Add input_spec declarations to dmri processing nodes

dmri/dp_node_dmri.m

@@ -4,6 +4,11 @@
     % and utilities for handling diffusion data, including automatic XPS file handling.
 
     methods
+
+        function obj = dp_node_dmri()
+            obj.input_spec.add('dmri_fn', 'file', 1, 1, 'Diffusion MRI nifti file');
+            obj.input_spec.add('xps_fn', 'file', 0, 1, 'Experimental parameter set file (auto-generated if not provided)');
+        end
 
         function input = po2i(obj, po)
             input = po;

dmri/dp_node_dmri_denoise.m

@@ -8,6 +8,8 @@
         function obj = dp_node_dmri_denoise()
             obj.input_test = {'dmri_fn', 'xps_fn'};
             obj.output_test = {'dmri_fn', 'xps_fn'};
+
+            obj.input_spec.add('dmri_fn', 'file', 1, 1, 'Diffusion MRI nifti file');
         end
 
         function output = i2o(obj, input) %#ok<INUSD>

dmri/dp_node_dmri_disco_synb0.m

@@ -17,6 +17,9 @@
             obj.license_fn = license_fn;
             obj.input_test = {'dmri_fn', 't1_fn'};
             obj.output_test = {'synb0_fn', 'topup_nii_fn'};
+
+            obj.input_spec.add('dmri_fn', 'file', 1, 1, 'Diffusion MRI nifti file');
+            obj.input_spec.add('t1_fn', 'file', 1, 1, 'T1-weighted nifti file');
         end
 
         % construct names of output files

dmri/dp_node_dmri_divide.m

@@ -14,6 +14,9 @@
             obj.suffix = suffix;
 
             if (suffix(1) ~= '_'), warning('probably want _suffix'); end
+
+            obj.input_spec.add('dmri_fn', 'file', 1, 1, 'Diffusion MRI nifti file');
+            obj.input_spec.add('divisor_fn', 'file', 1, 1, 'Divisor volume nifti file');
         end
 
         function output = i2o(obj, input)

dmri/dp_node_dmri_dti.m

@@ -13,6 +13,11 @@
             obj.input_test = {'dmri_fn'};
             obj.output_test = {'md_fn', 'fa_fn', 's0_fn', 'fa_col_fn'};
 
+            obj.input_spec.add('dmri_fn', 'file', 1, 1, 'Diffusion MRI nifti file');
+            obj.input_spec.add('xps_fn', 'file', 1, 1, 'Experimental parameter set file');
+            obj.input_spec.add('mask_fn', 'file', 0, 1, 'Brain mask file (optional)');
+            obj.input_spec.add('opt', 'struct', 0, 0, 'Options structure (optional)');
+
             if (nargin > 0)
                 obj.filter_sigma = filter_sigma;
             end

dmri/dp_node_dmri_flirt.m

@@ -8,6 +8,11 @@
         function obj = dp_node_dmri_flirt()
             obj.input_test = {'nii_fn'};
             obj.output_test = {'nii_fn'};
+
+            obj.input_spec.add('fa_fn', 'file', 1, 1, 'Fractional anisotropy map nifti file');
+            obj.input_spec.add('target_fn', 'file', 0, 1, 'Target registration template file (optional)');
+            obj.input_spec.add('dmri_fn', 'file', 0, 0, 'Diffusion MRI file (optional, passed through)');
+            obj.input_spec.add('mask_fn', 'file', 0, 0, 'Brain mask file (optional, passed through)');
         end
 
         function input = po2i(obj, po)

dmri/dp_node_dmri_flirt_apply.m

@@ -10,6 +10,13 @@
     % - mask_fn (optional)
 
     methods
+
+        function obj = dp_node_dmri_flirt_apply()
+            obj.input_spec.add('dmri_fn', 'file', 1, 1, 'Diffusion MRI nifti file');
+            obj.input_spec.add('matrix_fn', 'file', 1, 1, 'FLIRT transformation matrix file');
+            obj.input_spec.add('xps_fn', 'file', 0, 1, 'Experimental parameter set file (optional)');
+            obj.input_spec.add('mask_fn', 'file', 0, 1, 'Brain mask file (optional)');
+        end
 
