.. _page-menubar:

Menubar
=======

- :ref:`menu-section-file`
- :ref:`menu-section-functions`
- :ref:`menu-section-registration`
- :ref:`menu-section-segmentation`
- :ref:`menu-section-mapping`
- :ref:`menu-section-diffusion`
- :ref:`menu-section-views`
- :ref:`menu-section-window`

.. _menu-section-file:
File
----

	- Open...
	- Open template >
	- Open from format >

		- Open Nifti...
		- Open Nrrd...
		- Open Minc...
		- Open FreeSurfer MGH...
		- Open Sisyphe...
		- Open BrainVoyager VMR...
		- Open VTK...

	- Recent files >
	- Save
	- Save all
	- Save as...
	- Save to format >

		- Save Nifti...
		- Save Numpy...
		- Save Nrrd...
		- Save Minc...
		- Save VTK...

	- Close
	- Close all
	- Preferences...
	- Download manager...
	- Check for update...
	- Edit attributes...
	- ID replacement...
	- Anomynize...
	- Edit volume labels...
	- ROIs to label volume...
	- Volumes to label volume...
	- Label volume to ROIs...
	- Import >

		- Import Nifti...
		- Import Minc...
		- Import Nrrd...
		- Import Vtk...
		- Import Sisyphe (*.vol)

	- Export >

		- Export Nifti...
		- Export Minc...
		- Export Nrrd..
		- Export Vtk...
		- Export Numpy...

	- DICOM >

		- DICOM import...
		- DICOM RT import...
		- DICOM export...
		- DICOM Dataset...
		- Xml DICOM attributes...
		
	- Edit LUT...
	- Quit...

.. _menu-section-functions:
Functions
---------

	- Join single component volume(s)
	- Split multi component volume (s)
	- Flip axis...
	- Permute axis...
	- Remove neck slilces...
	- Datatype conversion...
	- Attributes conversion...
	- Filters >

		- Mean...
		- Median...
		- Gaussian...
		- Gradient magnitude...
		- Laplacian...
		- Anistropic diffusion...

	- Intensity processing >

		- Histogram intensity matching...
		- Regression intensity matching...
		- Inensity normalization...

	- Texture feature maps...
	- Bias field correction...
	- Voxel-by-voxel processing >

		- Mean volume...
		- Median volume...
		- Standard deviation volume...
		- Minimum volume...
		- Maximum volume...
		- Algebra...

	- Processing workflow...
	- Workflows >
	- Install plugin...
	- Remove plugin...
	- Plugins >

.. _menu-section-registration:
Registration
------------

	- Stereotactic frame detection...
	- AC-PC selection...
	- Volume reorientation...
	- Manual registration...
	- Rigid registration...
	- Affine registration...
	- Displacement field registration...
	- ICBM normalization...
	- Batch registration...
	- Time series realignment...
	- Eddy current correction...
	- Resample...
	- Asymmetry displacement field...
	- Displacement field jacobian determinant...

.. _menu-section-segmentation:
Segmentation
------------

	- KMeans clustering...
	- KMeans segmentation...
	- Skull striping...
	- Tissue segmentation...
	- Cortical thickness...
	- Registration based segmentation...
	- Structs >

		- Labelling >
		- User >

	- Depp learning segmentation >

		- Hippocampus segmentation...
		- Hypo-intensity lesion segmentation...
		- Medial temporal clustering...
		- TOF vessels segmentation...
		- Tumor clustering...
		- White matter hyper-intensities segmentation...

.. _menu-section-mapping:
Mapping
-------

	- Model >

		- fMRI conditions...
		- fMRI subjects/conditions...
		- fMRI groups/subjects/conditions...
		- One sample t-test...
		- Two sample t-test...
		- Paired t-test
		- GLM subjects/conditions...
		- GLM groups/subjects/conditions...
		- GLM groups...
		- GLM groups/subjects...
		- Models >

	- Contrast...
	- Result...
	- Conjunction...
	- t to z-map conversion...
	- Clean time series...
	- Seed-to-voxel time series correlation...
	- Time series correlation matrix...
	- Single-subject time series ICA...
	- Multi-subject time series ICA...
	- Dynamic suceptibility contrast...

.. _menu-section-diffusion:
Diffusion
---------

	- Gradients...
	- Preprocessing...
	- Diffusion model...
	- Bundle >

		- ROI based streamlines selection...
		- Filter based streamlines selection...
		- Template based streamlines selection...
		- Density map...
		- Path length map...
		- Connectivity matrix...

.. _menu-section-views:
Views
-----

	- Slice view >
	- Orthogonal  >
	- Synchronize view >
	- Projection view >
	- Multi-component view >
	- Database >
	- Screenshots >
	- IPython >

.. _menu-section-window:
Window
------

	- About
	- Minimize
	- Maximize
	- Full screen
	- Show/Hide Toolbar
	- Show/Hide Thumbnail
	- Show/Hide Dock
	- Show/Hide Status bar
	- Next tab
	- Previous tab
	- Slice view
	- Orthogonal view
	- Synchornized view
	- Projection view
	- Multi-component view
	- Database
	- Screenshots
	- IPython