Utilities_Visual_Check.txt

Visual Check
---------------------------

The current function provides batch operations to visually inspect artifacts and normalization quality, by calling *Display* from SPM. We've added keyboard operations to the *Display* figure that users can press up/down to switch fMRI volumes of one subject and press left/right to switch subjects. Before running the frame-by-frame inspection, the current function exports screenshots of selected slices overlaid by a semi-transparent brain mask for a glimpse of the overall image quality.

.. image:: _images/visual_check.png
   :align: right
     
**The function calls SPM Check Reg to visualize input volume, a keyboard callback is added to enable left/right and up/down to switch timepoint and subjects.**
    
* **mask**: could be whole brain mask or gray matter mask.
* **id index**: identifier to find unique string for each subject
* **filetype**: files in the filetype will be searched in input directories.
* **4D nifti files**: if the input data is 4D, check this item. Otherwise uncheck.
* **input dirs**: directories can be input either using a :file:`\*.txt` file or spm select window.
* **display orthogonal view**: check to display orthogonal view of selected slices and save screenshots. uncheck will only save screenshots to out dir.
* **mask color**: color of the transparent overlaid mask.
* **slices**: modified image n-th slice of x,y,z to save.
* **out dir**: output directory for saving results.
    
- **Keyboard Operation**:
    - **Up/Down**: last/next timepoint of the same subject.
    - **Left/Right**: same timepoint of last/next subject.
    
* **Buttons**:
    * **S**: Save parameters of the current panel to a :file:`\*.mat` file. The :file:`\*.mat` can be further loaded for the panel or be used in a script processing.
    * **L**: Load parameters from :file:`\*.mat` for the current panel.
    * **?**: Help information.