         function input = po2i(obj, po)
             input = po;

dmri/dp_node_dmri_md.m

@@ -16,6 +16,12 @@
     end
 
     methods
+
+        function obj = dp_node_md()
+            obj.input_spec.add('nii_fn', 'file', 1, 1, 'Nifti file for MD calculation');
+            obj.input_spec.add('bp', 'path', 1, 1, 'Base path');
+            obj.input_spec.add('mask_fn', 'file', 0, 1, 'Brain mask file (optional)');
+        end
 
         function output = i2o(obj, input)
 

dmri/dp_node_dmri_mec.m

@@ -4,6 +4,11 @@
     % Corrects for subject motion and scanner-related distortions during diffusion acquisition.
 
     methods
+
+        function obj = dp_node_dmri_mec()
+            obj.input_spec.add('dmri_fn', 'file', 1, 1, 'Diffusion MRI nifti file');
+            obj.input_spec.add('elastix_p', 'struct', 0, 0, 'ELASTIX parameters structure (optional)');
+        end
 
         function input = po2i(obj, po)
             input = po;

dmri/dp_node_dmri_mec_eb.m

@@ -5,6 +5,12 @@
     % by extrapolating from low b-value data for improved motion correction performance.
 
     methods
+
+        function obj = dp_node_dmri_mec_eb()
+            obj.input_spec.add('dmri_fn', 'file', 1, 1, 'Diffusion MRI nifti file');
+            obj.input_spec.add('elastix_p', 'struct', 0, 0, 'ELASTIX parameters structure (optional)');
+            obj.input_spec.add('mdm_opt', 'struct', 0, 0, 'MDM options structure (optional)');
+        end
 
         function input = po2i(obj, po)
             input = po2i@dp_node_dmri(obj, po);

dmri/dp_node_dmri_merge.m

@@ -13,6 +13,11 @@
         function obj = dp_node_dmri_merge(fields, output_fn)
             obj.merge_fields = fields;
             obj.output_fn = output_fn;
+
+            % Add input_spec for the dynamic merge fields
+            for i = 1:length(fields)
+                obj.input_spec.add(fields{i}, 'file', 1, 1, sprintf('Input diffusion MRI file %d', i));
+            end
         end
 
         function output = i2o(obj, input)

dmri/dp_node_dmri_normalise_seq.m

@@ -7,6 +7,10 @@
 
         function obj = dp_node_dmri_normalise_seq()
             obj.output_test = {'dmri_fn', 'xps_fn'};
+
+            obj.input_spec.add('dmri_fn', 'file', 1, 1, 'Diffusion MRI nifti file');
+            obj.input_spec.add('xps_fn', 'file', 1, 1, 'Experimental parameter set file');
+            obj.input_spec.add('mask_fn', 'file', 1, 1, 'Brain mask file');
         end
 
         function output = i2o(obj, input)

dmri/dp_node_dmri_powder_average.m

@@ -7,6 +7,10 @@
 
         function obj = dp_node_dmri_powder_average()
             obj.output_test = {'dmri_fn'};
+
+            obj.input_spec.add('dmri_fn', 'file', 1, 1, 'Diffusion MRI nifti file');
+            obj.input_spec.add('xps_fn', 'file', 1, 1, 'Experimental parameter set file');
+            obj.input_spec.add('mask_fn', 'file', 0, 1, 'Brain mask file (optional)');
         end
 
 

dmri/dp_node_dmri_qti.m

@@ -7,6 +7,10 @@
 
         function obj = dp_node_dmri_qti()
             obj.output_test = {'mki_fn', 'mka_fn', 'md_fn'};
+
+            obj.input_spec.add('dmri_fn', 'file', 1, 1, 'Diffusion MRI nifti file');
+            obj.input_spec.add('xps_fn', 'file', 1, 1, 'Experimental parameter set file');
+            obj.input_spec.add('mask_fn', 'file', 0, 1, 'Brain mask file (optional)');
         end
 
