@@ -3,4 +3,4 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Connectome Workbench is a visualization for neuroimaging data, esp. derived from HCP data."""
 from .metric import MetricResample
-from .cifti import CiftiSmooth
+from .cifti import CiftiSmooth, CiftiCorrelation, CiftiParcellate, CiftiSeparateMetric

@@ -154,3 +154,278 @@ class CiftiSmooth(WBCommand):
 input_spec = CiftiSmoothInputSpec
 output_spec = CiftiSmoothOutputSpec
 _cmd = "wb_command -cifti-smoothing"
+
+
+class CiftiCorrelationInputSpec(CommandLineInputSpec):
+in_file = File(
+exists=True,
+mandatory=True,
+argstr="%s ",
+position=0,
+desc="The input ptseries or dense series",
+)
+out_file = File(
+name_source=["in_file"],
+name_template="correlation_matrix_%s.nii",
+keep_extension=True,
+argstr=" %s",
+position=1,
+desc="The output CIFTI",
+)
+
+roi_override = traits.Bool(
+exists=True,
+argstr="-roi-override %s ",
+position=2,
+desc=" perform correlation from a subset of rows to all rows",
+)
+
+left_roi = File(
+exists=True,
+position=3,
+argstr="-left-roi %s",
+desc="Specify the left roi metric to use",
+)
+
+right_roi = File(
+exists=True,
+position=5,
+argstr="-right-roi %s",
+desc="Specify the right roi metric to use",
+)
+cerebellum_roi = File(
+exists=True,
+position=6,
+argstr="-cerebellum-roi %s",
+desc="specify the cerebellum meytric to use",
+)
+
+vol_roi = File(
+exists=True,
+position=7,
+argstr="-vol-roi %s",
+desc="volume roi to use",
+)
+
+cifti_roi = File(
+exists=True,
+position=8,
+argstr="-cifti-roi %s",
+desc="cifti roi to use",
+)
+weights_file = File(
+exists=True,
+position=9,
+argstr="-weights %s",
+desc="specify the cerebellum surface metricto use",
+)
+
+fisher_ztrans = traits.Bool(
+position=10,
+argstr="-fisher-z",
+desc=" fisherz transfrom",
+)
+no_demean = traits.Bool(
+position=11,
+argstr="-fisher-z",
+desc=" fisherz transfrom",
+)
+compute_covariance = traits.Bool(
+position=12,
+argstr="-covariance ",
+desc=" compute covariance instead of correlation",
+)
+
+
+class CiftiCorrelationOutputSpec(TraitedSpec):
+out_file = File(exists=True, desc="output CIFTI file")
+
+
+class CiftiCorrelation(WBCommand):
+r"""
+Compute correlation from CIFTI file
+The input cifti file must have a brain models mapping on the chosen
+dimension, columns for .ptseries or .dtseries,
+>>> cifticorr = CiftiCorrelation()
+>>> cifticorr.inputs.in_file = 'sub-01XX_task-rest.ptseries.nii'
+>>> cifticorr.inputs.out_file = 'sub_01XX_task-rest.pconn.nii'
+>>> cifticorr.cmdline
+wb_command -cifti-correlation sub-01XX_task-rest.ptseries.nii \
+'sub_01XX_task-rest.pconn.nii'
+"""
+
+input_spec = CiftiCorrelationInputSpec
+output_spec = CiftiCorrelationOutputSpec
+_cmd = "wb_command -cifti-correlation"
+
+
+class CiftiParcellateInputSpec(CommandLineInputSpec):
+in_file = File(
+exists=True,
+mandatory=True,
+argstr="%s ",
+position=0,
+desc="The input CIFTI file",
+)
+atlas_label = traits.File(
+mandatory=True,
+argstr="%s ",
+position=1,
+desc="atlas label, in mm",
+)
+direction = traits.Enum(
+"ROW",
+"COLUMN",
+mandatory=True,
+argstr="%s ",
+position=2,
+desc="which dimension to smooth along, ROW or COLUMN",
+)
+out_file = File(
+name_source=["in_file"],
+name_template="parcelated_%s.nii",
+keep_extension=True,
+argstr=" %s",
+position=3,
+desc="The output CIFTI",
+)
+
+spatial_weights = traits.Str(
+argstr="-spatial-weights ",
+position=4,
+desc=" spatial weight file",
+)
+
+left_area_surf = File(
+exists=True,
+position=5,
+argstr="-left-area-surface %s",
+desc="Specify the left surface to use",
+)
+
+right_area_surf = File(
+exists=True,
+position=6,
+argstr="-right-area-surface %s",
+desc="Specify the right surface to use",
+)
+cerebellum_area_surf = File(
+exists=True,
+position=7,
+argstr="-cerebellum-area-surf %s",
+desc="specify the cerebellum surface to use",
+)
+
+left_area_metric = File(
+exists=True,
+position=8,
+argstr="-left-area-metric %s",
+desc="Specify the left surface metric to use",
+)
+
+right_area_metric = File(
+exists=True,
+position=9,
+argstr="-right-area-metric %s",
+desc="Specify the right surface metric to use",
+)
+cerebellum_area_metric = File(
+exists=True,
+position=10,
+argstr="-cerebellum-area-metric %s",
+desc="specify the cerebellum surface metricto use",
+)
+
+cifti_weights = File(
+exists=True,
+position=11,
+argstr="-cifti-weights %s",
+desc="cifti file containing weights",
+)
+cor_method = traits.Str(
+position=12,
