Nipype integration of NIFTI_NORDIC

NIFTI_NORDIC_interface.py

@@ -0,0 +1,76 @@
+# Author: Monika Dörig, 2024
+
+
+from nipype.interfaces.base import (CommandLine, traits, TraitedSpec,
+                                    BaseInterface, BaseInterfaceInputSpec, File)
+import os
+
+
+class NiftiNordicInputSpec(BaseInterfaceInputSpec):
+    additional_path = traits.Str(desc='Additional path to be added with addpath in MATLAB', mandatory=True)
+    fn_magn_in = traits.File(exists=True, desc='Input magnitude file', mandatory=True)
+    fn_phase_in = traits.File(exists=True, desc='Input phase file', mandatory=True)
+    fn_out = traits.Str(desc='Output prefix or suffix', mandatory=True)
+    ARG = traits.File(exists=True, desc='Path to MATLAB struct file representing input parameters')
+
+
+class NiftiNordicOutputSpec(TraitedSpec):
+    # traits.Either allows for the possibility that the file might not exist (None) or that it exists and is a valid file (File(exists=True))
+    output_file = traits.Either(None, File(exists=True), desc='Denoised nii file')
+    add_info_file = traits.Either(None, File(exists=True), desc='Optional output file for additional info')
+    complex_phase_file = traits.Either(None, File(exists=True), desc='Optional output file - saves phase in similar format as input phase')
+    complex_magn_file = traits.Either(None, File(exists=True), desc='Optional output file - saves magn in similar format as input magn')
+    gfactor_map_file = traits.Either(None, File(exists=True), desc='Optional output file for gfactor map')
+    residual_mat_file = traits.Either(None, File(exists=True), desc='Optional output file for NORDIC residuals')
+
+class NiftiNordic(BaseInterface):
+    input_spec = NiftiNordicInputSpec
+    output_spec = NiftiNordicOutputSpec
+
+    # To handle the basename of .nii and .nii.gz files correctly
+    def get_base_filename(self, file_path):
+        base_name = os.path.basename(file_path)
+        base_name, ext = os.path.splitext(base_name)
+        if ext == '.gz':
+            base_name, _ = os.path.splitext(base_name)
+        return base_name
+
+    def _run_interface(self, runtime):
+        self.base_name = self.get_base_filename(self.inputs.fn_magn_in)
+
+        mlab_cmd = f"matlab -r \"addpath('{self.inputs.additional_path}'); try; NIFTI_NORDIC_nipype ('{self.inputs.fn_magn_in}', '{self.inputs.fn_phase_in}', '{self.base_name}{self.inputs.fn_out}','{self.inputs.ARG}' ); catch ME; disp(getReport(ME)); end; quit;\""
+        mlab = CommandLine(command=mlab_cmd, terminal_output='stream', resource_monitor=True)
+        result = mlab.run()  
+        return result.runtime
+
+    def _list_outputs(self):
+        outputs = self.output_spec().get()
+        # Save it in directory of Nipype Node
+        cwd = os.getcwd()
+
+        # Check if the output files exist (depending on the arguments) and assign outputs 
+        output = os.path.abspath(f"{cwd}/{self.base_name}{self.inputs.fn_out}.nii")
+        if os.path.exists(output):
+            outputs['output_file'] = output
+
+        info = os.path.abspath(f"{cwd}/{self.base_name}{self.inputs.fn_out}.mat")
+        if os.path.exists(info):
+            outputs['add_info_file'] = info
+
+        complex_phase = os.path.abspath(f"{cwd}/{self.base_name}{self.inputs.fn_out}_phase.nii")
+        if os.path.exists(complex_phase):
+            outputs['complex_phase_file'] = complex_phase
+
+        complex_magn = os.path.abspath(f"{cwd}/{self.base_name}{self.inputs.fn_out}_magn.nii")
+        if os.path.exists(complex_magn):
+            outputs['complex_magn_file'] = complex_magn
+
+        gfactor = os.path.abspath(f"{cwd}/gfactor_{self.base_name}{self.inputs.fn_out}.nii")
+        if os.path.exists(gfactor):
+            outputs['gfactor_map_file'] = gfactor     
+
+        residuals = os.path.abspath(f"{cwd}/RESIDUAL{self.base_name}{self.inputs.fn_out}.mat")
+        if os.path.exists(residuals):
+            outputs['residual_mat_file'] = residuals
+
+        return outputs

NIFTI_NORDIC.m → NIFTI_NORDIC_nipype.m

@@ -1,4 +1,16 @@
-function  NIFTI_NORDIC(fn_magn_in,fn_phase_in,fn_out,ARG)
+function NIFTI_NORDIC_nipype(fn_magn_in,fn_phase_in,fn_out,ARG_path)
+
+% Additional code for integration with the Nipype interface for NIFTI_NORDIC 
+% This customization is tailored to the specific requirements of it and may
+% need adaptations when the Nipype interface is modified
+
+if exist('ARG_path') 
+    arg_struct = load(ARG_path);
+    ARG = arg_struct.ARG;
+    ARG = structfun(@double, ARG, 'uniformoutput', 0); %fields need to be casted to double (from python struct with datatype int64) 
+    disp(ARG)
+end
+
 % fMRI
 %  fn_magn_in='name.nii.gz';
 %  fn_phase_in='name2.nii.gz';