help > Adding Markers and Slice Coordinates to "Cut out"
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Oct 14, 2021  11:10 AM | rosenkohl
Adding Markers and Slice Coordinates to "Cut out"
Dear community,

I have plotted fMRI z-score clusters by using the "cut out" option from the "templates". Now I am searching for the coordinates of the slices by which I have defined the cut out. These information would help for defining the exact cutout position. 
And also I was looking for the "cross hairs", I guess I can't add those in the "cutout" mode. Am I right?

Thanks in advance and all the best!
Oct 14, 2021  12:10 PM | Chris Rorden
RE: Adding Markers and Slice Coordinates to "Cut out"
You can solve both questions by selecting the "Multi-Planar (A+C+S+R)" item in the "View" menu. Interactive cross-hairs appear in the 2D slices and the rendering. Note that when you click on a location in the render view, the crosshairs move to this position and the coordinates appear in the title bar. You can also compute the coordinates by using the Python scripting. The "Cutout" example in the Scripting/Templates menu shows how to define the cut out as a fraction of your image size. From that, you can precisely derive the coordinates.
Attachment: Cutout.png
Oct 14, 2021  12:10 PM | rosenkohl
RE: Adding Markers and Slice Coordinates to "Cut out"
Thanks for the quick response! By choosing "Display" - "Multi-Planar" I wasn't able to reconstruct the bottom right figure (the whole brain) of the file you have sent, it only shows me the 2D slices (with cutouts) and no option to controle the cutout.
Oct 14, 2021  01:10 PM | Chris Rorden
RE: Adding Markers and Slice Coordinates to "Cut out"
Please upgrade to the current version (1.2.20211006).
Oct 16, 2021  11:10 AM | rosenkohl
RE: Adding Markers and Slice Coordinates to "Cut out"
That worked and it looks cool! Thanks! When in the "Multi-Planar A+P+S+R" view, is there a way to obtain the MNI coordinates of the point marked by the crosshairs?
Oct 16, 2021  11:10 AM | Chris Rorden
RE: Adding Markers and Slice Coordinates to "Cut out"
The Coordinates are always displayed in the title bar. So that "12×15×2" would indicate that you are 12mm right, 15mm anterior and 2mm superior of the origin. If your data is directly from an MRI scanner, the origin will be isocenter, if your data is direct from a CT scanner the origin will be table center, if your image has been normalized to a MNI template, the origin should be the anterior commissure.