open-discussion > MRIcron Mask Editing
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May 26, 2018  04:05 AM | Mugdha Kunte
MRIcron Mask Editing

My name is Mugdha Sanjay Kunte and I am working in National Institute of Mental Health and Neurosciences (NIMHANS) as a Technical Assistant.
I am working with SPM suit and have extracted cerebellum using the Suit toolbox. I am overlaying the mask(cerebellum) onto the structural image to ensure that it fits perfectly.
Unfortunately, there are a few regions that are excluded by the mask. I have been trying to edit the mask to include the regions that are left out, but the resulting images are still incomplete. Following are the steps I followed :
1. Open the structural image in MRIcron and overlay the cerebellum. This would show the extent of overlap between the two images. A few of the images do not superimpose completely.
2. Select the brush icon and fill in the incomplete regions and save the image (I tried saving the image using the save button under file drop down menu and saving it using the voi option, followed by nifti conversion). On opening this saved file, only the regions that have been recently added show up and the rest of the mask is absent.
Is there a way to add regions in the mask and save it?

Thank you for your help!
May 26, 2018  12:05 PM | Chris Rorden
RE: MRIcron Mask Editing
If you want to edit your mask you need to open it as a drawing. So instead of "Open the structural image in MRIcron and overlay the cerebellum." you should "Open the structural image in MRIcron and open the cerebellum cerebellum as a drawing." The Drawing/OpenVOI allows you to open an image so you can edit it with the drawing tools.

Note that you can open/save drawings in .nii, .nii.gz and .voi formats. The only difference between a ".nii.gz" and the ".voi" is the filename extension, but my software assumes that a .voi is a binary image.

You may also want to try the more modern MRIcroGL. It allows you to save multiple different colors of regions of interest and has a few other handy features.