+default="MEAN ",
+argstr="-method %s",
+desc=" correlation method, option inlcude MODE",
+)
+
+
+class CiftiParcellateOutputSpec(TraitedSpec):
+out_file = File(exists=True, desc="output CIFTI file")
+
+
+class CiftiParcellate(WBCommand):
+r"""
+Extract timeseries from CIFTI file
+The input cifti file must have a brain models mapping on the chosen
+dimension, columns for .dtseries,
+>>> ciftiparcel = CiftiParcellate()
+>>> ciftiparcel.inputs.in_file = 'sub-01XX_task-rest.dtseries.nii'
+>>> ciftiparcel.inputs.out_file = 'sub_01XX_task-rest.ptseries.nii'
+>>> ciftiparcel.inputs.atlas_label = 'schaefer_space-fsLR_den-32k_desc-400_atlas.dlabel.nii'
+>>> ciftiparcel.inputs.direction = 'COLUMN'
+>>> ciftiparcel.cmdline
+wb_command -cifti-parcellate sub-01XX_task-rest.dtseries.nii \
+schaefer_space-fsLR_den-32k_desc-400_atlas.dlabel.nii COLUMN \
+sub_01XX_task-rest.ptseries.nii
+"""
+input_spec = CiftiParcellateInputSpec
+output_spec = CiftiParcellateOutputSpec
+_cmd = "wb_command -cifti-parcellate"
+
+
+class CiftiSeparateMetricInputSpec(CommandLineInputSpec):
+in_file = File(
+exists=True,
+mandatory=True,
+argstr="%s ",
+position=0,
+desc="The input dense series",
+)
+direction = traits.Enum(
+"ROW",
+"COLUMN",
+mandatory=True,
+argstr="%s ",
+position=1,
+desc="which dimension to smooth along, ROW or COLUMN",
+)
+metric = traits.Str(
+mandatory=True,
+argstr=" -metric %s ",
+position=2,
+desc="which of the structure eg CORTEX_LEFT CORTEX_RIGHT"
+"check https://www.humanconnectome.org/software/workbench-command/-cifti-separate ",
+)
+out_file = File(
+name_source=["in_file"],
+name_template="correlation_matrix_%s.func.gii",
+keep_extension=True,
+argstr=" %s",
+position=3,
+desc="The gifti output, iether left and right",
+)
+
+
+class CiftiSeparateMetricOutputSpec(TraitedSpec):
+out_file = File(exists=True, desc="output CIFTI file")
+
+
+class CiftiSeparateMetric(WBCommand):
+r"""
+Extract left or right hemisphere surface from CIFTI file (.dtseries)
+other structure can also be extracted
+The input cifti file must have a brain models mapping on the chosen
+dimension, columns for .dtseries,
+>>> ciftiseparate = CiftiSeparateMetric()
+>>> ciftiseparate.inputs.in_file = 'sub-01XX_task-rest.dtseries.nii'
+>>> ciftiseparate.inputs.metric = "CORTEX_LEFT" # extract left hemisphere
+>>> ciftiseparate.inputs.out_file = 'sub_01XX_task-rest_hemi-L.func.gii'
+>>> ciftiseparate.inputs.direction = 'COLUMN'
+>>> ciftiseparate.cmdline
+wb_command -cifti-separate 'sub-01XX_task-rest.dtseries.nii' COLUMN \
+-metric CORTEX_LEFT 'sub_01XX_task-rest_hemi-L.func.gii'
+"""
+input_spec = CiftiSeparateMetricInputSpec
+output_spec = CiftiSeparateMetricOutputSpec
+_cmd = "wb_command -cifti-separate "

@@ -0,0 +1,93 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from ..cifti import CiftiCorrelation
+
+
+def test_CiftiCorrelation_inputs():
+input_map = dict(
+args=dict(
+argstr="%s",
+),
+cerebellum_roi=dict(
+argstr="-cerebellum-roi %s",
+extensions=None,
+position=6,
+),
+cifti_roi=dict(
+argstr="-cifti-roi %s",
+extensions=None,
+position=8,
+),
+compute_covariance=dict(
+argstr="-covariance ",
+position=12,
+),
+environ=dict(
+nohash=True,
+usedefault=True,
+),
+fisher_ztrans=dict(
+argstr="-fisher-z",
+position=10,
+),
+in_file=dict(
+argstr="%s ",
+extensions=None,
+mandatory=True,
+position=0,
+),
+left_roi=dict(
+argstr="-left-roi %s",
+extensions=None,
+position=3,
+),
+no_demean=dict(
+argstr="-fisher-z",
+position=11,
+),
+out_file=dict(
+argstr=" %s",
+extensions=None,
+keep_extension=True,
+name_source=["in_file"],
+name_template="correlation_matrix_%s.nii",
+position=1,
+),
+right_roi=dict(
+argstr="-right-roi %s",
+extensions=None,
+position=5,
+),
+roi_override=dict(
+argstr="-roi-override %s ",
+exists=True,
+position=2,
+),
+vol_roi=dict(
+argstr="-vol-roi %s",
+extensions=None,
+position=7,
+),
+weights_file=dict(
+argstr="-weights %s",
+extensions=None,
+position=9,
+),
+)
+inputs = CiftiCorrelation.input_spec()
+
+for key, metadata in list(input_map.items()):
+for metakey, value in list(metadata.items()):
+assert getattr(inputs.traits()[key], metakey) == value
+
+
+def test_CiftiCorrelation_outputs():
+output_map = dict(
+out_file=dict(
+extensions=None,
+),
+)
+outputs = CiftiCorrelation.output_spec()
+
+for key, metadata in list(output_map.items()):
+for metakey, value in list(metadata.items()):
+assert getattr(outputs.traits()[key], metakey) == value