Hi,
I have a problem when I try to calculated the network. Although I have many times to chang the direction, the BetT1 still always failed.
The detailed error has been described in the attached "log" file.
Thanks inadvance.
Good wish
Changhong

Dear,

I use the command of fsl 'fslswapdim' to change the direction of the image before brain extraction.
If you change the direction with mricron, then it is not compatible with fslswapdim, then it will run into error.

When you convert DICOM to NIfTI, mricron will produce 3 images.
Please the original one, don't use images with 'o' prefix or 'co' prefix.
Then it will not run into error.

And method:
You can do brain extraction yourself, and then remove the hool before f(skull_removal) in T1 options.
Then PANDA will not do brain extraction on your T1 image, and it will not run into error.

Best

Zaixu

Dear,
Thanks for your reply. I will try it again according to your directions.
Besides, I still not understand that how to use the "Test bvecs" tool when I used trackvis to fiber tracking. So if possible, can you send me the deatailed
manual.
Thanks again.
Best wishes,
Changhong Li

Dear,
 
  "Test bvecs" is used to check if the bvecs is correct for the fiber tracking.  As we all know, the bvecs determine the principal direction of the diffusion tensor and the local fiber direction is along the principal direction of the tensor. So in order to get the right fiber, we advice the uses check the bvecs before tractography. Specically, first open the 'V1' file by fslview, and then choose the "DTI dispay opthion"->"Display as"->"lines". and check the principle direction by linkng the local direction step by step in a specific location, such as corpus callosum.  It is importportant for both the deterministic and probabilistic tractography. But for the deterministic tractography, you also need to check the '.trk' file by opening the '.trk' by trackvis. And choose the corrected option of the "invert" and "Swap".
 
 
    Best Regards,
 
 Suyu