I tried posting to the listserv but after logging in (successfully) it gives me the message, “Sorry, you are not authorized to post to the FSL list from the email address ([log in to unmask]) you entered in the login screen.”

 

Just in case you are able to respond here, I would like to bother you for a second regarding a problem we have encountered with one participant when using sienax. It appears the SNR or contrast ratio of the T1 image is poor, and we are unable to get a good BET result. When manually using BET, we get poor results even shifting the center point to accommodate the extra neck (and using –N command and adjusting the –f all over the place) and eyeballs that are not being stripped out. I can manually skull strip the data using the mask procedure in fslview and with fslmaths subtraction, but I do not know how to supply sienax with this self-created skull-stripped image. Is that possible?

 

Also, given that the main use we are getting from sienax is the normalization ratio (to use with other ROI’s we are comparing), I am guessing this normalization ratio may not be reliable given the difficulties with BET due to low SNR contrast. Is this assumption correct? Is there a way to see an output of what the algorithm identified as skull and not-skull (such as when the bet procedure produces the .html file:// to inspect with a web browser)? Should I trust the normalization ratio given that the script uses the non-skull stripped image for normalization based on skull?

 

Thanks in advance!

 

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Joseph Gullett, M.S.

Doctoral Candidate

Department of Clinical and Health Psychology

University of Florida