 

dmri/dp_node_dmri_qti_pa.m

@@ -7,6 +7,10 @@
 
         function obj = dp_node_dmri_qti_pa()
             obj.output_test = {'mki_fn', 'mka_fn', 'md_fn'};
+
+            obj.input_spec.add('dmri_fn', 'file', 1, 1, 'Diffusion MRI nifti file');
+            obj.input_spec.add('xps_fn', 'file', 1, 1, 'Experimental parameter set file');
+            obj.input_spec.add('mask_fn', 'file', 0, 1, 'Brain mask file (optional)');
         end
 
         function output = i2o(obj, input)

dmri/dp_node_dmri_smooth.m

@@ -12,6 +12,9 @@
         function obj = dp_node_dmri_smooth(filter_sigma)
             if (nargin > 0), obj.filter_sigma = filter_sigma; end
             obj.output_test = {'dmri_fn'};
+
+            obj.input_spec.add('dmri_fn', 'file', 1, 1, 'Diffusion MRI nifti file');
+            obj.input_spec.add('mask_fn', 'file', 0, 1, 'Brain mask file (optional)');
         end
 
         function output = i2o(obj, input)

dmri/dp_node_dmri_subsample.m

@@ -15,6 +15,8 @@
             obj.suffix = suffix;
 
             if (suffix(1) ~= '_'), warning('probably want _suffix'); end
+
+            obj.input_spec.add('dmri_fn', 'file', 1, 1, 'Diffusion MRI nifti file');
         end
 
         function output = i2o(obj, input)

dmri/dp_node_dmri_subsample_b0.m

@@ -13,6 +13,10 @@
     % nii_fn
 
     methods
+
+        function obj = dp_node_dmri_subsample_b0()
+            obj.input_spec.add('dmri_fn', 'file', 1, 1, 'Diffusion MRI nifti file');
+        end
 
         function output = i2o(obj, input)
 

dmri/dp_node_dmri_topup2_apply.m

@@ -5,6 +5,13 @@
 
     methods
 
+        function obj = dp_node_dmri_topup2_apply()
+            obj.input_spec.add('ap_dmri_fn', 'file', 1, 1, 'Anterior-posterior diffusion MRI nifti file');
+            obj.input_spec.add('pa_dmri_fn', 'file', 1, 1, 'Posterior-anterior diffusion MRI nifti file');
+            obj.input_spec.add('topup_data_path', 'path', 1, 1, 'Path to TOPUP data files');
+            obj.input_spec.add('topup_spec_fn', 'file', 1, 1, 'TOPUP specification file');
+        end
+
         % construct names of output files
         function output = i2o(obj, input)
 

dmri/dp_node_dmri_topup2_b0.m

@@ -7,6 +7,11 @@
 
         function obj = dp_node_dmri_topup2_b0()
             obj.output_test = {'fieldmap_fn'};
+
+            obj.input_spec.add('topup_nii_fn', 'file', 1, 1, 'TOPUP input nifti file');
+            obj.input_spec.add('topup_spec_fn', 'file', 1, 1, 'TOPUP specification file');
+            obj.input_spec.add('topup_cnf', 'string', 0, 0, 'TOPUP configuration name (optional)');
+            obj.input_spec.add('topup_opt', 'struct', 0, 0, 'TOPUP options structure (optional)');
         end
 
         % construct names of output files

dmri/dp_node_dmri_topup2_io.m

@@ -13,6 +13,13 @@
                 'ap_json_fn', 'pa_json_fn', ...
                 'ap_xps_fn', 'pa_xps_fn'};
 
