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Where and what
Created in T1 preprocessing folder, for example
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The brainmasklots is the brainmask that has been dilated, which means expanded - puffed out is a good analogy.
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Identifying problem
If brainmask/brainmasklots look bad, check the c1 & c2 files (or p1 & p2). Here is an example:
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When we look at the CSF image (c3), we see the problem - gray matter has been classified as CSF:
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Possible solution
The most common reason segmentation fails is that the T1 is poor coregistration with the template. In the example about, running “Check coregistration” for “T1 coreg” shows that this subject is not well registered. The first step is then to go to projects, manual coreg, then copy and coreg when done.
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Problem - unusual brain
In rare cases segmentation fails when a participant has a brain shape that is very different from the template. In that case, it may be that using CAT will help, although this woudl mean running all subjects with CAT.
Otherwise, find the batch job that created the segmentations in the same folder and adjust parameters and run again manually.