Add nuisance parameter outputs to fsl_mrsi.

CHANGELOG.rst

@@ -3,6 +3,7 @@ This document contains the FSL-MRS release history in reverse chronological orde
 1.1.4 (WIP)
 ------------------------------
 - Fixed bug in mrs_tools split
+- fsl_mrsi now outputs fitting nuisance parameters: phases, and shifts & linewidths for each metabolite group.
 
 1.1.3 (Tuesday 29th June 2021)
 ------------------------------

fsl_mrs/scripts/fsl_mrsi

@@ -315,11 +315,13 @@ def main():
     # Generate the folders
     concs_folder = os.path.join(args.output, 'concs')
     uncer_folder = os.path.join(args.output, 'uncertainties')
+    nuisance_folder = os.path.join(args.output, 'nuisance')
     qc_folder = os.path.join(args.output, 'qc')
     fit_folder = os.path.join(args.output, 'fit')
 
     os.mkdir(concs_folder)
     os.mkdir(uncer_folder)
+    os.mkdir(nuisance_folder)
     os.mkdir(qc_folder)
     os.mkdir(fit_folder)
 
@@ -367,6 +369,65 @@ def main():
                             cleanup=True,
                             dtype=float))
 
+    # Fitting nuisance parameters
+    # Phases - p0, p1
+    p0_list = [res[0].getPhaseParams()[0] for res in results]
+    file_p0 = os.path.join(nuisance_folder, 'p0.nii.gz')
+    save_img_output(file_p0,
+                    mrsi.list_to_matched_array(
+                        p0_list,
+                        indicies=indicies,
+                        cleanup=True,
+                        dtype=float))
+
+    p1_list = [res[0].getPhaseParams()[1] for res in results]
+    file_p1 = os.path.join(nuisance_folder, 'p1.nii.gz')
+    save_img_output(file_p1,
+                    mrsi.list_to_matched_array(
+                        p1_list,
+                        indicies=indicies,
+                        cleanup=True,
+                        dtype=float))
+
+    # Grouped - shifts, widths (gamma, sigma, combined)
+    for group in range(results[0][0].g):
+        shiftn_list = [res[0].getShiftParams()[group] for res in results]
+        file_sn = os.path.join(nuisance_folder, f'shift_group{group}.nii.gz')
+        save_img_output(file_sn,
+                        mrsi.list_to_matched_array(
+                            shiftn_list,
+                            indicies=indicies,
+                            cleanup=True,
+                            dtype=float))
+
+        comb_n_list = [res[0].getLineShapeParams()[0][group] for res in results]
+        file_comb = os.path.join(nuisance_folder, f'combined_lw_group{group}.nii.gz')
+        save_img_output(file_comb,
+                        mrsi.list_to_matched_array(
+                            comb_n_list,
+                            indicies=indicies,
+                            cleanup=True,
+                            dtype=float))
+
+        gamma_n_list = [res[0].getLineShapeParams()[1][group] for res in results]
+        file_gam = os.path.join(nuisance_folder, f'gamma_group{group}.nii.gz')
+        save_img_output(file_gam,
+                        mrsi.list_to_matched_array(
+                            gamma_n_list,
+                            indicies=indicies,
+                            cleanup=True,
+                            dtype=float))
+
+        if results[0][0].model == 'voigt':
+            sigma_n_list = [res[0].getLineShapeParams()[2][group] for res in results]
+            file_sig = os.path.join(nuisance_folder, f'sigma_group{group}.nii.gz')
+            save_img_output(file_sig,
+                            mrsi.list_to_matched_array(
+                                sigma_n_list,
+                                indicies=indicies,
+                                cleanup=True,
+                                dtype=float))
+
     # qc - SNR & FWHM
     for metab in results[0][0].original_metabs:
         metab_fwhm_list = [res[0].getQCParams(metab=metab)[1]

fsl_mrs/tests/test_scripts_fsl_mrsi.py

@@ -41,9 +41,17 @@ def test_fsl_mrsi(tmp_path):
     assert (tmp_path / 'fit_out/qc').exists()
     assert (tmp_path / 'fit_out/uncertainties').exists()
     assert (tmp_path / 'fit_out/concs').exists()
+    assert (tmp_path / 'fit_out/nuisance').exists()
 
     assert (tmp_path / 'fit_out/concs/raw/NAA.nii.gz').exists()
     assert (tmp_path / 'fit_out/concs/molality/NAA.nii.gz').exists()
     assert (tmp_path / 'fit_out/uncertainties/NAA_sd.nii.gz').exists()
     assert (tmp_path / 'fit_out/qc/NAA_snr.nii.gz').exists()
     assert (tmp_path / 'fit_out/fit/fit.nii.gz').exists()
+
+    assert (tmp_path / 'fit_out/nuisance/p0.nii.gz').exists()
+    assert (tmp_path / 'fit_out/nuisance/p1.nii.gz').exists()
+    assert (tmp_path / 'fit_out/nuisance/shift_group0.nii.gz').exists()
+    assert (tmp_path / 'fit_out/nuisance/combined_lw_group0.nii.gz').exists()
+    assert (tmp_path / 'fit_out/nuisance/gamma_group0.nii.gz').exists()
+    assert (tmp_path / 'fit_out/nuisance/sigma_group0.nii.gz').exists()