Create Cifti Dense Time Series

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CREATE CIFTI DENSE TIMESERIES

caret_command -create-cifti-dense-timeseries

[input functional volume timeseries]

[input left midthickness surface]
[[input left surface roi]]
[cifti structure name]
[input left surface metric timeseries]

[input left subcortical structure volumetric roi]
[cifti structure name]


[input right midthickness surface]
[[input right surface roi]]
[cifti structure name]
[input right surface metric timeseries]

[input left subcortical structure volumetric roi]
[cifti structure name]


<output cifti dense timeseries>
[output cifti header text]
[output gifti external binary format matrix]

Combine surface and volume timeseries into a single CIFTI dense timeseries file. All inputs are optional but there must be at least one input. If any volume structures are specified, a volume timeseries must precede the inputs. For each surface, a surface, name, and metric timeseries are required. A metric roi is optional. For each volume, a volume ROI and name are required. CIFTI files can contain both surface and volume structures, or only one or the other. All structures must be given a name. Common names include (do they all have STRUCTURE in them or not?):
CIFTI_STRUCTURE_ACCUMBENS_LEFT
CIFTI_STRUCTURE_ACCUMBENS_RIGHT
CIFTI_STRUCTURE_AMYGDALA_LEFT
CIFTI_STRUCTURE_AMYGDALA_RIGHT
CIFTI_STRUCTURE_BRAIN_STEM
CIFTI_STRUCTURE_CAUDATE_LEFT
CIFTI_STRUCTURE_CAUDATE_RIGHT
CIFTI_STRUCTURE_CEREBELLUM
CIFTI_STRUCTURE_CEREBELLUM_LEFT
CIFTI_STRUCTURE_CEREBELLUM_RIGHT
CIFTI_STRUCTURE_CORTEX_LEFT
CIFTI_STRUCTURE_CORTEX_RIGHT
CIFTI_STRUCTURE_HIPPOCAMPUS_LEFT
CIFTI_STRUCTURE_HIPPOCAMPUS_RIGHT
CIFTI_STRUCTURE_OTHER
CIFTI_STRUCTURE_PALLIDUM_LEFT
CIFTI_STRUCTURE_PALLIDUM_RIGHT
CIFTI_STRUCTURE_PUTAMEN_LEFT
CIFTI_STRUCTURE_PUTAMEN_RIGHT
CIFTI_STRUCTURE_SUBCORTICAL_WHITE_MATTER_LEFT
CIFTI_STRUCTURE_SUBCORTICAL_WHITE_MATTER_RIGHT
CIFTI_STRUCTURE_THALAMUS_LEFT
CIFTI_STRUCTURE_THALMUS_RIGHT
CIFTI_STRUCTURE_DIENCEPHALON_VENTRAL_LEFT
CIFTI_STRUCTURE_DIENCEPHALON_VENTRAL_RIGHT

The only names that must be the same as above, if used, are CIFTI_STRUCTURE_CORTEX_LEFT and CIFTI_STRUCTURE_CORTEX_RIGHT so that viewers know the structure is a left or right surface (is this needed?). The CIFTI file output will be ordered in the order of the inputs. It is possible to also output a text CIFTI header and GIFTI external binary file for compatibility with Matlab. A CIFTI file output must be specified.
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