From 1aded9dd7b8a871fc59f6194909fb2413388aa1b Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 11 Sep 2025 10:56:05 +0000
Subject: [PATCH 1/3] Initial plan


From d0ced191c5be8ee3f31294c2be6897ab5951cc49 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 11 Sep 2025 11:02:40 +0000
Subject: [PATCH 2/3] Add input_spec declarations to first batch of dmri files

Co-authored-by: markus-nilsson <17831339+markus-nilsson@users.noreply.github.com>
---
 dmri/dp_node_dmri_denoise.m            | 2 ++
 dmri/dp_node_dmri_disco_synb0.m        | 3 +++
 dmri/dp_node_dmri_divide.m             | 3 +++
 dmri/dp_node_dmri_dti.m                | 5 +++++
 dmri/dp_node_dmri_flirt.m              | 5 +++++
 dmri/dp_node_dmri_flirt_apply.m        | 7 +++++++
 dmri/dp_node_dmri_mec.m                | 5 +++++
 dmri/dp_node_dmri_qti.m                | 4 ++++
 dmri/dp_node_dmri_smooth.m             | 3 +++
 dmri/dp_node_dmri_subsample.m          | 2 ++
 dmri/dp_node_dmri_topup2_apply.m       | 7 +++++++
 dmri/dp_node_dmri_topup2_b0.m          | 5 +++++
 dmri/dp_node_dmri_xps_from_bval_bvec.m | 3 +++
 13 files changed, 54 insertions(+)

diff --git a/dmri/dp_node_dmri_denoise.m b/dmri/dp_node_dmri_denoise.m
index f7232d8..e28d0df 100755
--- a/dmri/dp_node_dmri_denoise.m
+++ b/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>
diff --git a/dmri/dp_node_dmri_disco_synb0.m b/dmri/dp_node_dmri_disco_synb0.m
index cb4687b..b1cbf79 100755
--- a/dmri/dp_node_dmri_disco_synb0.m
+++ b/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
diff --git a/dmri/dp_node_dmri_divide.m b/dmri/dp_node_dmri_divide.m
index 9b2dbcc..8ba6dbe 100644
--- a/dmri/dp_node_dmri_divide.m
+++ b/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)
diff --git a/dmri/dp_node_dmri_dti.m b/dmri/dp_node_dmri_dti.m
index 5d66866..5c6afa7 100755
--- a/dmri/dp_node_dmri_dti.m
+++ b/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
diff --git a/dmri/dp_node_dmri_flirt.m b/dmri/dp_node_dmri_flirt.m
index cff2edb..bc172a9 100755
--- a/dmri/dp_node_dmri_flirt.m
+++ b/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)
diff --git a/dmri/dp_node_dmri_flirt_apply.m b/dmri/dp_node_dmri_flirt_apply.m
index cd0e71b..f682508 100755
--- a/dmri/dp_node_dmri_flirt_apply.m
+++ b/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;
diff --git a/dmri/dp_node_dmri_mec.m b/dmri/dp_node_dmri_mec.m
index 18609af..69e8c94 100755
--- a/dmri/dp_node_dmri_mec.m
+++ b/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;
diff --git a/dmri/dp_node_dmri_qti.m b/dmri/dp_node_dmri_qti.m
index 3a50130..8bb7ff6 100755
--- a/dmri/dp_node_dmri_qti.m
+++ b/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
 
 
diff --git a/dmri/dp_node_dmri_smooth.m b/dmri/dp_node_dmri_smooth.m
index c943a6b..cff3efb 100755
--- a/dmri/dp_node_dmri_smooth.m
+++ b/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)
diff --git a/dmri/dp_node_dmri_subsample.m b/dmri/dp_node_dmri_subsample.m
index 9a9cb7b..4a5c53e 100755
--- a/dmri/dp_node_dmri_subsample.m
+++ b/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)
diff --git a/dmri/dp_node_dmri_topup2_apply.m b/dmri/dp_node_dmri_topup2_apply.m
index 210a21b..e110a5b 100644
--- a/dmri/dp_node_dmri_topup2_apply.m
+++ b/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)
 
