Hi Mark,
Thank you for your reply. I did what you said, but the results were nonsense.
I checked the Q_form/S_form of all the files. In all the files, Q_form is the
same as S_form. But, Q_form/S_form of each file is different from the other. I
ran "fslcpgeom file1 file2", when I view file2, it is not a brain image, but some
noise. I ran "fslcpgeom file1 file2 -d" , the result was brain image but is was
streched or sheard, since file1 and file2 have different dimentions.
Actually, I am using a registration framework before segmentation. Since my
original image has not the same orientation and dimention as MNI reference
template, the registered image has different dimention and orientation
compared to my original image. If I segment this registered image by fsl, the
segmented image indeed has different orientation and dimention compared to
the original image. When I use fsl for both registration and segmentation using
run_first_all command, I am not able to compare the results of the
segmentation, since the first segmented image (my registration and fsl
segmentation) has different dimention and orientation compared to the second
segmented image (fsl registration and segmentation). May be this helps you to
guide me more.
Best,
Siamak
|