Keep working.

env.yml

@@ -24,11 +24,11 @@ dependencies:
   - graphviz=9.0
   - pandoc=3.1
   # Workflow dependencies: FSL (versions pinned in 6.0.7.7)
-  # We need SUSAN and MELODIC for Rapidtide
   - fsl-bet2=2111.4
-  - fsl-melodic=2111.3
   - fsl-miscmaths=2203.2
-  - fsl-susan=2111.0
+  # Workflow dependencies: ANTs
+  - ants=2.5
+  # Other dependencies
   - pip
   - pip:
     - templateflow==24.0

src/fmripost_rapidtide/_version.py

@@ -12,5 +12,5 @@
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.1.dev73+g29d61b9'
-__version_tuple__ = version_tuple = (0, 1, 'dev73', 'g29d61b9')
+__version__ = version = '0.1.dev21+g8ddc181.d20240903'
+__version_tuple__ = version_tuple = (0, 1, 'dev21', 'g8ddc181.d20240903')

src/fmripost_rapidtide/cli/__init__.py

@@ -1,13 +0,0 @@
-# SPDX-FileCopyrightText: 2023-present Chris Markiewicz <[email protected]>
-#
-# SPDX-License-Identifier: Apache-2.0
-import click
-
-from .. import __version__
-
-
-@click.group(context_settings={'help_option_names': ['-h', '--help']}, invoke_without_command=True)
-@click.version_option(version=__version__, prog_name='fmripost-rapidtide')
-@click.pass_context
-def fmripost_rapidtide(ctx: click.Context):
-    click.echo('Hello world!')

src/fmripost_rapidtide/config.py

@@ -594,7 +594,7 @@ class workflow(_Config):
     convergencethresh = None
     """Continue refinement until the MSE between regressors becomes <= THRESH."""
     maxpasses = None
-    """Terminate refinement after MAXPASSES passes, whether or not convergence has occured."""
+    """Terminate refinement after MAXPASSES passes, whether or not convergence has occurred."""
     glmsourcefile = None
     """Regress delayed regressors out of FILE instead of the initial fmri file used to estimate
     delays."""

src/fmripost_rapidtide/interfaces/rapidtide.py

@@ -138,8 +138,8 @@ class _RapidtideInputSpec(CommandLineInputSpec):
         argstr='--globalsignalmethod %s',
         mandatory=False,
     )
-    globalpcacomponents = traits.Int(
-        argstr='--globalpcacomponents %d',
+    globalpcacomponents = traits.Float(
+        argstr='--globalpcacomponents %f',
         mandatory=False,
     )
     numskip = traits.Int(
@@ -207,8 +207,8 @@ class _RapidtideInputSpec(CommandLineInputSpec):
         argstr='--sigmathresh %f',
         mandatory=False,
     )
-    pcacomponents = traits.Int(
-        argstr='--pcacomponents %d',
+    pcacomponents = traits.Float(
+        argstr='--pcacomponents %f',
         mandatory=False,
     )
     convergencethresh = traits.Float(

src/fmripost_rapidtide/workflows/rapidtide.py

@@ -34,6 +34,7 @@ def init_rapidtide_wf(
     *,
     bold_file: str,
     metadata: dict,
+    mem_gb: dict,
 ):
     """Build a workflow that runs `Rapidtide`_.
 
@@ -87,6 +88,7 @@ def init_rapidtide_wf(
     confounds_file
     """
 
+    from nipype.interfaces.base import Undefined
     from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 
     from fmripost_rapidtide.interfaces.nilearn import SplitDseg
@@ -146,45 +148,46 @@ def init_rapidtide_wf(
             datatstep=metadata['RepetitionTime'],
             autosync=config.workflow.autosync,
             filterband=config.workflow.filterband,
-            passvec=config.workflow.passvec,
-            stopvec=config.workflow.stopvec,
-            numestreps=config.workflow.numestreps,
+            filterfreqs=config.workflow.passvec or Undefined,
+            filterstopfreqs=config.workflow.stopvec or Undefined,
+            numnull=config.workflow.numestreps,
             detrendorder=config.workflow.detrendorder,
-            gausssigma=config.workflow.gausssigma,
-            confoundfilespec=config.workflow.confoundfilespec,
-            confound_power=config.workflow.confound_power,
-            confound_deriv=config.workflow.confound_deriv,
+            spatialfilt=config.workflow.gausssigma,
+            confoundfile=config.workflow.confoundfilespec or Undefined,
+            confoundpowers=config.workflow.confound_power,
+            confoundderiv=config.workflow.confound_deriv,
             globalsignalmethod=config.workflow.globalsignalmethod,
             globalpcacomponents=config.workflow.globalpcacomponents,
             numtozero=config.workflow.numtozero,
             timerange=config.workflow.timerange,
             corrweighting=config.workflow.corrweighting,
             simcalcrange=config.workflow.simcalcrange,
-            fixeddelayvalue=config.workflow.fixeddelayvalue,
-            lag_extrema=config.workflow.lag_extrema,
-            widthmax=config.workflow.widthmax,
+            fixdelay=config.workflow.fixeddelayvalue or Undefined,
+            searchrange=config.workflow.lag_extrema,
+            sigmalimit=config.workflow.widthmax,
             bipolar=config.workflow.bipolar,
             lagminthresh=config.workflow.lagminthresh,
             lagmaxthresh=config.workflow.lagmaxthresh,
             ampthresh=config.workflow.ampthresh,
             sigmathresh=config.workflow.sigmathresh,
             pcacomponents=config.workflow.pcacomponents,
-            convergencethresh=config.workflow.convergencethresh,
+            convergencethresh=config.workflow.convergencethresh or Undefined,
             maxpasses=config.workflow.maxpasses,
-            glmsourcefile=config.workflow.glmsourcefile,
+            glmsourcefile=config.workflow.glmsourcefile or Undefined,
             glmderivs=config.workflow.glmderivs,
             outputlevel=config.workflow.outputlevel,
-            territorymap=config.workflow.territorymap,
-            respdelete=config.workflow.respdelete,
+            territorymap=config.workflow.territorymap or Undefined,
+            autorespdelete=config.workflow.respdelete,
         ),
         name='rapidtide',
+        mem_gb=mem_gb['resampled'],
     )
     workflow.connect([
         (inputnode, rapidtide, [
             ('bold_std', 'in_file'),
             ('brain_mask_std', 'brainmask'),
-            ('confounds', 'motpars'),
-            ('skip_vols', 'skip_vols'),
+            ('confounds', 'motionfile'),
+            ('skip_vols', 'numskip'),
         ]),
         (split_tissues, rapidtide, [
             ('gm', 'graymattermask'),