RF: Move most PET GLM logic to GLMFit

Author: effigies

nipype/interfaces/freesurfer/model.py

@@ -404,17 +404,17 @@ class GLMFitInputSpec(FSTraitedSpec):
     mrtm1 = InputMultiPath(
         traits.Tuple(File(exists=True), File(exists=True)),
         argstr="--mrtm1 %s %s...",
-        desc="Reference time activity curve and frame times",
+        desc="RefTac TimeSec : perform MRTM1 kinetic modeling",
     )
     mrtm2 = InputMultiPath(
         traits.Tuple(File(exists=True), File(exists=True), traits.Float),
         argstr="--mrtm2 %s %s %f...",
-        desc="Reference time activity curve, frame times and k2p",
+        desc="RefTac TimeSec k2prime : perform MRTM2 kinetic modeling",
     )
     logan = InputMultiPath(
         traits.Tuple(File(exists=True), File(exists=True), traits.Float),
         argstr="--logan %s %s %f...",
-        desc="Reference time activity curve, frame times and tstar",
+        desc="RefTac TimeSec tstar   : perform Logan kinetic modeling",
     )
     force_perm = traits.Bool(
         argstr="--perm-force",
@@ -438,10 +438,9 @@ class GLMFitInputSpec(FSTraitedSpec):
     sim_done_file = File(
         argstr="--sim-done %s", desc="create file when simulation finished"
     )
-    nii_gz = traits.Bool(
-        argstr='--nii.gz',
-        desc='save outputs as nii.gz',
-    )
+    _ext_xor = ['nii', 'nii_gz']
+    nii = traits.Bool(argstr='--nii', desc='save outputs as nii', xor=_ext_xor)
+    nii_gz = traits.Bool(argstr='--nii.gz', desc='save outputs as nii.gz', xor=_ext_xor)
 
 
 class GLMFitOutputSpec(TraitedSpec):
@@ -463,6 +462,8 @@ class GLMFitOutputSpec(TraitedSpec):
     frame_eigenvectors = File(desc="matrix of frame eigenvectors from residual PCA")
     singular_values = File(desc="matrix singular values from residual PCA")
     svd_stats_file = File(desc="text file summarizing the residual PCA")
+    k2p_file = File(desc="estimate of k2p parameter")
+    bp_file = File(desc="Binding potential estimates")
 
 
 class GLMFit(FSCommand):
@@ -497,22 +498,33 @@ def _list_outputs(self):
             glmdir = os.path.abspath(self.inputs.glm_dir)
         outputs["glm_dir"] = glmdir
 
+        if isdefined(self.inputs.nii_gz):
+            ext = '.nii.gz'
+        if isdefined(self.inputs.nii):
+            ext = '.nii'
+        else:
+            ext = '.mgh'
+
         # Assign the output files that always get created
-        outputs["beta_file"] = os.path.join(glmdir, "beta.mgh")
-        outputs["error_var_file"] = os.path.join(glmdir, "rvar.mgh")
-        outputs["error_stddev_file"] = os.path.join(glmdir, "rstd.mgh")
-        outputs["mask_file"] = os.path.join(glmdir, "mask.mgh")
+        outputs["beta_file"] = os.path.join(glmdir, f"beta.{ext}")
+        outputs["error_var_file"] = os.path.join(glmdir, f"rvar.{ext}")
+        outputs["error_stddev_file"] = os.path.join(glmdir, f"rstd.{ext}")
+        outputs["mask_file"] = os.path.join(glmdir, f"mask.{ext}")
         outputs["fwhm_file"] = os.path.join(glmdir, "fwhm.dat")
         outputs["dof_file"] = os.path.join(glmdir, "dof.dat")
         # Assign the conditional outputs
-        if isdefined(self.inputs.save_residual) and self.inputs.save_residual:
-            outputs["error_file"] = os.path.join(glmdir, "eres.mgh")
-        if isdefined(self.inputs.save_estimate) and self.inputs.save_estimate:
-            outputs["estimate_file"] = os.path.join(glmdir, "yhat.mgh")
+        if self.inputs.save_residual:
+            outputs["error_file"] = os.path.join(glmdir, "eres.{ext}")
+        if self.inputs.save_estimate:
+            outputs["estimate_file"] = os.path.join(glmdir, "yhat.{ext}")
+        if any((self.inputs.mrtm1, self.inputs.mrtm2, self.inputs.logan)):
+            outputs["bp_file"] = os.path.join(glmdir, f"bp.{ext}")
+        if self.inputs.mrtm1:
+            outputs["k2p_file"] = os.path.join(glmdir, "k2prime.dat")
 
         # Get the contrast directory name(s)
+        contrasts = []
         if isdefined(self.inputs.contrast):
-            contrasts = []
             for c in self.inputs.contrast:
                 if split_filename(c)[2] in [".mat", ".dat", ".mtx", ".con"]:
                     contrasts.append(split_filename(c)[1])
@@ -522,19 +534,19 @@ def _list_outputs(self):
             contrasts = ["osgm"]
 
         # Add in the contrast images
-        outputs["sig_file"] = [os.path.join(glmdir, c, "sig.mgh") for c in contrasts]
-        outputs["ftest_file"] = [os.path.join(glmdir, c, "F.mgh") for c in contrasts]
+        outputs["sig_file"] = [os.path.join(glmdir, c, f"sig.{ext}") for c in contrasts]
+        outputs["ftest_file"] = [os.path.join(glmdir, c, f"F.{ext}") for c in contrasts]
         outputs["gamma_file"] = [
-            os.path.join(glmdir, c, "gamma.mgh") for c in contrasts
+            os.path.join(glmdir, c, f"gamma.{ext}") for c in contrasts
         ]
         outputs["gamma_var_file"] = [
-            os.path.join(glmdir, c, "gammavar.mgh") for c in contrasts
+            os.path.join(glmdir, c, f"gammavar.{ext}") for c in contrasts
         ]
 
