open-discussion > brain mask error: ImageMath cannot be started
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Nov 18, 2019  06:11 PM | ameliaqian
brain mask error: ImageMath cannot be started
I am doing QC using DTIPrep and it work well except brain mask. I use bet2 from FSL, DiffusionWeightedVolumeMasking from slicer 4.4.0, ImageMath from DTIPrep. Based on the posts on forum, I chose BRAINMASK_method as 3 FSL_bet(IDWI).


The QC report shows: DTIPrepPackage/ImageMath cannot be started. (I attached a image of report). How can I solve this issue?
Attachment: QCreport.png
Nov 19, 2019  06:11 AM | Martin Styner
RE: brain mask error: ImageMath cannot be started
ImageMath is a small tool on the DTIPrep package and it needs to find it in order to apply the computed brain masks. It looks like it finds it correctly (assuming that you have indeed ImageMath under the path listed in that line in the QCreport), but cannot start it. Not sure what the issue is as this is not a message from ImageMath, but from the system. Maybe you do not execution privileges for ImageMath? 

If you look at the properties of that executable, you should see whether you can/are allowed to execute it or not.

Martin
Nov 19, 2019  07:11 AM | ameliaqian
RE: brain mask error: ImageMath cannot be started
I checked the property of ImageMath. It is executable.


I remembered several days ago, the QC report showed "Brain Mask FSL: DTIPrep/bet2 cannot be started". Then I changed some settings. Now it shows "ImageMath had an issue". I have no idea why it changed and how to solve it.