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Hi,

It looks like your images are in different spaces.
You need to get them into the same space first.
You can do that by applying one of the transformations from the registration, using applywarp.
Something like:
  applywarp -i test -r dtifit_FA --premat=str2diff.mat -o test_diff
Here I am assuming that test is in the structural space and not in the diffusion space, but dtifit_FA is in the diffusion space.  If that assumption is not correct then you'll need to change the above command appropriately.

If you think they are already in the same space then look at the output of fslinfo in the images and see if their sizes (dims and pixdims) are the same or not, as this might indicate something different from what you expect.

If you need more help then have a look at the FSL Course practical on registration.

All the best,
Mark


On 25 Aug 2017, at 09:28, Isobel French <[log in to unmask]> wrote:

Dear Experts,

I am trying to extract FA and MD values using the fdt_paths file. What is the right procedure for this? Are the following steps below correct?

a)Threshold and/or binarize it to create a mask, then multiply with the dti_FA file.

b)Then use fslstats to extract the mean FA value from your result.

However, when I try I get the following error:

neuros-iMac-3:AHM/23954/C1PPNL2] neuro% fslmaths test.nii.gz -mul dtifit_FA PPN_FA

WARNING:: Inconsistent orientations for individual images in pipeline!
          Will use voxel-based orientation which is probably incorrect - *PLEASE CHECK*!

Image Exception : #3 :: Attempted to multiply images/ROIs of different sizes
libc++abi.dylib: terminate called throwing an exception
Abort

[neuros-iMac-3:AHM/23954/C1PPNL2] neuro%

How do I correct the orientation between the images? By the way the fdt_paths file was obtained via a structural image using the strr2diff.mat.

Please advise. Tqvm.

Best regards,


Isobel French

Researcher
Neurosurgery Research Unit, Division of Neurosurgery
Department of Surgery, Faculty of Medicine
University Malaya

Suite 15 T8-4a 
Level 4, Menara Timur
University of Malaya Medical Center

016-7937605
03-79493138