Hi,

In order to visualize the resulting segmentation with AMIDE. Is it correct to put the probability map above the original T1 sequence, or should I make any transformation? Because in some cases, the images are rotated.


Laura

The images are in native T1 space. So no transformation is needed.
If the images are rotated, just change the deader info (load the image to matlab via nifti and check if the pmap's and T1's headers are the same -- I am not sure why this is happening for your case though)

And what is supposed to be different among the headers or what must be changed?

The headers must be the same. All the processing is done in native T1 space.
Hence all the intermediate and final output files should have the same header as the T1 image. If this is not the case, then the processing resulted in wrong outputs somewhere.
We never observed this mis-match in my evaluations -- and nothing of that sorts was reported earlier on this forum. However, I am mentioning this because, this is the only way the images will rotate -- and you mentioned that such rotation pblm did occur in your case.

Hi Laura, 

I happened to face the same issue right now and haven't solve the issue despite changes in cut values and trying different preproc bias values (60, 80, 100, 120,140). I was wondering if you managed to overcome this problem previously, and if so, may I ask how did you do it?

Best regards,
Jeremy

Apologies, I replied to the wrong thread earlier