Dear experts,

I am a new user of DTIPrep and I am having some problems when I set the BRAINMASK_bCheck option to Yes in the protocol.

In the QC Report it is written: 

Brain Mask FSL
/home/rita/Desktop/DTIPrep-1.2.11/bin/ImageMath crashes.

I checked all the paths and if the files are executable. Everything looks fine to me.

Also, I am having some errors during dtiprocess and dtiestim (picture attached). Only _Baseline, _DTI and _IDWI files are created.


Thanks in advance!
Rita

ImageMath: This might be an issue due to ANTS having also a tool/executable called ImageMath (and of course, the two tools are not compatible, even though they do similar tasks). If you have the ANTS ImageMath in your PATH, then that could be the source of your issue. Solution would be to either remove ANTS from your PATH when running DTIPrep or ensure that the DTIPrep path is mentioned before the ANTS path.

dtiestim seems to have worked, though not dtiprocess. Best turn off writing the frobenius norm image in the DTIPrep protocol (probably a version issue on dtiprocess).

Martin
Originally posted by ritagv: