Aaron,

I have seen this problem before whereby the signal in the pericallosal artery is enhanced due to inflow artifacts (flow of fully magnetized protons into the imaging slice) which makes the artery indistinguishable from the corpus callosum.  This appears in some pulse sequences and not others, which leads me to believe that the problem can be prevented by using a well-designed 3D T1W sequence.  Unfortunately, there is not much that can be done after the fact other than manually correcting Yuki's output.

Babak

Babak, 

Thank you for your feedback! Is there a way that we could manually edit the output of Yuki? On the image there are multiple + symbols. Is there a way that we could adjust those to appropriately refit the margins to exclude the pericallosal artery? I provided an image to show an example of the problem that we have occuring. 

Thank you,

Aaron

Aaron,

In this case you have to manually draw corpus callosum (CC) and then run the yuki again. Here are the steps.

• Open the MSP file (in your case it may be named as cos002a1001_msp.nii) in an image-editing tool (ITKSNAP or FSLVIEW), where you can draw and save a segmentation. My preference is ITKSNAP.
• Draw the CC manually on the the MSP image and save the segmentation as a file cos002a1001_cc_corrected.nii (This corrected image should be a binary image)
• Now you can run the yuki with -cc option as follows:
• yuki -ppm -cc cos002a1001_cc_corrected.nii -i cos002a1001.nii -csv cos002a1001_corrected.csv -H
• The important option here is the -cc option that you should use to mention the corrected binary CC image.

I hope it will solve your problem. Please let me know if you still have any question.


Regards,


--
Asim

Thanks for the reply Asim.  I would add that in Step 2 you won't have to draw the CC manually from scratch.  You can load the imperfect cos002a1001_cc.nii generated by yuki into ITKSNAP as a segmentation image and mend it using brush tools and after you're happy with it save it as cos002a1001_cc_corrected.nii.

Babak