         # Add in the PCA results, if relevant
         if isdefined(self.inputs.pca) and self.inputs.pca:
             pcadir = os.path.join(glmdir, "pca-eres")
-            outputs["spatial_eigenvectors"] = os.path.join(pcadir, "v.mgh")
+            outputs["spatial_eigenvectors"] = os.path.join(pcadir, f"v.{ext}")
             outputs["frame_eigenvectors"] = os.path.join(pcadir, "u.mtx")
             outputs["singluar_values"] = os.path.join(pcadir, "sdiag.mat")
             outputs["svd_stats_file"] = os.path.join(pcadir, "stats.dat")

nipype/interfaces/freesurfer/petsurfer.py

@@ -519,23 +519,17 @@ def _format_arg(self, name, spec, value):
 
 
 class MRTMInputSpec(GLMFitInputSpec):
-
     mrtm1 = InputMultiPath(
-        traits.Tuple(
-            File(exists=True, mandatory=True), File(exists=True, mandatory=True)
-        ),
+        traits.Tuple(File(exists=True), File(exists=True)),
+        mandatory=True,
         argstr="--mrtm1 %s %s...",
         desc="RefTac TimeSec : perform MRTM1 kinetic modeling",
     )
 
 
-class MRTMOutputSpec(GLMFitInputSpec):
-
-    k2p = File(desc="estimate of k2p parameter")
-
-
 class MRTM(GLMFit):
     """Perform MRTM1 kinetic modeling.
+
     Examples
     --------
     >>> mrtm = MRTM()
@@ -546,35 +540,17 @@ class MRTM(GLMFit):
     'mri_glmfit --glmdir mrtm --y tac.nii --mrtm1 ref_tac.dat timing.dat'
     """
 
-    _cmd = "mri_glmfit"
     input_spec = MRTMInputSpec
-    output_spec = MRTMOutputSpec
-
-    def _list_outputs(self):
-        outputs = self.output_spec().get()
-        outputs['k2p'] = os.path.join(self.inputs.glm_dir, 'k2prime.dat')
-        return outputs
 
 
 class MRTM2InputSpec(GLMFitInputSpec):
-
     mrtm2 = InputMultiPath(
         traits.Tuple(File(exists=True), File(exists=True), traits.Float),
         mandatory=True,
         argstr="--mrtm2 %s %s %f...",
         desc="RefTac TimeSec k2prime : perform MRTM2 kinetic modeling",
     )
 
-    _ext_xor = ['nii', 'nii_gz']
-    nii = traits.Bool(argstr='--nii', desc='save outputs as nii', xor=_ext_xor)
-    nii_gz = traits.Bool(argstr='--nii.gz', desc='save outputs as nii.gz', xor=_ext_xor)
-    yhat_save = traits.Bool(argstr="--save-yhat", desc="save signal estimate (yhat)")
-
-
-class MRTM2OutputSpec(GLMFitInputSpec):
-    bp = File(desc="BP estimates")
-    yhat = File(desc="Fitted values (yhat) to the TACs")
-
 
 class MRTM2(GLMFit):
     """Perform MRTM2 kinetic modeling.
@@ -588,21 +564,7 @@ class MRTM2(GLMFit):
     'mri_glmfit --glmdir mrtm2 --y tac.nii --mrtm2 ref_tac.dat timing.dat 0.078720'
     """
 
-    _cmd = "mri_glmfit"
     input_spec = MRTM2InputSpec
-    output_spec = MRTM2OutputSpec
-
-    def _list_outputs(self):
-        outputs = self.output_spec().get()
-        if isdefined(self.inputs.nii_gz):
-            ext = '.nii.gz'
-        if isdefined(self.inputs.nii):
-            ext = '.nii'
-        else:
-            ext = '.mgh'
-        outputs['bp'] = os.path.join(self.inputs.glm_dir, 'bp', ext)
-        outputs['yhat'] = os.path.join(self.inputs.glm_dir, 'yhat', ext)
-        return outputs
 
 
 class LoganRefInputSpec(GLMFitInputSpec):
@@ -613,14 +575,6 @@ class LoganRefInputSpec(GLMFitInputSpec):
         desc="RefTac TimeSec tstar   : perform Logan kinetic modeling",
     )
 
-    _ext_xor = ['nii', 'nii_gz']
-    nii = traits.Bool(argstr='--nii', desc='save outputs as nii', xor=_ext_xor)
-    nii_gz = traits.Bool(argstr='--nii.gz', desc='save outputs as nii.gz', xor=_ext_xor)
-
-
-class LoganRefOutputSpec(GLMFitInputSpec):
-    bp_file = File(desc="BP estimates")
-
 
 class LoganRef(GLMFit):
     """Perform Logan reference kinetic modeling.
@@ -634,17 +588,4 @@ class LoganRef(GLMFit):
     'mri_glmfit --glmdir logan --y tac.nii --logan ref_tac.dat timing.dat 2600'
     """
 
-    _cmd = "mri_glmfit"
     input_spec = LoganRefInputSpec
-    output_spec = LoganRefOutputSpec
-
-    def _list_outputs(self):
-        outputs = self.output_spec().get()
-        if isdefined(self.inputs.nii_gz):
-            ext = '.nii.gz'
-        if isdefined(self.inputs.nii):
-            ext = '.nii'
-        else:
-            ext = '.mgh'
-        outputs['bp'] = os.path.join(self.inputs.glm_dir, 'bp', ext)
-        return outputs