**fScan Reference Manual, Chapter 1 (Topics): Contents **
===== Introductory Topics -- Summary List =====

|[[jvs:fscan:manual:chapter1:introduction|Introduction]]|Beginner's guide to fScan|
|[[jvs:fscan:manual:chapter1:tutorial|Tutorial]]|A tutorial guide to fScan|
|[[jvs:fscan:manual:chapter1:menus|Menus]]|Using taskbars and dialogs|
|[[jvs:fscan:manual:chapter1:rois|ROIs]]|Using regions-of-interest|
|[[jvs:fscan:manual:chapter1:timing|Timing]]|Handling reference timing data|
|[[jvs:fscan:manual:chapter1:blocks|Blocks]]|Block-design analysis|
|[[jvs:fscan:manual:chapter1:events|Events]]|Event-related analysis|
|[[jvs:fscan:manual:chapter1:programming|Programming]]|Scripting fScan commands|
|[[jvs:fscan:manual:chapter1:launching|Launching]]|Launching other programs from fScan|
|[[jvs:fscan:manual:chapter1:colormaps|ColorMaps]]|Using color tables|
|[[jvs:fscan:manual:chapter1:clipboard|Clipboard]]|Using the Copy/Paste clipboard|
|[[jvs:fscan:manual:chapter1:atlases|Atlases]]|Using atlases|
|[[jvs:fscan:manual:chapter1:glossaries|Glossaries]]|Using glossaries|
|[[jvs:fscan:manual:chapter1:lists|Lists]]|Using data lists|
|[[jvs:fscan:manual:chapter1:images|Images]]|Using image data|
|[[jvs:fscan:manual:chapter1:fMRI|fMRI]]|Processing 4-D image series|
|[[jvs:fscan:manual:chapter1:surfaces|Surfaces]]|Using 3D surface-reconstructed data|
|[[jvs:fscan:manual:chapter1:masking|Masking]]|Using image masks|
|[[jvs:fscan:manual:chapter1:thresholding|Thresholding]]|Using intensity thresholding|
|[[jvs:fscan:manual:chapter1:history|History]]|Data provenance records|
|[[jvs:fscan:manual:chapter1:database|Database]]|Accessing database information|
|[[jvs:fscan:manual:chapter1:cmdline|CmdLine]]|Starting fScan using a command line|
|[[jvs:fscan:manual:chapter1:starting|StartUp]]|Start-up processing steps|
|[[jvs:fscan:manual:chapter2|CmdSummary]]|List of commands|
|[[jvs:fscan:manual:chapter1:cmdsummary|oldCmdSummary]]|Old list of commands|
|[[jvs:fscan:manual:chapter1:infiles|InFiles]]|Input file formats recognized|
|[[jvs:fscan:manual:chapter1:outfiles|Outfiles]]|Saving data|
|[[jvs:fscan:manual:chapter1:workspace file|Workspace File]]|Using workspaces|
|[[jvs:fscan:manual:chapter1:ample|AMPLE]]|Amplitude mapping as percentage of local excitation|
|[[jvs:fscan:manual:chapter1:cortmap|Cortmap]]|Patient mapping protocol|
|[[jvs:fscan:manual:chapter1:aligning|Aligning]]|Aligning image data sets|
|[[jvs:fscan:manual:chapter1:processing|Processing]]|  |
|[[jvs:fscan:manual:chapter1:variables|Variables]]|Using fScan internal variables|
|[[jvs:fscan:manual:chapter1:stringsubst|StringSubst]]|String substitutions in interactive commands|
|[[jvs:fscan:manual:chapter1:relatedprogs|RelatedPrograms]]|Handy shell scripts and other programs|
|[[jvs:fscan:manual:chapter1:dbax|DBAX]]|Interacting with the DBAX imaging database web-service|
|[[jvs:fscan:manual:chapter1:headmotion|Head motion]]|Comments on head motion|



**See Also:**\\
[[jvs:fscan|fScan Home]],
[[jvs:fscan:manual|fScan Manual]],
[[jvs:fscan:manual:help|Manual Help]]