Calculate patch radius from number of volumes in DWI run (#892)

* Work on patch radius. * Determine n_volumes and use it. * Fix type. * Convert to integer. * Update boilerplate. * Fix style issue. * Enforce odd integer value. * Update boilerplate. * Remove unused variables. * Capitalize start of sentence. * Apply suggestions from code review Co-authored-by: Matt Cieslak <[email protected]> --------- Co-authored-by: Matt Cieslak <[email protected]>
PennLINC · Dec 2, 2024 · 8bb6c0d · 8bb6c0d
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diff --git a/qsiprep/cli/parser.py b/qsiprep/cli/parser.py
@@ -99,6 +99,23 @@ def _min_one(value, parser):
             raise parser.error("Argument can't be less than one.")
         return value
 
+    def _int_or_auto(value, parser):
+        """Ensure an argument is an integer or 'auto'."""
+        if value.lower() == 'auto':
+            return value
+        try:
+            value = int(value)
+        except ValueError as exc:
+            raise parser.error('Argument must be an integer or "auto".') from exc
+
+        if value < 1:
+            raise parser.error('Argument must be greater than zero.')
+
+        if value % 2 == 0:
+            raise parser.error('Argument must be an odd integer.')
+
+        return value
+
     def _to_gb(value):
         scale = {'G': 1, 'T': 10**3, 'M': 1e-3, 'K': 1e-6, 'B': 1e-9}
         digits = ''.join([c for c in value if c.isdigit()])
@@ -154,6 +171,7 @@ def _bids_filter(value, parser):
     PathExists = partial(_path_exists, parser=parser)
     IsFile = partial(_is_file, parser=parser)
     PositiveInt = partial(_min_one, parser=parser)
+    IntOrAuto = partial(_int_or_auto, parser=parser)
     BIDSFilter = partial(_bids_filter, parser=parser)
 
     # Arguments as specified by BIDS-Apps
@@ -349,18 +367,25 @@ def _bids_filter(value, parser):
     g_conf.add_argument(
         '--dwi-denoise-window',
         action='store',
+        type=IntOrAuto,
         default='auto',
-        help='window size in voxels for image-based denoising, integer or "auto".'
-        'If "auto", 5 will be used for dwidenoise and auto-configured for '
-        'patch2self based on the number of b>0 images.',
+        help=(
+            'Window size in voxels for image-based denoising: odd integer or "auto". '
+            'Any non-"auto" value must be an odd, positive integer. '
+            'If using the "dwidenoise" denoising method, '
+            'the "auto" option will calculate a window size '
+            'based on the number of volumes according to the method described by the '
+            'dwidenoise documentation. '
+            'If using the "patch2self" denoising method, this argument will not be used.'
+        ),
     )
     g_conf.add_argument(
         '--denoise-method',
         action='store',
         choices=['dwidenoise', 'patch2self', 'none'],
         default='dwidenoise',
         help='Image-based denoising method. Either "dwidenoise" (MRtrix), '
-        '"patch2self" (DIPY) or none. (default: dwidenoise)',
+        '"patch2self" (DIPY) or "none". (default: dwidenoise)',
     )
     g_conf.add_argument(
         '--unringing-method',
@@ -692,10 +717,14 @@ def parse_args(args=None, namespace=None):
 
     # Validate the tricky options here
     if config.workflow.dwi_denoise_window != 'auto':
-        try:
-            _ = int(config.workflow.dwi_denoise_window)
-        except ValueError:
-            raise Exception("--dwi-denoise-window must be an integer or 'auto'")
+        if config.workflow.denoise_method == 'patch2self':
+            config.loggers.cli.error(
+                'The --dwi-denoise-window option is not used when --denoise-method=patch2self'
+            )
+        elif config.workflow.denoise_method == 'none':
+            config.loggers.cli.warning(
+                'The --dwi-denoise-window option is not used when --denoise-method=none'
+            )
 
     bids_dir = config.execution.bids_dir
     output_dir = config.execution.output_dir

diff --git a/qsiprep/data/boilerplate.bib b/qsiprep/data/boilerplate.bib
@@ -394,13 +394,15 @@ @article{msmt5tt
 }
 
 @article{mrtrix3,
-  title = {MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation},
-  author = {J-Donald and Smith, Robert and Raffelt, David and Tabbara, Rami and Dhollander, Thijs and Pietsch, Maximilian and Christiaens, Daan and Jeurissen, Ben and Yeh, Chun-Hung and Connelly, Alan"},
-  journal = {NeuroImage},
-  volume = {202},
-  pages = {116137},
-  year = {2019},
-  issn={1053-8119},
+  title={MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation},
+  author={Tournier, J-Donald and Smith, Robert and Raffelt, David and Tabbara, Rami and Dhollander, Thijs and Pietsch, Maximilian and Christiaens, Daan and Jeurissen, Ben and Yeh, Chun-Hung and Connelly, Alan},
+  journal={Neuroimage},
+  volume={202},
+  pages={116137},
+  year={2019},
+  publisher={Elsevier},
+  url={https://doi.org/10.1016/j.neuroimage.2019.116137},
+  doi={10.1016/j.neuroimage.2019.116137}
 }
 
 @article{originalcsd,
@@ -535,7 +537,8 @@ @article{patch2self
   author={Fadnavis, Shreyas and Batson, Joshua and Garyfallidis, Eleftherios},
   journal={Advances in Neural Information Processing Systems},
   volume={33},
-  year={2020}
+  year={2020},
+  url={https://proceedings.neurips.cc/paper_files/paper/2020/file/bc047286b224b7bfa73d4cb02de1238d-Paper.pdf},
 }
 
 @article{noddi,
@@ -640,3 +643,15 @@ @article{power2017simple
   url={https://doi.org/10.1016/j.neuroimage.2016.08.009},
   doi={10.1016/j.neuroimage.2016.08.009}
 }
+
+@article{cordero2019complex,
+  title={Complex diffusion-weighted image estimation via matrix recovery under general noise models},
+  author={Cordero-Grande, Lucilio and Christiaens, Daan and Hutter, Jana and Price, Anthony N and Hajnal, Jo V},
+  journal={Neuroimage},
+  volume={200},
+  pages={391--404},
+  year={2019},
+  publisher={Elsevier},
+  url={https://doi.org/10.1016/j.neuroimage.2019.06.039},
+  doi={10.1016/j.neuroimage.2019.06.039}
+}
diff --git a/qsiprep/workflows/dwi/hmc.py b/qsiprep/workflows/dwi/hmc.py
@@ -635,7 +635,7 @@ def init_dwi_model_hmc_wf(
         name='outputnode',
     )
     workflow.__desc__ = (
-        'The the SHORELine method was used to estimate head motion in b>0 '
+        'The SHORELine method was used to estimate head motion in b>0 '
         'images. This entails leaving out each b>0 image and reconstructing '
         'the others using 3dSHORE [@merlet3dshore]. The signal for the left-'
         f'out image serves as the registration target. A total of {num_iters} '