+            obj.input_spec.add('ap_dmri_fn', 'file', 1, 1, 'Anterior-posterior diffusion MRI nifti file');
+            obj.input_spec.add('pa_dmri_fn', 'file', 1, 1, 'Posterior-anterior diffusion MRI nifti file');
+            obj.input_spec.add('ap_json_fn', 'file', 1, 1, 'Anterior-posterior JSON parameter file');
+            obj.input_spec.add('pa_json_fn', 'file', 1, 1, 'Posterior-anterior JSON parameter file');
+            obj.input_spec.add('ap_xps_fn', 'file', 1, 1, 'AP experimental parameter set file');
+            obj.input_spec.add('pa_xps_fn', 'file', 1, 1, 'PA experimental parameter set file');
+
             % disable the execution
             obj.get_dpm('execute').do_run_execute = 0;
 

dmri/dp_node_dmri_topup2_prep.m

@@ -4,6 +4,14 @@
     % handling. Formats AP/PA acquisitions for the improved TOPUP processing pipeline.
 
     methods
+
+        function obj = dp_node_dmri_topup2_prep()
+            obj.input_spec.add('ap_dmri_fn', 'file', 1, 1, 'Anterior-posterior diffusion MRI nifti file');
+            obj.input_spec.add('pa_dmri_fn', 'file', 1, 1, 'Posterior-anterior diffusion MRI nifti file');
+            obj.input_spec.add('ap_json_fn', 'file', 1, 1, 'Anterior-posterior JSON parameter file');
+            obj.input_spec.add('pa_json_fn', 'file', 1, 1, 'Posterior-anterior JSON parameter file');
+            obj.input_spec.add('nii', 'struct', 0, 0, 'Nifti structure (optional)');
+        end
 
         function output = i2o(~, input)
 

dmri/dp_node_dmri_topup_apply.m

@@ -12,6 +12,11 @@
     methods
 
         function obj = dp_node_dmri_topup_apply(name, suffix)
+
+            obj.input_spec.add('nii_ap_fn', 'file', 0, 1, 'Anterior-posterior nifti file (optional)');
+            obj.input_spec.add('nii_pa_fn', 'file', 0, 1, 'Posterior-anterior nifti file (optional)');
+            obj.input_spec.add('topup_data_path', 'path', 1, 1, 'Path to TOPUP data files');
+            obj.input_spec.add('topup_spec_fn', 'file', 1, 1, 'TOPUP specification file');
 
             if (nargin > 0)
 

dmri/dp_node_dmri_topup_b0.m

@@ -7,6 +7,11 @@
 
         function obj = dp_node_dmri_topup_b0()
             obj.output_test = {'fieldmap_fn'};
+
+            obj.input_spec.add('topup_nii_fn', 'file', 1, 1, 'TOPUP input nifti file');
+            obj.input_spec.add('topup_spec_fn', 'file', 1, 1, 'TOPUP specification file');
+            obj.input_spec.add('topup_cnf', 'string', 0, 0, 'TOPUP configuration name (optional)');
+            obj.input_spec.add('topup_opt', 'struct', 0, 0, 'TOPUP options structure (optional)');
         end
 
         % construct names of output files

dmri/dp_node_dmri_topup_prep.m

@@ -10,6 +10,12 @@
             obj.input_test = {...
                 'nii_ap_fn', 'nii_pa_fn', ...
                 'xps_ap_fn', 'xps_pa_fn'};
+
+            obj.input_spec.add('nii_ap_fn', 'file', 1, 1, 'Anterior-posterior nifti file');
+            obj.input_spec.add('nii_pa_fn', 'file', 1, 1, 'Posterior-anterior nifti file');
+            obj.input_spec.add('xps_ap_fn', 'file', 0, 1, 'AP experimental parameter set file (auto-generated if not provided)');
+            obj.input_spec.add('xps_pa_fn', 'file', 0, 1, 'PA experimental parameter set file (auto-generated if not provided)');
+            obj.input_spec.add('nii', 'struct', 0, 0, 'Nifti structure (optional)');
 
