Hi,
It is fine to use RAS images, and normal that fslreorient2std would do nothing in this case. I would strongly recommend that you do *not* change the orientation information at all, since there is a very strong risk of swapping left and right in that case and you will not be able to tell. So I would delete the versions of the image where you’ve modified the orientation information and revert to the original images.
As for why the linear registration is failing, that is not clear to me.
It is concerning that the automatic cropping doesn’t work.
This could be due to the way that the images were acquired or some artifact.
The cropping part does struggle if there is any ghosting or artifacts in the S-I direction.
So I would turn the cropping part off when you use fsl_anat.
It would be helpful to have the exact command line call that you’ve used.
One possibility is that you have a problem with your brain extract, although from the image that looks OK.
Another possibility is problematic bias field or other artifacts.
But at the moment it would probably be useful to see what happens with a simple call to flirt.
So if you take your brain extracted image, do the following:
flirt -in your_brain_extracted_image.nii.gz -ref $FSLDIR//data/standard/MNI152_T1_2mm_brain.nii.gz -out test_flirt.nii.gz
Then tell us what these results are like.
All the best,
Mark
> On 14 Feb 2020, at 05:31, J <[log in to unmask]> wrote:
>
> Hello,
>
> Here is another update on my progress. Please please help. I can't figure out why my images are not aligning.
>
> I noticed that my T1 images where in RAS orientation when I opened up the headers. So, I changed the image data orientation to -X, Y+, Z +
>
> The FOV for the image 208 x 300 x 320
>
> Voxel size is 0.8 x .8 x .8
>
> When I changed the orientation, the image registration still failed!
>
> For some reason, the fslreorient2std part of the scrip didn't change any orientations, I had to do this manually in mango.
>
> Please help, I can't figure out why the images are not registering.
>
> ALso, I normalize the structural images to MNI 2 mm voxels
>
> Does any of this explain the failing registration?
>
> Thanks,
>
> J
>
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