Hello,

Thank you for making your toolbox available!

I have been having some difficulty successfully running the toolbox, however. We have a set of training images that we have used in the past for other WMH toolboxes. We converted the dicom files and then ran the T1/T2 nifti files from 9 pilot subjects through your toolbox, both as a complete batch and individually. Regardless, of the 9 pilot subject sets, only one will provide the 3 EV quantification values. The .txt files for the other 8 subjects are blank where there should be numbers. 
 
We have played around with the default settings, particularly the cleaning threshold, but still no luck with the other 8 sets.
Any recommendations? Is it possible that there may have been something we did not account for before running the sets through W2MHS (perhaps during the dicom-to-nifti conversion)?
 
Thank you!
 
- Jason

Hello.

I wonder if the output of WhyD_postproc is itself empty, i.e. the input the the quantification step are images with no/erroneous WMH detections ? Please check the 'pmap' and 'unrectify' files themselves to see if this is what is going on ?
Else, it might be the case that different images have different bias fields, which is unlikely but might cause these issues. If so, changing pre-processing hyper-parameters may help resolve the issue.
Please let me know if either of these solve the issue! Thanks for your interest.

Vamsi

Thank you!
 
It appears that we needed to reslice our images again before feeding it through the analysis.

Ok. Please let us know if there are any more issues.