         end
 

dmri/dp_node_dmri_topup_prep_collect.m

@@ -5,6 +5,10 @@
 
 
     methods
+
+        function obj = dp_node_dmri_topup_prep_collect()
+            obj.input_spec.add('nii', 'struct', 0, 0, 'Nifti structure (optional)');
+        end
 
         function output = i2o(~, input)           
             output.topup_nii_fn = fullfile(input.op, 'topupinput.nii.gz');

dmri/dp_node_dmri_topup_prep_one.m

@@ -32,6 +32,9 @@
             obj.epi_time = time;
 
             obj.input_test = {'nii_fn','xps_fn'};
+
+            obj.input_spec.add('nii_fn', 'file', 1, 1, 'Nifti file');
+            obj.input_spec.add('xps_fn', 'file', 1, 1, 'Experimental parameter set file');
 
         end
 

dmri/dp_node_dmri_xps.m

@@ -7,6 +7,8 @@
 
         function obj = dp_node_dmri_xps()
             obj.output_test = {'dmri_fn', 'xps_fn'};
+
+            obj.input_spec.add('dmri_fn', 'file', 1, 1, 'Diffusion MRI nifti file');
         end
 
         function output = i2o(obj, input)

dmri/dp_node_dmri_xps_force.m

@@ -11,6 +11,9 @@
 
         function obj = dp_node_dmri_xps_force(xps)
             obj.xps = xps;
+
+            % This node forces a specific XPS and doesn't use any input fields
+            % from the data, so no input_spec needed beyond the base path/op
         end
 
         function output = execute(obj, ~, output)

dmri/dp_node_dmri_xps_from_bval_bvec.m

@@ -11,6 +11,9 @@
 
         function obj = dp_node_dmri_xps_from_bval_bvec(b_delta)
             obj.b_delta = b_delta;
+
+            obj.input_spec.add('bval_fn', 'file', 1, 1, 'B-value file');
+            obj.input_spec.add('bvec_fn', 'file', 1, 1, 'B-vector file');
         end
 
         function output = execute(obj, input, output)

dmri/dp_node_dmri_xps_from_gdir.m

@@ -7,6 +7,9 @@
 
         function obj = dp_node_dmri_xps_from_gdir()
             obj.input_test = {'dmri_fn'};
+
+            obj.input_spec.add('dmri_fn', 'file', 1, 1, 'Diffusion MRI nifti file');
+            obj.input_spec.add('gdir_fn', 'file', 0, 1, 'Gradient direction file (auto-detected if not provided)');
         end
 
         function po = po2i(~, po)

dmri/dp_node_dmri_xps_from_json.m

@@ -15,6 +15,8 @@
 
         function obj = dp_node_dmri_xps_from_json()
             obj.output_test = {'xps_fn', 'status_file_fn'};
+
+            obj.input_spec.add('dmri_fn', 'file', 1, 1, 'Diffusion MRI nifti file (with associated JSON file)');
         end
 
         function output = i2o(obj, input)

dmri/dp_node_dmri_xps_make.m

@@ -9,6 +9,11 @@
 
         function obj = dp_node_dmri_xps_make()
             obj.input_test = {'dmri_fn'};
+
+            obj.input_spec.add('dmri_fn', 'file', 1, 1, 'Diffusion MRI nifti file');
+            obj.input_spec.add('bval_fn', 'file', 0, 1, 'B-value file (auto-detected if not provided)');
+            obj.input_spec.add('bvec_fn', 'file', 0, 1, 'B-vector file (auto-detected if not provided)');
+            obj.input_spec.add('id', 'string', 0, 0, 'Subject/session identifier');
         end
 
         function po = po2i(~, po)

dmri/dp_node_make_xps.m

@@ -5,6 +5,12 @@
     % XXX: Will be removed in future releases
 
     methods
+
+        function obj = dp_node_make_xps()
+            obj = obj@dp_node_dmri_xps_make();
+
+            obj.input_spec.add('nii_fn', 'file', 1, 1, 'Nifti file (legacy input)');
+        end
 
         function input = po2i(obj, po)
             input = po;