Hi Andreas,
It is extremely different to get good registrations manually (as you
have to work in 3D and you only see 2D planes), and you'll most
certainly not be able to achieve the accuracy of an automated method
(especially not of robust_register/robust_template, which are pretty
damn accurate, if you ask me :-). So I strongly advise against that
(unless you want to show that manual registration messes things up).
Now to answer your question: You could theoretically use
mri_robust_template to construct the template from your three inputs.
Then stop the stream, mri_concatenate_lta your transform from image_i to
image_0 with the transform that roubst_template gives you from image_0
to template. Then reconstruct the template using mri_robust_template
with --ixform (passing these transforms) and --noit to not iterate, this
will recreate the median template image.
Also replace the lta files in the base/mri/transforms with the new ones
that you got from the concatenation, so that the base and later the long
streams know.
Resume the recon-all stream.
This, obviously, has never been tested and requires some looking into
recon-all to make sure you do things right. E.g. you need to use the
norm.mgz of the inputs and make sure you overwrite the norm_template or
similar (the one that get's created in the base step).
Best, Martin
On 04/09/2014 05:35 AM, Andreas Werner wrote:
Dear Experts,
i am analyzing a longitudinal study (three timepoints for each
participant).
I manually register the second and third timepoint to the first
timepoint using freeview.
Question: Is it possible to use these manually created transformation
matrices to create a common template that is equidistant from all
three timepoints to balance interpolation ? If so, which commands do I
need to use ?
(As I understand mri_robust_template does this, but I would like
to use manual rather than automatic registration.)
Many thanks in advance!
Andreas
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Martin Reuter, Ph.D.
Instructor in Neurology
Harvard Medical School
Assistant in Neuroscience
Dept. of Radiology, Massachusetts General Hospital
Dept. of Neurology, Massachusetts General Hospital
Research Affiliate
Computer Science and Artificial Intelligence Lab,
Dept. of Electrical Engineering and Computer Science,
Massachusetts Institute of Technology
A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129
Phone: +1-617-724-5652
Email:
mreu...@nmr.mgh.harvard.edu
reu...@mit.edu
Web : http://reuter.mit.edu
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