MException Message

Skip to first unread message

Crystal Franklin

Apr 22, 2020, 8:14:20 AM4/22/20
Dear All,

I am new user and I am trying to process my first dataset with the NODDI toolbox.  The data has been pre-processed using FSL tools (topup, eddy, etc.).  When I run the eddy corrected data, it seems to run fine until the batch_fitting_single command.  It will run, but I notice the below message will show up at different times in the matlab window:

MException with properties:

    identifier: ' '
       message: 'All b=0 measurements are negative'
           cause: {0x1 cell}
            stack: [3x1 struct]

The data continues running and I get output images.  I have tried playing with the mask and doubled checked that the b-value is actually 0 and I still get the same error message. 

Any suggestions on how to resolve this?

Thanks in advance,

Hui Zhang

Apr 25, 2020, 9:58:12 AM4/25/20
Hi Crystal,

This message can happen for two reasons:

1) the b-values of non-diffusion-weighted measurements are recorded not as 0 in the bval file.

This often happens with the b-values for these measurements are not exactly 0, instead they take a small value such as 5.

From your email, it looks like this isn't your problem.  But if it is, you will not get any sensible NODDI maps.  To fix this problem, one can call FSL2Procotol with one extra argument

protocol = FSL2Protocol(bval, bvec, b0threshold);

2) for some of the voxels, none of their b=0 measurements is greater than 0.

This often happens for the voxels at the edge of binary brain mask.  If this is the case, you will be able to get sensible NODDI maps for the other voxels.  So you can safely ignore this error message.


You received this message because you are subscribed to the Google Groups "NODDI" group.
To unsubscribe from this group and stop receiving emails from it, send an email to
To view this discussion on the web visit
Reply all
Reply to author
0 new messages