diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 6ee756a17c0c7a0d9f1288ba79937d92ee462bc0..c66cfbd3075736f07aebc64c57cceaa01f93474c 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -1,5 +1,10 @@
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.
diff --git a/fsl_mrs/scripts/fsl_mrs_preproc.py b/fsl_mrs/scripts/fsl_mrs_preproc.py
index d1dd2f58b276d0689769b74ecf6c55949cbbf5cb..cdb03a2664a0522a4a705dc3b90f040de2086f09 100755
--- a/fsl_mrs/scripts/fsl_mrs_preproc.py
+++ b/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:
diff --git a/fsl_mrs/scripts/fsl_mrs_preproc_edit.py b/fsl_mrs/scripts/fsl_mrs_preproc_edit.py
index e84a266b79f99095004e624cb3a02ca7629a8aca..8e4ccbd637f32cbb9935eb17a3cd50ecca5f23a1 100644
--- a/fsl_mrs/scripts/fsl_mrs_preproc_edit.py
+++ b/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))
diff --git a/fsl_mrs/tests/test_scripts_preproc.py b/fsl_mrs/tests/test_scripts_preproc.py
index af3b2f1dbfdd87d520889147f5e78d1477e38a5c..a4b0fc708b34eb111dbcfe65f84b19cd2be7b98f 100644
--- a/fsl_mrs/tests/test_scripts_preproc.py
+++ b/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):
diff --git a/fsl_mrs/tests/test_scripts_preproc_edit.py b/fsl_mrs/tests/test_scripts_preproc_edit.py
index 225a9e10f1533ffe2f3851eb9f314ef949d5864a..6ca42fc893bc3683439dcf9d66e6d767c8c76a81 100644
--- a/fsl_mrs/tests/test_scripts_preproc_edit.py
+++ b/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']])
diff --git a/requirements.txt b/requirements.txt
index 4c472d4715ae26240cb56d8ce429259d8f270a17..a68e49cc7caa11c4b62e265b30dbbc20423034ad 100644
--- a/requirements.txt
+++ b/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