On 2/10/2020 11:20 AM, Christian O'Reilly, Dr wrote:

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Hi,

How can I convert a LTA file type 0 (LINEAR_VOX_TO_VOX) to a type 1 (LINEAR_RAS_TO_RAS)?

Use lta_convert

Also, given a volume x.nii.gz and a file y.lta, how do I obtaijn z.nii.gz as the original volume x.nii.gz transformed according to y.lta? I tried with mri_vol2vol but somehow I could not figure a way to make it work properly.

Should be mri_vol2vol --mov x.nii.gz --reg y.lta --target y.nii.gz --o x-in-y.nii.gz

Also, given a volume containing a full head and a second volume containing a stripped skull, what is the best approach with FreeSurfer to transform the brain so that it is properly registered with the full head (using an affine transform)? I tried many different ways to get it done with mri_robust_register and also with bbregister, but somehow I could not get a satisfactory result (i.e., I could always get a much better fit by hand using freeview)....

Need more info about the nature of the data. where did it come from? are they two different scans? differnt sesssions?

Thank you!

Christian

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