Update.

env.yml

@@ -23,9 +23,6 @@ dependencies:
   # Utilities
   - graphviz=9.0
   - pandoc=3.1
-  # Workflow dependencies: FSL (versions pinned in 6.0.7.7)
-  - fsl-bet2=2111.4
-  - fsl-miscmaths=2203.2
   # Workflow dependencies: ANTs
   - ants=2.5
   # Other dependencies

scripts/fetch_templates.py

@@ -44,10 +44,10 @@ def fetch_MNI6():
     """
     template = 'MNI152NLin6Asym'
 
-    tf.get(template, resolution=(1, 2), desc=None, suffix='T1w')
+    tf.get(template, resolution=(1, 2), desc=[None, 'brain'], suffix='T1w')
     tf.get(template, resolution=(1, 2), desc='brain', suffix='mask')
     # CIFTI
-    tf.get(template, resolution=2, atlas='HCP', suffix='dseg')
+    # tf.get(template, resolution=2, atlas='HCP', suffix='dseg')
     # Transform from MNI152NLin2009cAsym to MNI152NLin6Asym
     tf.get(
         template, mode='image', suffix='xfm', extension='.h5', **{'from': 'MNI152NLin2009cAsym'}

src/fmripost_rapidtide/cli/parser.py

@@ -235,7 +235,7 @@ def _bids_filter(value, parser):
     )
     filt_opts.add_argument(
         '--filterfreqs',
-        dest='passvec',
+        dest='filterfreqs',
         action='store',
         nargs=2,
         type=float,
@@ -249,7 +249,7 @@ def _bids_filter(value, parser):
     )
     filt_opts.add_argument(
         '--filterstopfreqs',
-        dest='stopvec',
+        dest='filterstopfreqs',
         action='store',
         nargs=2,
         type=float,
@@ -266,7 +266,7 @@ def _bids_filter(value, parser):
     sigcalc_opts = g_rapidtide.add_argument_group('Significance calculation options')
     sigcalc_opts.add_argument(
         '--numnull',
-        dest='numestreps',
+        dest='numnull',
         action='store',
         type=int,
         metavar='NREPS',
@@ -288,7 +288,7 @@ def _bids_filter(value, parser):
     )
     preproc.add_argument(
         '--spatialfilt',
-        dest='gausssigma',
+        dest='spatialfilt',
         action='store',
         type=float,
         metavar='GAUSSSIGMA',
@@ -302,7 +302,7 @@ def _bids_filter(value, parser):
     )
     preproc.add_argument(
         '--confoundfile',
-        dest='confoundfilespec',
+        dest='confoundfile',
         metavar='CONFFILE',
         help=(
             'Read additional (non-motion) confound regressors out of CONFFILE file '
@@ -314,15 +314,15 @@ def _bids_filter(value, parser):
     )
     preproc.add_argument(
         '--confoundpowers',
-        dest='confound_power',
+        dest='confoundpowers',
         metavar='N',
         type=int,
         help='Include powers of each confound regressor up to order N.',
         default=1,
     )
     preproc.add_argument(
         '--confoundderiv',
-        dest='confound_deriv',
+        dest='confoundderiv',
         action='store_false',
         help='Toggle whether derivatives will be used in confound regression.',
         default=True,
@@ -433,7 +433,7 @@ def _bids_filter(value, parser):
     fixdelay = corr_fit.add_mutually_exclusive_group()
     fixdelay.add_argument(
         '--fixdelay',
-        dest='fixeddelayvalue',
+        dest='fixdelay',
         action='store',
         type=float,
         metavar='DELAYTIME',
@@ -442,7 +442,7 @@ def _bids_filter(value, parser):
     )
     fixdelay.add_argument(
         '--searchrange',
-        dest='lag_extrema',
+        dest='searchrange',
         action=IndicateSpecifiedAction,
         nargs=2,
         type=float,
@@ -452,7 +452,7 @@ def _bids_filter(value, parser):
     )
     corr_fit.add_argument(
         '--sigmalimit',
-        dest='widthmax',
+        dest='sigmalimit',
         action='store',
         type=float,
         metavar='SIGMALIMIT',
@@ -620,7 +620,7 @@ def _bids_filter(value, parser):
     )
     experimental.add_argument(
         '--autorespdelete',
-        dest='respdelete',
+        dest='autorespdelete',
         action='store_true',
         help='Attempt to detect and remove respiratory signal that strays into the LFO band.',
         default=False,

src/fmripost_rapidtide/config.py

@@ -544,21 +544,21 @@ class workflow(_Config):
     crosscorrelation."""
     filterband = None
     """Filter data and regressors to specific band. Use "None" to disable filtering."""
-    passvec = None
+    filterfreqs = None
     """Filter data and regressors to retain LOWERPASS to UPPERPASS."""
-    stopvec = None
+    filterstopfreqs = None
     """Filter data and regressors to with stop frequencies LOWERSTOP and UPPERSTOP."""
-    numestreps = None
+    numnull = None
     """Estimate significance threshold by running NREPS null correlations."""
     detrendorder = None
     """Set order of trend removal (0 to disable)."""
-    gausssigma = None
+    spatialfilt = None
     """Spatially filter fMRI data prior to analysis using GAUSSSIGMA in mm."""
-    confoundfilespec = None
+    confoundfile = None
     """Read additional (non-motion) confound regressors out of CONFFILE file."""
-    confound_power = None
+    confoundpowers = None
     """Include powers of each confound regressor up to order N."""
-    confound_deriv = None
+    confoundderiv = None
     """Toggle whether derivatives will be used in confound regression."""
     globalsignalmethod = None
     """The method for constructing the initial global signal regressor - straight summation."""
@@ -573,11 +573,11 @@ class workflow(_Config):
     """Method to use for cross-correlation weighting."""
     simcalcrange = None
     """Limit correlation calculation to data between timepoints START and END in the fmri file."""
-    fixeddelayvalue = None
+    fixdelay = None
     """Don't fit the delay time - set it to DELAYTIME seconds for all voxels."""
-    lag_extrema = None
+    searchrange = None
     """Limit fit to a range of lags from LAGMIN to LAGMAX."""
-    widthmax = None
+    sigmalimit = None
     """Reject lag fits with linewidth wider than SIGMALIMIT Hz."""
     bipolar = None
     """Bipolar mode - match peak correlation ignoring sign."""
@@ -605,7 +605,7 @@ class workflow(_Config):
     territorymap = None
     """This specifies a territory map. Each territory is a set of voxels with the same integral
     value."""
-    respdelete = None
+    autorespdelete = None
     """Attempt to detect and remove respiratory signal that strays into the LFO band."""
     err_on_warn = False
     """Cast Rapidtide warnings to errors."""

src/fmripost_rapidtide/data/io_spec.json

@@ -63,17 +63,6 @@
                     ".nii"
                 ]
             },
-            "dseg": {
-                "datatype": "anat",
-                "res": "2",
-                "space": "MNI152NLin6Asym",
-                "desc": null,
-                "suffix": "dseg",
-                "extension": [
-                    ".nii.gz",
-                    ".nii"
-                ]
-            },
             "confounds": {
                 "datatype": "func",
                 "echo": null,
@@ -89,6 +78,33 @@
                 "extension": [
                     ".tsv"
                 ]
+            },
+            "dseg_mni152nlin6asym": {
+                "datatype": "anat",
+                "task": null,
+                "run": null,
+                "res": "2",
+                "space": "MNI152NLin6Asym",
+                "desc": null,
+                "suffix": "dseg",
+                "extension": [
+                    ".nii.gz",
+                    ".nii"
+                ]
+            },
+            "anat_dseg": {
+                "datatype": "anat",
+                "task": null,
+                "run": null,
+                "space": null,
+                "res": null,
+                "den": null,
+                "desc": null,
+                "suffix": "dseg",
+                "extension": [
+                    ".nii.gz",
+                    ".nii"
+                ]
             }
         },
         "transforms": {

src/fmripost_rapidtide/interfaces/nilearn.py

@@ -19,7 +19,7 @@ class _MeanImageInputSpec(BaseInterfaceInputSpec):
     )
     mask_file = File(
         exists=True,
-        mandatory=True,
+        mandatory=False,
         desc='A binary brain mask.',
     )
     out_file = File(
@@ -44,11 +44,19 @@ class MeanImage(NilearnBaseInterface, SimpleInterface):
     output_spec = _MeanImageOutputSpec
 
     def _run_interface(self, runtime):
+        import nibabel as nb
         from nilearn.masking import apply_mask, unmask
+        from nipype.interfaces.base import isdefined
+
+        if isdefined(self.inputs.mask_file):
+            data = apply_mask(self.inputs.bold_file, self.inputs.mask_file)
+            mean_data = data.mean(axis=0)
+            mean_img = unmask(mean_data, self.inputs.mask_file)
+        else:
+            in_img = nb.load(self.inputs.bold_file)
+            mean_data = in_img.get_fdata().mean(axis=3)
+            mean_img = nb.Nifti1Image(mean_data, in_img.affine, in_img.header)
 
-        data = apply_mask(self.inputs.bold_file, self.inputs.mask_file)
-        mean_data = data.mean(axis=0)
-        mean_img = unmask(mean_data, self.inputs.mask_file)
         self._results['out_file'] = os.path.join(runtime.cwd, self.inputs.out_file)
         mean_img.to_filename(self._results['out_file'])
 

src/fmripost_rapidtide/interfaces/rapidtide.py

@@ -15,10 +15,16 @@ class _RapidtideInputSpec(CommandLineInputSpec):
     in_file = File(
         exists=True,
         argstr='%s',
-        position=-1,
+        position=-2,
         mandatory=True,
         desc='File to denoise',
     )
+    outputname = traits.Str(
+        argstr='%s',
+        position=-1,
+        mandatory=True,
+        desc='Output name',
+    )
     # Set by the workflow
     denoising = traits.Bool(
         argstr='--denoising',
@@ -151,7 +157,7 @@ class _RapidtideInputSpec(CommandLineInputSpec):
         mandatory=False,
     )
     timerange = traits.List(
-        traits.Float,
+        traits.Int,
         argstr='--timerange %s',
         mandatory=False,
         minlen=2,
@@ -166,7 +172,7 @@ class _RapidtideInputSpec(CommandLineInputSpec):
         mandatory=False,
     )
     simcalcrange = traits.List(
-        traits.Float,
+        traits.Int,
         argstr='--simcalcrange %s',
         mandatory=False,
         minlen=2,
@@ -177,7 +183,7 @@ class _RapidtideInputSpec(CommandLineInputSpec):
         mandatory=False,
     )
     searchrange = traits.List(
-        traits.Float,
+        traits.Int,
         argstr='--searchrange %s',
         mandatory=False,
         minlen=2,
@@ -264,10 +270,14 @@ class Rapidtide(CommandLine):
     def _list_outputs(self):
         outputs = self._outputs().get()
         out_dir = os.getcwd()
-        outputs['delay_map'] = os.path.join(out_dir, 'desc-maxtime_map.nii.gz')
+        outputname = self.inputs.outputname
+        outputs['delay_map'] = os.path.join(out_dir, f'{outputname}_desc-maxtime_map.nii.gz')
         outputs['regressor_file'] = os.path.join(
             out_dir,
-            'desc-refinedmovingregressor_timeseries.tsv.gz',
+            f'{outputname}_desc-refinedmovingregressor_timeseries.tsv.gz',
+        )
+        outputs['denoised'] = os.path.join(
+            out_dir,
+            f'{outputname}_desc-lfofilterCleaned_bold.nii.gz'
         )
-        outputs['denoised'] = os.path.join(out_dir, 'desc-lfofilterCleaned_bold.nii.gz')
         return outputs

src/fmripost_rapidtide/workflows/base.py

@@ -383,6 +383,7 @@ def init_single_run_wf(bold_file):
     # Run rapidtide
     rapidtide_wf = init_rapidtide_wf(bold_file=bold_file, metadata=bold_metadata, mem_gb=mem_gb)
     rapidtide_wf.inputs.inputnode.confounds = functional_cache['confounds']
+    rapidtide_wf.inputs.inputnode.dseg_std = functional_cache['dseg_mni152nlin6asym']
     rapidtide_wf.inputs.inputnode.skip_vols = skip_vols
 
     mni6_buffer = pe.Node(niu.IdentityInterface(fields=['bold', 'bold_mask']), name='mni6_buffer')
@@ -395,6 +396,8 @@ def init_single_run_wf(bold_file):
         from niworkflows.interfaces.header import ValidateImage
         from templateflow.api import get as get_template
 
+        raise Exception()
+
         workflow.__desc__ += """\
 Raw BOLD series were resampled to MNI152NLin6Asym:res-2, for rapidtide denoising.
 """