diff --git a/dmri/dp_node_dmri_topup2_b0.m b/dmri/dp_node_dmri_topup2_b0.m
index 1025a6c..31cce34 100644
--- a/dmri/dp_node_dmri_topup2_b0.m
+++ b/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
diff --git a/dmri/dp_node_dmri_xps_from_bval_bvec.m b/dmri/dp_node_dmri_xps_from_bval_bvec.m
index 91930a0..0321294 100644
--- a/dmri/dp_node_dmri_xps_from_bval_bvec.m
+++ b/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)

From 4e50953c4e1acc3b4ee1be2f9250a13ab4fab3b8 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 11 Sep 2025 11:09:26 +0000
Subject: [PATCH 3/3] Complete input_spec implementation for all applicable
 dmri files

Co-authored-by: markus-nilsson <17831339+markus-nilsson@users.noreply.github.com>
---
 dmri/dp_node_dmri.m                    | 5 +++++
 dmri/dp_node_dmri_md.m                 | 6 ++++++
 dmri/dp_node_dmri_mec_eb.m             | 6 ++++++
 dmri/dp_node_dmri_merge.m              | 5 +++++
 dmri/dp_node_dmri_normalise_seq.m      | 4 ++++
 dmri/dp_node_dmri_powder_average.m     | 4 ++++
 dmri/dp_node_dmri_qti_pa.m             | 4 ++++
 dmri/dp_node_dmri_subsample_b0.m       | 4 ++++
 dmri/dp_node_dmri_topup2_io.m          | 7 +++++++
 dmri/dp_node_dmri_topup2_prep.m        | 8 ++++++++
 dmri/dp_node_dmri_topup_apply.m        | 5 +++++
 dmri/dp_node_dmri_topup_b0.m           | 5 +++++
 dmri/dp_node_dmri_topup_prep.m         | 6 ++++++
 dmri/dp_node_dmri_topup_prep_collect.m | 4 ++++
 dmri/dp_node_dmri_topup_prep_one.m     | 3 +++
 dmri/dp_node_dmri_xps.m                | 2 ++
 dmri/dp_node_dmri_xps_force.m          | 3 +++
 dmri/dp_node_dmri_xps_from_gdir.m      | 3 +++
 dmri/dp_node_dmri_xps_from_json.m      | 2 ++
 dmri/dp_node_dmri_xps_make.m           | 5 +++++
 dmri/dp_node_make_xps.m                | 6 ++++++
 21 files changed, 97 insertions(+)

diff --git a/dmri/dp_node_dmri.m b/dmri/dp_node_dmri.m
index 8c2eea8..473dbef 100755
--- a/dmri/dp_node_dmri.m
+++ b/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;
diff --git a/dmri/dp_node_dmri_md.m b/dmri/dp_node_dmri_md.m
index 41f0d3a..0927416 100755
--- a/dmri/dp_node_dmri_md.m
+++ b/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)
 
diff --git a/dmri/dp_node_dmri_mec_eb.m b/dmri/dp_node_dmri_mec_eb.m
index 7575bc1..a488b10 100755
--- a/dmri/dp_node_dmri_mec_eb.m
+++ b/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);
diff --git a/dmri/dp_node_dmri_merge.m b/dmri/dp_node_dmri_merge.m
index 06a800c..db0df1c 100755
--- a/dmri/dp_node_dmri_merge.m
+++ b/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)
diff --git a/dmri/dp_node_dmri_normalise_seq.m b/dmri/dp_node_dmri_normalise_seq.m
index 248d2a3..5d67bd8 100644
--- a/dmri/dp_node_dmri_normalise_seq.m
+++ b/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)
diff --git a/dmri/dp_node_dmri_powder_average.m b/dmri/dp_node_dmri_powder_average.m
index 1af3d9a..b221777 100755
--- a/dmri/dp_node_dmri_powder_average.m
+++ b/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
 
