Look in the file menu for functions that let you load / save anatomy files, analyses, ROIs and so on. There are also functions that let you print the currently displayed image, import / export data, ROIs, write out information about the session in a Readme.txt file, and quit the current session of mrLoadRet.

• Load: Select an anatomy file on which overlays will be rendered. Normally, this will be your inplane anatomy file which was collected during the scanning session at the same slice locations as your functional data.
• Load from volume directory; Select a volume anatomy file on which overlays will be rendered. By default, the file dialog window opens in the volumeDirectory folder specified in your preferences. Make sure that the qform and sform matrices of the file you select are correct. Normally, you will use the volume anatomy file that was used as the target in your alignment steps (see mrAlign documentation).
• Use current scan Lets you use the current functional scan as the background image. You will be prompted to select a time point from the 4D volume; the first frame in the sequence is 1. If you select time point '0', the mean 3D image across time will be used.
• Load flat Load flat patches created by the steps described in the
• Load Surface Load OFF surfaces created with TFI/SurfRelax. You will be prompted for an outer surface filename. Provide the gray matter (GM) surface from one subject/hemisphere. You will then be prompted to select the matching inner surface (white matter, WM), curvature, and anatomy file. See documentation for mrSurfaceViewer for more details.
• Save Save the currently used anatomy image with a default filename
• Save As… Save the currently used anatomy image and specify a filename

• Load Load an analysis that was computed and saved earlier. Standard analyses that can be created by functions accessible in the GUI Analysis menu are Time Series Statistics (e.g. mean, median, across time), Correlation Analysis (standard Fourier-based analysis), Event related analysis, and GLM analysis (generalized linear models to produce statistical parametric maps).
• Save Save the currently selected analysis.
• Save All Save all analysis that have been opened in this session.

Edit details of the scanning session such as a description, the subject id, operator, magnet and pulse sequence. Those were usually when running mrInitRet or mrInit.

Manipulate groups (such as Raw, MotionComp, and Averages

• New Group - create a new group
• Delete Group - delete an existing group, e.g. if you realize that there were some mistakes in averaging across scans, you can delete the group Averages. The function will clean up the appropriate entries in the view variable that goes along with your session.
• Edit Group - This allows you to edit details for each scan in a Group: the scan description, the total number of frames and the junk frames (also called 'dummies') at the beginning of each scan that get disregarded in any analysis.
• Info - show information about each scan in each the current group. For the Average group, this will also show you which files contributed to each average. This is quite an important tool for debugging and checking your analyses.

Edit important preferences that affect the overall behavior of mrLoadRet. You will see a menu like the following:

Open up a new window, if you want to e.g. look at the same data set in the coronal and sagittal views simultaneously

Open up a new graphing window, into which results from new calls to the interrogator functions or functions form the Plots menu get rendered.

• Motion Compensation For more info see: Motion Compensation.
• Average Time Series For more info see: Average Time Series
• Concatenate Time Series For more info see: Concatenate Time Series
• Time Series Statistics For more info see: Time Series Statistics
• Correlation Analysis For more info see: Correlation Analysis
• Event Related Analysis For more info see: Event Related Analysis
• GLM Analysis For more info see: GLM Analysis