Path(vol_dir).glob("*.nii.gz"))
+        if not nifti_files:
+            raise RuntimeError("No NIfTI file generated by dcm2niix.")
+        if len(nifti_files) > 1:
+            raise RuntimeError("Multiple NIfTI files generated; expected one 4D NIfTI.")
+
+        bval_files = list(vol_dir.glob("*.bval"))
+        bvec_files = list(vol_dir.glob("*.bvec"))
+        bval_path = str(bval_files[0]) if bval_files else None
+        bvec_path = str(bvec_files[0]) if bvec_files else None
+
+
+        return vol_dir / "dicom2nifti.nii.gz", bval_path, bvec_path
+
+    except subprocess.CalledProcessError as e:
+        raise RuntimeError(f"dcm2niix failed: {e.stderr}")
+
 
 def read_nifti_file(input_file):
     """
@@ -81,22 +121,35 @@ def loop_over_first_n_minus_1_dimensions(arr):
 
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(description="Read a 4D NIfTI phantom file along with BIDS JSON, b-vector, and b-value files.")
-    parser.add_argument("input_file", type=str, help="Path to the input 4D NIfTI file.")
-    parser.add_argument("bvec_file", type=str, help="Path to the b-vector file.")
-    parser.add_argument("bval_file", type=str, help="Path to the b-value file.")
+    parser.add_argument("input_file", type=Path, help="Path to the input 4D NIfTI file or DICOM files 4D images like fMRI and DTI/DKI are supported..")
+    parser.add_argument("bvec_file", type=Path, help="Path to the b-vector file.")
+    parser.add_argument("bval_file", type=Path, help="Path to the b-value file.")
     parser.add_argument("--affine", type=float, nargs="+", help="Affine matrix for NIfTI image.")
     parser.add_argument("--algorithm", type=str, default="OJ_GU_seg", help="Select the algorithm to use.")
     parser.add_argument("--algorithm_args", nargs=argparse.REMAINDER, help="Additional arguments for the algorithm.")
 
     args = parser.parse_args()
 
     try:
+        if args.input_file.is_dir():
+            # Convert DICOM to NIfTI using dicom2niix
+            nifti_file, bval_path, bvec_path = dicom_to_niix(args.input_file) # read dir
+            if bval_path is None or bvec_path is None:
+                raise RuntimeError("dcm2niix did not generate bval/bvec files.")
+            bval_file = Path(bval_path)
+            bvec_file = Path(bvec_path)
+        else:
+            # Assume input is already a NIfTI file
+            nifti_file = args.input_file
+            bval_file = args.bval_file
+            bvec_file = args.bvec_file
+
         # Read the 4D NIfTI file
-        data, _ = read_nifti_file(args.input_file)
+        data, _ = read_nifti_file(nifti_file)
 
         # Read the b-vector, and b-value files
-        bvecs = read_bvec_file(args.bvec_file)
-        bvals = read_bval_file(args.bval_file)
+        bvecs = read_bvec_file(bvec_file)
+        bvals = read_bval_file(bval_file)
 
         # Pass additional arguments to the algorithm