Dear DTIPrep experts,
  I am trying to run brainmasking from the DTIPrep Pipeline modifying the defaults. It turns that braimaksing does not seem to strip skull. Using the "Slicer" flag it seems to run ok according to QCReport, but image QCed still has skull. Using any of the FSL options ends up with image math failure in the QCReport.
  Any solution? I've checked the protocol paths and everything seems to be where it should be . Usually I leave the "Brainmask_MaskedImage" field empty but I also have added a subject-specific mask in this field and it does the same.

Thanks in advance.

The Slicer brain masking is not the best (which is likely why there's still skull in the image,I assume that something was removed?). For the FSL option, our tool ImageMath is used. Unfortunately there are other tools that have also an ImageMath binary (e.g. ANTs or Rview), so you need to make sure that the path to DTIPrep's ImageMath folder has to be before the paths of the other tools.

I usually use bet with IDWI

Martin

Hi,
  After troubleshooting some issues with the paths of the tools, it turns that brainmask does not work because he cannot find subj_IDWI.nrrd. I noticed that when I check "compute the DTI" (usually I uncheck this last step), a subj_IDWI.nrrd file is generated. Does it make sense?

 Also, when trying to do visual inspection, it only saves the changes to a subj_QCed_VC.nrrd file if the DTI tensor had previously been computed. Does that make sense also or it is just something related to my computer?

Thanks

Hi Martin,

I am also having a similar issue. The rest of DTIprep runs smoothly, but I keep getting brains that are not properly skull stripped. I am getting the following error message: 


Brain Mask

Brain Mask FSL
/Path/To/ImageMath
ImageMath cannot be started. 

Any ideas what issue this may be? Also, you mention that the ImageMath folder has to be before the paths of other tools - what do you mean by this? Does ImageMath need to be a directory above other tools?

Thank you for your help!
Giorgia
Originally posted by Martin Styner:

same issue with brain masking. 

FSL_bet path

shall I set it to my fsl folder: /usr/local/fsl or bet2 folder: /usr/local/fsl/bin/bet2

Any comments?

Originally posted by Yingying Wang: to the bet2 binary and thus the second of your options