added synthseg options to contianers

reghbali · Sep 9, 2024 · db56fae · db56fae
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diff --git a/README.md b/README.md
@@ -239,6 +239,16 @@ data directory structure (press enter for default) (alfe, bids) [alfe]:
 The directory structure that pyALFE expects in the input directory and will follow when creating the output. See [Inupt directory](#input-directory) for information on ALFE and BIDS.
 This config value can be overwritten when calling `payalfe run` via `-dds` or `--data-dir-structure` option.
 
+#### Tissue Segmentation
+```bash
+tissue segmentation method (press enter for default) (prior, synthseg) [prior]:
+```
+
+The tissue segmentation method that will be used by pyALFE. The default is based on the method described in this [paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8346689/), a UNet
+that receives a template-based **prior** map tissue alongside the image . pyALFE
+also supports [SynthSeg](https://www.sciencedirect.com/science/article/pii/S1361841523000506) via [FreeSurfer](https://surfer.nmr.mgh.harvard.edu/fswiki/SynthSeg). To use SynthSeg, you have to have FreeSurfer >= v7
+installed.
+
 ### Running the pipeline
 To run PyALFE for an accession
 

diff --git a/docs/guides/tutorial.md b/docs/guides/tutorial.md
@@ -1,8 +1,7 @@
 # Tutorial
 
-In this tutorial, you will download sample data, install pyalfe, and run it on this data.
-This tutorial requires `git`, `python>=3.9`, [greedy](https://sourceforge.net/projects/greedy-reg/files/),
-and [c3d](https://sourceforge.net/projects/c3d/).
+In this tutorial, you will download sample data, install pyalfe, configure it, and run it on this data.
+This tutorial requires `git`, `python>=3.9`, [greedy](https://sourceforge.net/projects/greedy-reg/files/).
 
 
 ## Data download and directory setup
@@ -15,7 +14,7 @@ This will create a directory named `pyalfe-test-data` and downloads the tutorial
 data inside it. The data is the MRI scan of a glioblastoma patient and is
 taken from the [UPenn-GBM dataset](https://www.nature.com/articles/s41597-022-01560-7).
 
