Merge branch 'bf/preproc_noalign' into 'master'

BF: preproc(edit) noalign

See merge request !131

CHANGELOG.rst

 This document contains the FSL-MRS release history in reverse chronological order.
 
+2.4.3 (Friday 21st March 2025)
+------------------------------
+- Fixed bug introduced in 2.4.2 where the option to suppress alignment step in `fsl_mrs_preproc{_edit}` only suppressed some alignment.
+- Update minimum hlsvdpropy version to 2.0.2
+
 2.4.2 (Monday 17th March 2025)
 ------------------------------
 - Added a `freeshift_lorentzian` model with inter-metabolite shifts (freeshift) and lorentzian lineshape.

fsl_mrs/scripts/fsl_mrs_preproc.py

@@ -275,13 +275,21 @@ def main():
                 covariance=covariance,
                 no_prewhiten=no_prewhiten)
 
-    verbose_print('... Align Dynamics (1st iteration) ...')
-    supp_data = nifti_mrs_proc.align(
-        supp_data,
-        'DIM_DYN',
-        ppmlim=args.align_limits,
-        window=args.align_window,
-        report=report_dir)
+    if args.align:
+        verbose_print('... Align Dynamics (1st iteration) ...')
+        supp_data = nifti_mrs_proc.align(
+            supp_data,
+            'DIM_DYN',
+            ppmlim=args.align_limits,
+            window=args.align_window,
+            report=report_dir)
+
+        if has_multiple_dynamics(ref_data):
+            ref_data = nifti_mrs_proc.align(ref_data, 'DIM_DYN', ppmlim=(0, 8))
+        if args.quant is not None and has_multiple_dynamics(quant_data):
+            quant_data = nifti_mrs_proc.align(quant_data, 'DIM_DYN', ppmlim=(0, 8))
+        if args.ecc is not None and has_multiple_dynamics(ecc_data):
+            ecc_data = nifti_mrs_proc.align(ecc_data, 'DIM_DYN', ppmlim=(0, 8))
 
     # Bad average removal on the suppressed data
     if args.unlike:
@@ -307,23 +315,15 @@ def main():
         verbose_print(f'{bd_shape}/{supp_shape + bd_shape} '
                       'bad averages identified and removed.')
 
-    # Frequency and phase align the FIDs
-    if args.align:
-        verbose_print('... Align Dynamics (2nd iteration) ...')
-        supp_data = nifti_mrs_proc.align(
-            supp_data,
-            'DIM_DYN',
-            ppmlim=args.align_limits,
-            window=args.align_window,
-            report=report_dir)
-
-        if has_multiple_dynamics(ref_data):
-            ref_data = nifti_mrs_proc.align(ref_data, 'DIM_DYN', ppmlim=(0, 8))
-
-        if args.quant is not None and has_multiple_dynamics(quant_data):
-            quant_data = nifti_mrs_proc.align(quant_data, 'DIM_DYN', ppmlim=(0, 8))
-        if args.ecc is not None and has_multiple_dynamics(ecc_data):
-            ecc_data = nifti_mrs_proc.align(ecc_data, 'DIM_DYN', ppmlim=(0, 8))
+        # After removal repeat frequency and phase align the FIDs
+        if args.align:
+            verbose_print('... Align Dynamics (2nd iteration) ...')
+            supp_data = nifti_mrs_proc.align(
+                supp_data,
+                'DIM_DYN',
+                ppmlim=args.align_limits,
+                window=args.align_window,
+                report=report_dir)
 
     # Average the data (if asked to do so)
     if args.average:

fsl_mrs/scripts/fsl_mrs_preproc_edit.py

@@ -263,17 +263,19 @@ def main():
                 no_prewhiten=no_prewhiten)
 
     # Frequency and phase align the FIDs in the ON/OFF condition
-    verbose_print('... Align Dynamics ...')
-    supp_data = nifti_mrs_proc.align(
-        supp_data,
-        'DIM_DYN',
-        ppmlim=args.align_ppm_dynamic,
-        niter=4,
-        window=args.align_window_dynamic,
-        report=report_dir,
-        report_all=True)
+    if args.align:
+        verbose_print('... Align Dynamics ...')
+        supp_data = nifti_mrs_proc.align(
+            supp_data,
+            'DIM_DYN',
+            ppmlim=args.align_ppm_dynamic,
+            niter=4,
+            window=args.align_window_dynamic,
+            report=report_dir,
+            report_all=True)
 
     if args.dynamic_align and args.align:
+        verbose_print('... Align Dynamics using spectral model ...')
         # Run dynamic fitting based alignment
         edit_0, edit_1 = ntools.split(supp_data, 'DIM_EDIT', 0)
 
@@ -296,7 +298,7 @@ def main():
 
         supp_data = ntools.merge([edit_0_aligned, edit_1_aligned], 'DIM_EDIT')
 
-    elif args.align:
+    if args.align:
         if 'DIM_DYN' in ref_data.dim_tags:
             ref_data = nifti_mrs_proc.align(ref_data, 'DIM_DYN', ppmlim=(0, 8))
 

fsl_mrs/tests/test_scripts_preproc.py

@@ -97,16 +97,14 @@ def test_noalign(tmp_path):
          '--ecc', ecc,
          '--noalign',
          '--overwrite',
-         '--report',
          '--verbose'])
 
     assert retcode == 0
-    assert (tmp_path / 'mergedReports.html').exists()
     assert (tmp_path / 'metab.nii.gz').exists()
-    assert (tmp_path / 'wref.nii.gz').exists()
 
     proc_nii = mrs_io.read_FID(tmp_path / 'metab.nii.gz')
     assert proc_nii.shape == (1, 1, 1, 4096)
+    assert all(['.align' not in step['Details'] for step in proc_nii.hdr_ext['ProcessingApplied']])
 
 
 def test_window_align_preproc(tmp_path):

fsl_mrs/tests/test_scripts_preproc_edit.py

@@ -241,8 +241,7 @@ def test_noalign(tmp_path):
          '--verbose'])
 
     assert retcode == 0
-    assert (tmp_path / 'diff.nii.gz').exists()
     assert (tmp_path / 'edit_0.nii.gz').exists()
-    assert (tmp_path / 'edit_1.nii.gz').exists()
-    assert (tmp_path / 'wref.nii.gz').exists()
-    assert (tmp_path / 'options.txt').exists()
+
+    proc_nii = mrs_io.read_FID(tmp_path / 'edit_0.nii.gz')
+    assert all(['.align, dim=DIM_DYN' not in step['Details'] for step in proc_nii.hdr_ext['ProcessingApplied']])

requirements.txt

@@ -6,7 +6,7 @@ pandas
 jinja2
 beautifulsoup4
 nibabel>=5.3
-hlsvdpropy
+hlsvdpropy>=2.0.2
 fslpy>=3.9.0
 pillow
 spec2nii>=0.8.5