🔧 Update config to allow choosing mri_robust_template for longitudi…

…nal (new default) [skip ci]
FCP-INDI · Nov 13, 2024 · 9d09358 · 9d09358
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Showing 7 changed files with 123 additions and 43 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -24,12 +24,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Required positional parameter "wf" in input and output of `ingress_pipeconfig_paths` function, where a node to reorient templates is added to the `wf`.
 - Required positional parameter "orientation" to `resolve_resolution`.
 - Optional positional argument "cfg" to `create_lesion_preproc`.
+- Added `mri_robust_template` for longitudinal template generation.
 
 ### Changed
 
 - Moved `pygraphviz` from requirements to `graphviz` optional dependencies group.
 - Automatically tag untagged `subject_id` and `unique_id` as `!!str` when loading data config files.
 - Made orientation configurable (was hard-coded as "RPI").
+- Made `mri_robust_template` default implementation for longitudinal template generation.
 
 ### Fixed
 

diff --git a/CPAC/longitudinal/robust_template.py b/CPAC/longitudinal/robust_template.py
@@ -0,0 +1,18 @@
+# -*- coding: utf-8 -*-
+# Copyright (C) 2024  C-PAC Developers
+
+# This file is part of C-PAC.
+
+# C-PAC is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by the
+# Free Software Foundation, either version 3 of the License, or (at your
+# option) any later version.
+
+# C-PAC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
+# License for more details.
+
+# You should have received a copy of the GNU Lesser General Public
+# License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
+"""Create longitudinal template using ``mri_robust_template``."""
diff --git a/CPAC/longitudinal/wf/anat.py b/CPAC/longitudinal/wf/anat.py
@@ -43,6 +43,8 @@
     name="mask_T1w_longitudinal_template",
     config=["longitudinal_template_generation"],
     switch=["run"],
+    option_key="using",
+    option_val="C-PAC legacy",
     inputs=["desc-brain_T1w"],
     outputs=["space-T1w_desc-brain_mask"],
 )
@@ -97,6 +99,8 @@ def select_session(
     name="mask_longitudinal_T1w_brain",
     config=["longitudinal_template_generation"],
     switch=["run"],
+    option_key="using",
+    option_val="C-PAC legacy",
     inputs=["space-longitudinal_desc-brain_T1w"],
     outputs=["space-longitudinal_desc-brain_mask"],
 )
@@ -122,6 +126,8 @@ def mask_longitudinal_T1w_brain(
     name="warp_longitudinal_T1w_to_template",
     config=["longitudinal_template_generation"],
     switch=["run"],
+    option_key="using",
+    option_val="C-PAC legacy",
     inputs=[
         (
             "space-longitudinal_desc-brain_T1w",
@@ -178,6 +184,8 @@ def warp_longitudinal_T1w_to_template(
     name="warp_longitudinal_seg_to_T1w",
     config=["longitudinal_template_generation"],
     switch=["run"],
+    option_key="using",
+    option_val="C-PAC legacy",
     inputs=[
         (
             "from-longitudinal_to-T1w_mode-image_desc-linear_xfm",
@@ -376,12 +384,14 @@ def anat_longitudinal_wf(
         template_node.inputs.set(
             avg_method=config.longitudinal_template_generation["average_method"],
             dof=config.longitudinal_template_generation["dof"],
-            interp=config.longitudinal_template_generation["interp"],
-            cost=config.longitudinal_template_generation["cost"],
+            interp=config.longitudinal_template_generation["legacy-specific"]["interp"],
+            cost=config.longitudinal_template_generation["legacy-specific"]["cost"],
             convergence_threshold=config.longitudinal_template_generation[
                 "convergence_threshold"
             ],
-            thread_pool=config.longitudinal_template_generation["thread_pool"],
+            thread_pool=config.longitudinal_template_generation["legacy-specific"][
+                "thread_pool"
+            ],
             unique_id_list=list(session_wfs.keys()),
         )
 

