**fScan Reference Manual, Chapter 1 (Topics): Tutorial**
==== Step 4: Align ====

For more information, see [[jvs:fscan:manual:chapter1:overlay_and_alignment|Overlay and Alignment]].

 **4.1** Once the overlay has been set, click on the align icon in the **Overlay** taskbar. This will open the **Alignment** taskbar. 
 
 **4.2** There are various methods to make the proper adjustments. 

 **4.3** Click either the "Move", "Rotate", or "Scale" icons, use the up/down and right/left arrow icons to move the overlay accordingly.

 **4.4** To rotate the image, select a point on the overlay and click the "Pin" icon.
  
 **4.5** Select the "Rotate" icon. Make adjustments accordingly with arrow keys. 

***Note**: Alignment can be made with the "Rotate" and "Move" icons to correct any movement that may have occured in scanning, but the "Scale" tool should not prove necessary as the same subject, Sam, was scanned for functional and anatomical images and probably didn't grow or shrink too much in the process.

 **4.6** Once aligment is finished, select the "remove alignment and save changes" icon in the **Align** taskbar. 
 
 **4.7** Open the **Cortmap** taskbar and select the "Copy Alignment" icon to replicate this alignment with all of the functional images. 
 
 **4.8** Undo the current overlay on the bia3_7335_1_300 image by clicking the "turn off current overlay" icon in the **Overlay** taskbar. 
 
 **4.9** Check the alignment on all of the functional images by repeating the overlay with bia3_7335_1_7, bia3_7335_1_8, and bia3_7335_1_9. If an alignment seems off on one of the overlays, adjust it using the same method in steps 1-7. 
 
 **4.10** When the alignments is well-adjusted for all of them, save the alignment in a workspace file by going to the **File** taskbar and selecting the "Save WDF" icon. 
 
 **4.11** A window will pop up. Type in 'Aligned.wdf' and save. This will save the WDF to your current directory. 
 
 **4.12** To open this in fScan from your directory, simply type in: //fscan Aligned.wdf -D//

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**See Also:**\\


[[jvs:fscan|fScan Home]], 
[[jvs:fscan:manual|fScan Manual]], 
[[jvs:fscan:manual:chapter1|Topics]], 
[[jvs:fscan:manual:help|Manual Help]]