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Error in running MCX on specific MRI anatomy

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Yuanyuan Gao
Posts: 5
(@yuanyuan216)
Active Member
Joined: 2 years ago

Hi Yichuan and Giulia,

The error message means that mcx code expects at least 4 tissue types. I recommend inputting at least head, grey, and white matter. 

If you use SPM, you should use files starting with 'mwc', which is probably what Yichuan has been using (in native space and warped tissues). The problem is that the head file from SPM is actually background file, where background is defined as 1s, and the head is defined as 0s. But AV expects the background to be 0s and the head to be 1s. So a simple matlab code to swap the 0s and 1s should be run on the SPM output background file before importing to AV. (Let me know if you need the code)

If you are using freesurfer, you can use watershed command to get a single segmentation file to feed into AV.

Let me know if that works for you.

 

Yuanyuan

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