diff --git a/CPAC/pipeline/schema.py b/CPAC/pipeline/schema.py
@@ -848,22 +848,32 @@ def sanitize(filename):
         },
         "longitudinal_template_generation": {
             "run": bool1_1,
+            "using": In({"mri_robust_template", "C-PAC legacy"}),
             "average_method": In({"median", "mean", "std"}),
             "dof": In({12, 9, 7, 6}),
-            "interp": In({"trilinear", "nearestneighbour", "sinc", "spline"}),
-            "cost": In(
+            "convergence_threshold": Number,
+            "max_iter": int,
+            "legacy-specific": Maybe(
                 {
-                    "corratio",
-                    "mutualinfo",
-                    "normmi",
-                    "normcorr",
-                    "leastsq",
-                    "labeldiff",
-                    "bbr",
+                    "interp": Maybe(
+                        In({"trilinear", "nearestneighbour", "sinc", "spline"})
+                    ),
+                    "cost": Maybe(
+                        In(
+                            {
+                                "corratio",
+                                "mutualinfo",
+                                "normmi",
+                                "normcorr",
+                                "leastsq",
+                                "labeldiff",
+                                "bbr",
+                            }
+                        )
+                    ),
+                    "thread_pool": Maybe(int),
                 }
             ),
-            "thread_pool": int,
-            "convergence_threshold": Number,
         },
         "functional_preproc": {
             "run": bool1_1,
@@ -1418,6 +1428,17 @@ def schema(config_dict):
                 raise OSError(msg) from error
     except KeyError:
         pass
+    try:
+        # check for incompatible longitudinal options
+        lgt = partially_validated["longitudinal_template_generation"]
+        if lgt["using"] == "mri_robust_template":
+            error_msg = "{value} is not implemented for longitudinal {key} in `mri_robust_template`."
+            for key, value in [("average_method", "std"), ("dof", 9), ("max_iter", -1)]:
+                if lgt[key] == value:
+                    msg = error_msg.format(key=key, value=value)
+                    raise NotImplementedError(msg)
+    except KeyError:
+        pass
     return partially_validated
 
 

diff --git a/CPAC/resources/configs/1.7-1.8-nesting-mappings.yml b/CPAC/resources/configs/1.7-1.8-nesting-mappings.yml
@@ -322,12 +322,15 @@ longitudinal_template_dof:
    - dof
 longitudinal_template_interp:
    - longitudinal_template_generation
+   - legacy-specific
    - interp
 longitudinal_template_cost:
    - longitudinal_template_generation
+   - legacy-specific
    - cost
 longitudinal_template_thread_pool:
    - longitudinal_template_generation
+   - legacy-specific
    - thread_pool
 longitudinal_template_convergence_threshold:
    - longitudinal_template_generation

diff --git a/CPAC/resources/configs/pipeline_config_blank.yml b/CPAC/resources/configs/pipeline_config_blank.yml
@@ -14,7 +14,6 @@ pipeline_setup:
 
   # Desired orientation for the output data. "RPI", "LPI", "RAI", "LAI", "RAS", "LAS", "RPS", "LPS"
   desired_orientation: RPI
-
   output_directory:
 
     # Quality control outputs
@@ -1515,30 +1514,43 @@ longitudinal_template_generation:
   # at once.
   run: Off
 
-  # Freesurfer longitudinal template algorithm using FSL FLIRT
+  # Implementation to use
+  # Options: mri_robust_template, C-PAC legacy
+  using: mri_robust_template
+
   # Method to average the dataset at each iteration of the template creation
-  # Options: median, mean or std
+  # Options: median, mean
+  # Additional option if using "C-PAC legacy": std
   average_method: median
 
   # Degree of freedom for FLIRT in the template creation
-  # Options: 12 (affine), 9 (traditional), 7 (global rescale) or 6 (rigid body)
+  # Options: 12 (affine), 7 (global rescale), or 6 (rigid body)
+  # Additional option if using "C-PAC legacy": 9 (traditional)
   dof: 12
 