-2. Create an output directory where you have write access
+2. Create the output directory
 ```bash
 mkdir -p pyalfe-output
 ```
@@ -38,8 +37,46 @@ Download models
 pyalfe download models
 ```
 
+Configure pyalfe by running
+```bash
+pyalfe configrue
+```
+and simply pressing enter for all the prompts for default values.
 
 ## Run
 ```bash
 pyalfe run UPENNGBM0000511 --input-dir pyalfe-test-data  --output-dir pyalfe-output
 ```
+
+## Pipeline output
+You can now inspect the pipeline output by changing directory to
+
+```bash
+cd pyalfe-output/UPENNGBM0000511
+```
+and exploring the `FLAIR`, `T1`, `T1Post`, `T2`, `ADC` subdirectories.
+
+For instance, the individual FLAIR lesion measures can be found at:
+```bash
+FLAIR/quantification/UPENNGBM0000511_SummaryLesionMeasures.csv
+```
+
+FLAIR lesion segmentation can be found at:
+```bash
+FLAIR/abnormalmap/UPENNGBM0000511_FLAIR_abnormal_seg.nii.gz
+```
+
+Summary T1Post (enhancing) lesion measures can be found at:
+```bash
+T1Post/quantification/UPENNGBM0000511_IndividualLesionMeasures.csv
+```
+
+Brain volumetric measures can be found at:
+```bash
+T1/quantification/UPENNGBM0000511_volumeMeasures.csv
+```
+
+The tissue segmentation can be found at:
+```bash
+T1/UPENNGBM0000511_T1_tissue_seg.nii.gz
+```
diff --git a/docs/guides/usage.md b/docs/guides/usage.md
@@ -147,6 +147,14 @@ The directory structure that pyALFE expects in the input directory and will foll
 This config value can be overwritten when calling `payalfe run` via `-dds` or `--data-dir-structure` option.
 
 #### Tissue Segmentation
+```bash
+tissue segmentation method (press enter for default) (prior, synthseg) [prior]:
+```
+
+The tissue segmentation method that will be used by pyALFE. The default is based on the method described in this [paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8346689/), a UNet
+that receives a template-based **prior** map tissue alongside the image . pyALFE
+also supports [SynthSeg](https://www.sciencedirect.com/science/article/pii/S1361841523000506) via [FreeSurfer](https://surfer.nmr.mgh.harvard.edu/fswiki/SynthSeg). To use SynthSeg, you have to have FreeSurfer >= v7
+installed.
 
 ### Running the pipeline
 To run PyALFE for an accession

diff --git a/pyalfe/containers.py b/pyalfe/containers.py
@@ -11,7 +11,7 @@
 )
 from pyalfe.image_processing import Convert3DProcessor, NilearnProcessor
 from pyalfe.image_registration import GreedyRegistration, AntsRegistration
-from pyalfe.inference import NNUnetV2
+from pyalfe.inference import NNUnetV2, SynthSeg
 from pyalfe.models import MODELS_PATH
 from pyalfe.pipeline import PyALFEPipelineRunner, DicomProcessingPipelineRunner
 from pyalfe.tasks.dicom_processing import DicomProcessing
@@ -26,6 +26,7 @@
     TissueWithPriorSegementation,
     SingleModalitySegmentation,
     MultiModalitySegmentation,
+    SynthSegTissueSegmentation,
 )
 from pyalfe.tasks.skullstripping import Skullstripping
 from pyalfe.tasks.t1_postprocessing import T1Postprocessing
@@ -92,6 +93,10 @@ def image_processor(self):
             return Convert3DProcessor()
         elif self.config.options.image_processor == 'nilearn':
             return NilearnProcessor()
+        else:
+            raise ValueError(
+                f'Invalid image processor {self.config.options.image_processor}'
+            )
 
     @property
     def image_registration(self):
@@ -145,16 +150,23 @@ def enhancement_model(self):
 
     @cached_property
     def tissue_model(self):
-        return NNUnetV2(
-            model_dir=str(
-                MODELS_PATH.joinpath(
-                    'nnunetv2',
-                    'Dataset510_Tissue_W_Prior',
-                    'nnUNetTrainer__nnUNetPlans__3d_fullres',
-                )
-            ),
-            folds=(3,),
-        )
+        if self.config.options.tissue_segmentation == 'prior':
+            return NNUnetV2(
+                model_dir=str(
+                    MODELS_PATH.joinpath(
+                        'nnunetv2',
+                        'Dataset510_Tissue_W_Prior',
+                        'nnUNetTrainer__nnUNetPlans__3d_fullres',
+                    )
+                ),
+                folds=(3,),
+            )
+        elif self.config.options.tissue_segmentation == 'synthseg':
+            return SynthSeg()
+        else:
+            raise ValueError(
+                f'Invalid tissue segmentation {self.config.options.tissue_segmentation}'
+            )
 
     @cached_property
     def initialization(self):
@@ -225,15 +237,30 @@ def enhancement_segmentation(self):
 
     @cached_property
     def tissue_segmentation(self):
-        return TissueWithPriorSegementation(
-            inference_model=self.tissue_model,
-            image_processor=self.image_processor,
-            pipeline_dir=self.pipeline_dir,
-            image_type_input='trim_upsampled',
-            image_type_output='tissue_seg',
-            template_name='Tissue',
-            overwrite=self.config.options.overwrite_images,
-        )
+        if self.config.options.tissue_segmentation == 'prior':
+            return TissueWithPriorSegementation(
+                inference_model=self.tissue_model,
+                image_processor=self.image_processor,
+                pipeline_dir=self.pipeline_dir,
+                image_type_input='trim_upsampled',
+                image_type_output='tissue_seg',
+                template_name='Tissue',
+                overwrite=self.config.options.overwrite_images,
+            )
+        elif self.config.options.tissue_segmentation == 'synthseg':
+            return SynthSegTissueSegmentation(
+                inference_model=self.tissue_model,
+                image_processor=self.image_processor,
+                pipeline_dir=self.pipeline_dir,
+                image_type_input='trim_upsampled',
+                image_type_output='tissue_seg',
+                template_name='Tissue',
+                overwrite=self.config.options.overwrite_images,
+            )
+        else:
+            raise ValueError(
+                f'Invalid tissue segmentation {self.config.options.tissue_segmentation}'
+            )
 
     @cached_property
     def t1_postprocessing(self):

diff --git a/pyalfe/main.py b/pyalfe/main.py
@@ -334,10 +334,14 @@ def configure():
     None
     """
     input_dir = click.prompt(
-        'Enter input image directory', type=click.Path(exists=True, resolve_path=True)
+        'Enter input image directory ' '(press enter to skip)',
+        default='',
+        type=click.Path(resolve_path=True),
     )
     output_dir = click.prompt(
-        'Enter output image directory', type=click.Path(exists=True, resolve_path=True)
+        'Enter output image directory' '(press enter to skip)',
+        default='',
+        type=click.Path(resolve_path=True),
     )
     modalities = click.prompt(
         'Enter modalities separated by comma (press enter for default)',