Dear FSL experts,
Like many, I'm trying to register into the standard space scans with extensive lesions. So far, I have followed the instructions that was previous given in another email, and they have been working well. Basically, I have created a mask by manually drawing a ROI over the stroke area, inverted the mask with the following command "fslmaths originalmask -mul -1 -add 1 -thr 0.5 -bin invertedmask", and registered using FLIRT and putting my inverted mask into the weighting option as an input.
Like I said, it has been working well for 2 subjects, but didn't for 2 others. In the latter case, when I look at the data in FSLview, the image is no longer aligned: it has suffered a severe rotation making the axial view now the coronal view with a 90 degree rotation, and so on for the other views.
Now, I also tried to do the registration with a betted anatomical scan. Here the orientation is fine, but the registration itself doesn't look good.
Any suggestions would be useful.
Thank you in advance,
Kindest regards,
Jean-Sebastien
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