image registration problem

[Shengwei Zhang]

Hi Gary,

I'm using DTITK to register tensor images. But when I run the affine
registration, I found that the background of the image changed from 0
to 0.001. The input image is in float type and non-brain area are set
to 0.

Also, when I run the diffieo registration, everything seems to go well
except that some messages like:

/usr/local/bin/dtitk/scripts/dti_diffeomorphic_sn: line 35: [: :
integer expression expected
/usr/local/bin/dtitk/scripts/dti_diffeomorphic_reg: line 28: [: :
integer expression expected
/usr/local/bin/dtitk/scripts/dti_diffeomorphic_sn: line 46: [: :
integer expression expected

occurred for some subjects. The results seem reasonable. Just
wondering if it is working as expected.

Thanks in advance.

Shengwei

[hui Zhang]

Hi Shengwei,

DTI-TK indeed changes the background to an isotropic tensor with diagonal terms equal to 0.001 and off-diagonal ones to 0.0.  This is important for the log-euclidean tensor interpolation.  

The value 0.001 itself is arbitrary, just so that it is significantly smaller than the real diffusivity values seen in tissue.  Incidentally, I came to realize that this also makes adhering to the choice of diffusivity unit of DTI-TK very important.  Affine registration can fail if the proper diffusivity unit is not set, as found here:

http://groups.google.com/group/dtitk/browse_thread/thread/6649839b917cbe05#

Thanks for pointing out the warning messages.  They are indeed harmless, just mean that you didn't set up the DTITK_USE_QSUB variable.  Nevertheless, I added a note on this in the Installation page just now.

http://groups.google.com/group/dtitk/web/installation

Gary