[Anonymous]

This error is most likely related to incorrect estimation of diffusion brain mask. Can you please check the file <fileprefix>.dwi.RSA.mask.nii.gz and see if looks like reasonable mask for diffusion data (<fileprefix>.dwi.RSA.nii.gz)? I am guessing that it would be highly incorrect.

If that is the case, then please edit the mask manually in BrainSuite to cover brain-area reasonably in diffusion data. Then you should use this mask as input in BDP via –dwi-mask flag.

[bokkyuki@usc.edu]

Hello!

It is working if I edit the mask manually, but it took a lot of time to edit the mask manually. I ran this process with earlier version of BDP (14a), and it generated correct dwi mask. So I wonder if the wrong dwi mask from the new version of BDP is a kind of an error.

[Anonymous]

Hi, couple of things regarding this:

First, the algorithm of BDP for automatic masking did change in 15a as compared to 14a, which was also based on feedback from BDP users. We tried to make it more robust to variety to datasets in our test-sets. However, it is possible that the performance for your dataset is not optimal with this change. If you can send us a sample dataset, on our support email address, then we can include it in our test-set.

Having said that, if you have masks from 14a run then you can directly use the generated masks with any version of BDP. It should work without any problem.

Also, in case you are editing masks manually, you do not need to make very precise masks. You can just use thresholding in mask-tool – just make sure you are not missing big chunks of brain.

[carnico]

Hi to all,

I think I’ve the same problem.

The <fileprefix>.dwi.RSA.nii.gz to me looks reasonable. (https://www.dropbox.com/s/fdhhn9l1futgst9/Screen%20Shot%202017-04-08%20at%2010.22.02.png?dl=0)

I try to run the command line with a mask defined by me:

/Applications/BrainSuite16a1/bdp/bdp.sh t1.bfc.nii.gz –dwi-mask dti_brain_mask.nii.gz –tensor –FRT –FRACT –nii dti.nii -g dti.bvec -b dti.bval

and changing the dwi masking method:

/Applications/BrainSuite16a1/bdp/bdp.sh t1.bfc.nii.gz –dwi-masking-method intensity –tensor –FRT –FRACT –nii dti.nii -g dti.bvec -b dti.bval

but same error appear.

This is the outputlog link:

log

Do you have any suggestion?

Best Regards

Nicolò

[divarada]

Hi Nicolò,

Sorry for the late response.
This looks like a mask issue, even though your mask inputs are reasonable there could be processing steps changing the mask.
Here are a few things I can think of
1. Can you check if your t1.mask.nii.gz looks reasonable ?
2. Since the program crashed, can you check if BDP created a temporary mask file called epi_mask.nii.gz. BDP deletes these files but may be in this case it stopped before deleting. If you do find such a file, how does it look?
4. Run BDP to save intermediate png files using the flag –png-out or –p. This will save snapshots of the masks prior to this failure. Can you check the output <name>.approx_align.png. I have to warn you that this is a very memory intensive process.

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