-  # Interpolation parameter for FLIRT in the template creation
-  # Options: trilinear, nearestneighbour, sinc or spline
-  interp: trilinear
-
-  # Cost function for FLIRT in the template creation
-  # Options: corratio, mutualinfo, normmi, normcorr, leastsq, labeldiff or bbr
-  cost: corratio
-
-  # Number of threads used for one run of the template generation algorithm
-  thread_pool: 2
-
   # Threshold of transformation distance to consider that the loop converged
   # (-1 means numpy.finfo(np.float64).eps and is the default)
   convergence_threshold: -1
 
+  # Maximum iterations
+  # Stop after this many iterations, even if still above convergence_threshold
+  # Additional option if using "C-PAC legacy": -1 means loop forever until reaching convergence threshold
+  max_iter: 5
+
+  # Options for C-PAC legacy implementation that are not configurable in mri_robust_template
+  legacy-specific:
+
+    # Interpolation parameter for FLIRT in the template creation
+    # Options: trilinear, nearestneighbour, sinc or spline
+    interp:
+
+    # Cost function for FLIRT in the template creation
+    # Options: corratio, mutualinfo, normmi, normcorr, leastsq, labeldiff or bbr
+    cost:
+
+    # Number of threads used for one run of the template generation algorithm
+    thread_pool:
+
 # OUTPUTS AND DERIVATIVES
 # -----------------------
 post_processing:

diff --git a/CPAC/resources/configs/pipeline_config_default.yml b/CPAC/resources/configs/pipeline_config_default.yml
@@ -13,6 +13,8 @@ pipeline_setup:
   # This string will be sanitized and used in filepaths
   pipeline_name: cpac-default-pipeline
 
+  # Desired orientation for the output data. "RPI", "LPI", "RAI", "LAI", "RAS", "LAS", "RPS", "LPS"
+  desired_orientation: RPI
   output_directory:
 
     # Directory where C-PAC should write out processed data, logs, and crash reports.
@@ -248,30 +250,42 @@ longitudinal_template_generation:
   # at once.
   run: Off
 
-  # Freesurfer longitudinal template algorithm using FSL FLIRT
+  # Implementation to use
+  # Options: mri_robust_template, C-PAC legacy
+  using: mri_robust_template
+
   # Method to average the dataset at each iteration of the template creation
-  # Options: median, mean or std
+  # Options: median, mean
+  # Additional option if using "C-PAC legacy": std
   average_method: median
 
   # Degree of freedom for FLIRT in the template creation
-  # Options: 12 (affine), 9 (traditional), 7 (global rescale) or 6 (rigid body)
+  # Options: 12 (affine), 7 (global rescale), or 6 (rigid body)
+  # Additional option if using "C-PAC legacy": 9 (traditional)
   dof: 12
 
-  # Interpolation parameter for FLIRT in the template creation
-  # Options: trilinear, nearestneighbour, sinc or spline
-  interp: trilinear
-
-  # Cost function for FLIRT in the template creation
-  # Options: corratio, mutualinfo, normmi, normcorr, leastsq, labeldiff or bbr
-  cost: corratio
-
-  # Number of threads used for one run of the template generation algorithm
-  thread_pool: 2
-
   # Threshold of transformation distance to consider that the loop converged
   # (-1 means numpy.finfo(np.float64).eps and is the default)
   convergence_threshold: -1
 
+  # Maximum iterations
+  # Stop after this many iterations, even if still above convergence_threshold
+  # Additional option if using "C-PAC legacy": -1 means loop forever until reaching convergence threshold
+  max_iter: 5
+
+  # Options for C-PAC legacy implementation that are not configurable in mri_robust_template
+  legacy-specific:
+
+    # Interpolation parameter for FLIRT in the template creation
+    # Options: trilinear, nearestneighbour, sinc or spline
+    interp: trilinear
+
+    # Cost function for FLIRT in the template creation
+    # Options: corratio, mutualinfo, normmi, normcorr, leastsq, labeldiff or bbr
+    cost: corratio
+
+    # Number of threads used for one run of the template generation algorithm
+    thread_pool: 2
 
 anatomical_preproc: