Refactor longitudinal pipeline to live within ReconAll interface.

Author: l-espana

nipype/interfaces/freesurfer/longitudinal.py

@@ -253,211 +253,3 @@ def _list_outputs(self):
         outputs = self.output_spec().get()
         outputs["out_file"] = os.path.abspath(self.inputs.out_file)
         return outputs
-
-
-class BaseReconAllInputSpec(ReconAllInputSpec):
-    base_template_id = traits.Str(
-        argstr="-base %s",
-        desc="base template name",
-        mandatory=True,
-    )
-    base_timepoint_ids = InputMultiObject(
-        traits.Str(),
-        argstr="-base-tp %s...",
-        desc="processed time point to use in template",
-        mandatory=True,
-    )
-
-class BaseReconAllOutputSpec(FreeSurferSource.output_spec):
-    subjects_dir = Directory(exists=True, desc="FreeSurfer subjects directory")
-    subject_id = traits.Str(desc="Subject template name")
-
-class BaseReconAll(CommandLine):
-    """Uses the longitudinal pipeline of recon-all to create a template for a given number of subject's sessions.
-
-    Examples
-    --------
-    >>> from nipype.interfaces.freesurfer.longitudinal import BaseReconAll
-    >>> baserecon = BaseReconAll()
-    >>> baserecon.inputs.base_id = 'sub-template'
-    >>> baserecon.inputs.timepoints = ['ses-1','ses-2']
-    >>> baserecon.inputs.directive = 'all'
-    >>> baserecon.inputs.subjects_dir = '.'
-    >>> baserecon.cmdline
-    'recon-all -all -base sub-template -sd . -tp ses-1 -tp ses-2'
-    """
-
-    _cmd = "recon-all"
-    input_spec = BaseReconAllInputSpec
-    output_spec = BaseReconAllOutputSpec
-    _can_resume = True
-    force_run = False
-
-    def _gen_subjects_dir(self):
-        return os.getcwd()
-
-
-    def _gen_filename(self, name):
-        if name == "subjects_dir":
-            return self._gen_subjects_dir()
-        return None
-
-
-    def _list_outputs(self):
-        if isdefined(self.inputs.subjects_dir):
-            subjects_dir = self.inputs.subjects_dir
-        else:
-            subjects_dir = self._gen_subjects_dir()
-
-        if isdefined(self.inputs.hemi):
-            hemi = self.inputs.hemi
-        else:
-            hemi = "both"
-
-        outputs = self._outputs().get()
-
-        outputs.update(
-            FreeSurferSource(subject_id=self.inputs.base_id,
-                subjects_dir=subjects_dir, hemi=hemi)._list_outputs()
-        )
-        outputs["subject_id"] = self.inputs.base_id
-        outputs["subjects_dir"] = subjects_dir
-        return outputs
-
-
-    def _is_resuming(self):
-        subjects_dir = self.inputs.subjects_dir
-        if not isdefined(subjects_dir):
-            subjects_dir = self._gen_subjects_dir()
-        if os.path.isdir(os.path.join(subjects_dir, self.inputs.base_id, "mri")):
-            return True
-        return False
-
-
-    def _format_arg(self, name, trait_spec, value):
-        return super(BaseReconAll, self)._format_arg(name, trait_spec, value)
-
-
-    @property
-    def cmdline(self):
-        cmd = super(BaseReconAll, self).cmdline
-
-        if not self._is_resuming():
-            return cmd
-
-        subjects_dir = self.inputs.subjects_dir
-        if not isdefined(subjects_dir):
-            subjects_dir = self._gen_subjects_dir()
-
-        directive = self.inputs.directive
-        if not isdefined(directive):
-            steps = []
-
-        iflogger.info(f"recon-all: {cmd}")
-        return cmd
-
-
-class LongReconAllInputSpec(ReconAllInputSpec):
-    longitudinal_timepoint_id = traits.Str(
-        argstr="-long %s",
-        desc="longitudinal session/timepoint id",
-        mandatory=True
-        position=1
-    )
-    longitudinal_template_id = traits.Str(
-        argstr="%s",
-        desc="longitudinal base template id",
-        mandatory=True,
-        position=2
-    )
-
-
-class LongReconAllOutputSpec(FreeSurferSource.output_spec):
-    subjects_dir = Directory(exists=True, desc="FreeSurfer subjects directory")
-    subject_id = traits.Str(desc="Subject template name")
-
-
-class LongReconAll(CommandLine):
-    """Uses FreeSurfer's longitudinal recon-all to process a subject given
-    the previously processed base template.
-
-    Examples
-    ---------
-
-    >>> from nipype.interfaces.freesurfer.longitudinal import LongReconAll
-    >>> longrecon = LongReconAll()
-    >>> longrecon.inputs.long_id = "ses-1"
-    >>> longrecon.inputs.base_id = "sub-template"
-    >>> longrecon.inputs.directive = "all"
-    >>> longrecon.inputs.subjects_dir = "."
-    >>> longrecon.cmdline
-    'recon-all -all -long ses-1 sub-template -sd .'
-    """
-
-    _cmd = "recon-all"
-    input_spec = LongReconAllInputSpec
-    output_spec = LongReconAllOutputSpec
-    _can_resume = True
-    force_run = False
-
-    def _gen_subjects_dir(self):
-        return os.getcwd()
-
-    def _gen_filename(self, name):
-        if name == "subjects_dir":
-            return self._gen_subjects_dir()
-        return None
-
-    def _list_outputs(self):
-        subject_id = f"{self.inputs.long_id}.long.{self.inputs.base_id}"
-
-        if isdefined(self.inputs.subjects_dir):
-            subjects_dir = self.inputs.subjects_dir
-        else:
-            subjects_dir = self._gen_subjects_dir()
-
-        if isdefined(self.inputs.hemi):
-            hemi = self.inputs.hemi
-        else:
-            hemi = "both"
-
-        outputs = self._outputs().get()
-
-        outputs.update(
-            FreeSurferSource(
-                subject_id=subject_id, subjects_dir=subjects_dir, hemi=hemi
-            )._list_outputs()
-        )
-        outputs["subject_id"] = subject_id
-        outputs["subjects_dir"] = subjects_dir
-        return outputs
-
-    def _is_resuming(self):
-        subjects_dir = self.inputs.subjects_dir
-        subject_id = f"{self.inputs.long_id}.long.{self.inputs.base_id}"
-        if not isdefined(subjects_dir):
-            subjects_dir = self._gen_subjects_dir()
-        if os.path.isdir(os.path.join(subjects_dir, subject_id, "mri")):
-            return True
-        return False
-
-    def _format_arg(self, name, trait_spec, value):
-        return super(LongReconAll, self)._format_arg(name, trait_spec, value)
-
-    @property
-    def cmdline(self):
-        cmd = super(LongReconAll, self).cmdline
-
-        if not self._is_resuming():
-            return cmd
-
-        subjects_dir = self.inputs.subjects_dir
-        if not isdefined(subjects_dir):
-            subjects_dir = self._gen_subjects_dir()
-
-        directive = self.inputs.directive
-        if not isdefined(directive):
-            steps = []
-
-        iflogger.info(f"recon-all: {cmd}")
-        return cmd

nipype/interfaces/freesurfer/preprocess.py

@@ -25,6 +25,7 @@
     CommandLine,
     CommandLineInputSpec,
     isdefined,
+    InputMultiObject,
 )
 from .base import FSCommand, FSTraitedSpec, FSTraitedSpecOpenMP, FSCommandOpenMP, Info
 from .utils import copy2subjdir
@@ -816,7 +817,7 @@ def _gen_filename(self, name):
 
 class ReconAllInputSpec(CommandLineInputSpec):
     subject_id = traits.Str(
-        "recon_all", argstr="-subjid %s", desc="subject name", usedefault=True
+        "recon_all", argstr="-subjid %s", desc="subject name",
     )
     directive = traits.Enum(
         "all",
@@ -927,6 +928,31 @@ class ReconAllInputSpec(CommandLineInputSpec):
     )
     flags = InputMultiPath(traits.Str, argstr="%s", desc="additional parameters")
 
+    # Longitudinal runs
+    base_template_id = traits.Str(
+        argstr="-base %s",
+        desc="base template id",
+        xor=["subject_id","longitudinal_timepoint_id"],
+        requires=["base_timepoint_ids"],
+    )
+    base_timepoint_ids = InputMultiObject(
+        traits.Str(),
+        argstr="-base-tp %s...",
+        desc="processed timepoint to use in template",
+    )
+    longitudinal_timepoint_id = traits.Str(
+        argstr="-long %s",
+        desc="longitudinal session/timepoint id",
+        xor=["subject_id","base_template_id"],
+        requires=["longitudinal_template_id"],
+        position=1
+    )
+    longitudinal_template_id = traits.Str(
+        argstr="%s",
+        desc="longitudinal base tempalte id",
+        position=2
+    )
+
     # Expert options
     talairach = traits.Str(desc="Flags to pass to talairach commands", xor=["expert"])
     mri_normalize = traits.Str(
@@ -1019,7 +1045,7 @@ class ReconAll(CommandLine):
     >>> reconall.inputs.subject_id = 'foo'
     >>> reconall.inputs.directive = 'all'
     >>> reconall.inputs.subjects_dir = '.'
-    >>> reconall.inputs.T1_files = 'structural.nii'
+    >>> reconall.inputs.T1_files = ['structural.nii']
     >>> reconall.cmdline
     'recon-all -all -i structural.nii -subjid foo -sd .'
     >>> reconall.inputs.flags = "-qcache"
@@ -1049,7 +1075,7 @@ class ReconAll(CommandLine):
     >>> reconall_subfields.inputs.subject_id = 'foo'
     >>> reconall_subfields.inputs.directive = 'all'
     >>> reconall_subfields.inputs.subjects_dir = '.'
-    >>> reconall_subfields.inputs.T1_files = 'structural.nii'
+    >>> reconall_subfields.inputs.T1_files = ['structural.nii']
     >>> reconall_subfields.inputs.hippocampal_subfields_T1 = True
     >>> reconall_subfields.cmdline
     'recon-all -all -i structural.nii -hippocampal-subfields-T1 -subjid foo -sd .'
@@ -1060,6 +1086,24 @@ class ReconAll(CommandLine):
     >>> reconall_subfields.inputs.hippocampal_subfields_T1 = False
     >>> reconall_subfields.cmdline
     'recon-all -all -i structural.nii -hippocampal-subfields-T2 structural.nii test -subjid foo -sd .'
+
+    Base template creation for longitudinal pipeline:
+    >>> baserecon = ReconAll()
+    >>> baserecon.inputs.base_template_id = 'sub-template'
+    >>> baserecon.inputs.base_timepoint_ids = ['ses-1','ses-2']
+    >>> baserecon.inputs.directive = 'all'
+    >>> baserecon.inputs.subjects_dir = '.'
+    >>> baserecon.cmdline
+    'recon-all -all -base sub-template -base-tp ses-1 -base-tp ses-2 -sd .'
+
+    Longitudinal timepoint run:
+    >>> longrecon = ReconAll()
+    >>> longrecon.inputs.longitudinal_timepoint_id = 'ses-1'
+    >>> longrecon.inputs.longitudinal_template_id = 'sub-template'
+    >>> longrecon.inputs.directive = 'all'
+    >>> longrecon.inputs.subjects_dir = '.'
+    >>> longrecon.cmdline
+    'recon-all -all -long ses-1 sub-template -sd .'
     """
 
     _cmd = "recon-all"
@@ -1523,21 +1567,53 @@ def _list_outputs(self):
 
         outputs = self._outputs().get()
 
-        outputs.update(
-            FreeSurferSource(
-                subject_id=self.inputs.subject_id, subjects_dir=subjects_dir, hemi=hemi
-            )._list_outputs()
-        )
-        outputs["subject_id"] = self.inputs.subject_id
+        # If using longitudinal pipeline, update subject id accordingly,
+        # otherwise use original/default subject_id
+        if isdefined(self.inputs.base_template_id):
+            outputs.update(
+                FreeSurferSource(
+                    subject_id=self.inputs.base_template_id, subjects_dir=subjects_dir,
+                    hemi=hemi
+                )._list_outputs()
+            )
+            outputs["subject_id"] = self.inputs.base_template_id
+        elif isdefined(self.inputs.longitudinal_timepoint_id):
+            subject_id=f"{self.inputs.longitudinal_timepoint_id}.long.{self.inputs.longitudinal_template_id}"
+            outputs.update(
+                FreeSurferSource(
+                    subject_id=subject_id, subjects_id=subjects_dir, hemi=hemi
+                )._list_outputs()
+            )
+            outputs["subject_id"] = subject_id
+        else:
+            outputs.update(
+                FreeSurferSource(
+                    subject_id=self.inputs.subject_id, subjects_dir=subjects_dir, hemi=hemi
+                )._list_outputs()
+            )
+            outputs["subject_id"] = self.inputs.subject_id
+
         outputs["subjects_dir"] = subjects_dir
         return outputs
 
     def _is_resuming(self):
         subjects_dir = self.inputs.subjects_dir
         if not isdefined(subjects_dir):
             subjects_dir = self._gen_subjects_dir()
-        if os.path.isdir(os.path.join(subjects_dir, self.inputs.subject_id, "mri")):
-            return True
+
+        # Check for longitudinal pipeline
+        if not isdefined(self.inputs.subject_id):
+            if isdefined(self.inputs.base_template_id):
+                if os.path.isdir(os.path.join(subjects_dir, self.inputs.base_template_id, "mri")):
+                    return True
+            elif isdefined(self.inputs.longitudinal_template_id):
+                if os.path.isdir(os.path.join(subjects_dir,
+                    f"{self.inputs.longitudinal_timepoint_id}.long.{self.inputs.longitudinal_template_id}",
+                    "mri")):
+                    return True
+        else:
+            if os.path.isdir(os.path.join(subjects_dir, self.inputs.subject_id, "mri")):
+                return True
         return False
 
     def _format_arg(self, name, trait_spec, value):