 
diff --git a/dmri/dp_node_dmri_qti_pa.m b/dmri/dp_node_dmri_qti_pa.m
index dd2b674..a4e843d 100755
--- a/dmri/dp_node_dmri_qti_pa.m
+++ b/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)
diff --git a/dmri/dp_node_dmri_subsample_b0.m b/dmri/dp_node_dmri_subsample_b0.m
index fa0fc25..6a728d5 100755
--- a/dmri/dp_node_dmri_subsample_b0.m
+++ b/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)
 
diff --git a/dmri/dp_node_dmri_topup2_io.m b/dmri/dp_node_dmri_topup2_io.m
index 77163d1..491785f 100644
--- a/dmri/dp_node_dmri_topup2_io.m
+++ b/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;
 
diff --git a/dmri/dp_node_dmri_topup2_prep.m b/dmri/dp_node_dmri_topup2_prep.m
index faac3ba..21ca1e0 100644
--- a/dmri/dp_node_dmri_topup2_prep.m
+++ b/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)
 
diff --git a/dmri/dp_node_dmri_topup_apply.m b/dmri/dp_node_dmri_topup_apply.m
index 55d0722..32eeb91 100755
--- a/dmri/dp_node_dmri_topup_apply.m
+++ b/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)
 
diff --git a/dmri/dp_node_dmri_topup_b0.m b/dmri/dp_node_dmri_topup_b0.m
index 2b54f2e..254c8fb 100755
--- a/dmri/dp_node_dmri_topup_b0.m
+++ b/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
diff --git a/dmri/dp_node_dmri_topup_prep.m b/dmri/dp_node_dmri_topup_prep.m
index f9fadfe..4bee6fb 100755
--- a/dmri/dp_node_dmri_topup_prep.m
+++ b/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
 
diff --git a/dmri/dp_node_dmri_topup_prep_collect.m b/dmri/dp_node_dmri_topup_prep_collect.m
index d1cefad..dde5fda 100644
--- a/dmri/dp_node_dmri_topup_prep_collect.m
+++ b/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');
diff --git a/dmri/dp_node_dmri_topup_prep_one.m b/dmri/dp_node_dmri_topup_prep_one.m
index d3cbddf..b9fd83a 100644
--- a/dmri/dp_node_dmri_topup_prep_one.m
+++ b/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
 
diff --git a/dmri/dp_node_dmri_xps.m b/dmri/dp_node_dmri_xps.m
index c856c5f..c24be6b 100755
--- a/dmri/dp_node_dmri_xps.m
+++ b/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)
diff --git a/dmri/dp_node_dmri_xps_force.m b/dmri/dp_node_dmri_xps_force.m
index aa6103b..02c64ac 100755
--- a/dmri/dp_node_dmri_xps_force.m
+++ b/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)
diff --git a/dmri/dp_node_dmri_xps_from_gdir.m b/dmri/dp_node_dmri_xps_from_gdir.m
index dd08b47..d0be9f7 100644
--- a/dmri/dp_node_dmri_xps_from_gdir.m
+++ b/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)
diff --git a/dmri/dp_node_dmri_xps_from_json.m b/dmri/dp_node_dmri_xps_from_json.m
index cf31ccd..5245e15 100755
--- a/dmri/dp_node_dmri_xps_from_json.m
+++ b/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)
diff --git a/dmri/dp_node_dmri_xps_make.m b/dmri/dp_node_dmri_xps_make.m
index c5bc771..88030dd 100755
--- a/dmri/dp_node_dmri_xps_make.m
+++ b/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)
diff --git a/dmri/dp_node_make_xps.m b/dmri/dp_node_make_xps.m
index ac9d172..d672ff9 100755
--- a/dmri/dp_node_make_xps.m
+++ b/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;