Hi Ruthi, that is possible in several ways. The question is what images do you want to map and for what purposes. For easy transfer of control points or edits, it should be OK, or external data that you created and want to take along (fMRI or other images). But if you plan to map images that are part of the stream and then further process it, that may be problematic (again because of potential biases that may sneak in).
So to go from old base to new you can a) register the base images (e.g. norm.mgz) and then use the transform to map stuff (I think this would do the trick: mri_robust_register --mov <oldnorm.mgz> --dst <newnorm.mgz> --lta old2new.lta --mapmov old2new.mgz --sat 6 you can then use mri_convert or vol2vol to map stuff using the lta (make sure to use nearest neighbor interpolation for label maps and cubic interpolation for images). In mri_convert -rt cubic or -rt nearest b) you can concatenate the existing transform from a cross sectional to the old base (actually the inverse) with the new transform from that time point to the new base. The problem here is (although it should not matter much) that you again need to select a specific time point and that is again a potential source of bias. Also if you accidentally select a time point with motion artifacts or other problems this could be unstable. So I recommend option a). Best Martin > On Oct 11, 2015, at 6:20 AM, Adam, Ruth <ruth.a...@med.uni-muenchen.de> wrote: > > Thank you Martin! > In that case, is there an easy way to register volumes marked on the old 2 > time-points base to a new 3 time-points base? > Have a nice week. > > Best, > ruthi > > Message: 3 > Date: Thu, 8 Oct 2015 20:18:47 +0200 > From: Martin Reuter <mreu...@nmr.mgh.harvard.edu > <mailto:mreu...@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] longitudinal stream: adding a time point > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Message-ID: <4599ef79-c8d8-4448-ade3-3941caa18...@nmr.mgh.harvard.edu > <mailto:4599ef79-c8d8-4448-ade3-3941caa18...@nmr.mgh.harvard.edu>> > Content-Type: text/plain; charset="us-ascii" > > Hi Ruthi, > > it is possible to add time points retrospectively without re-creating the > base. However this will likely induce a processing bias, as the 3rd time > point is treated differently from the first two. How big that is going to be > nobody knows (it depends on your data and on the number of time points). The > more time points are in the base, the less of a problem it should be, but > with only 2, adding a 3rd may not be good. > > Here is how you can do it > recon-all -long <tpNsubjid> <longbasesubjid> -addtp -all > but I recommend against it. If you do, you definitely need to describe this > in the publication as it is not the standard procedure. You should also run > several cases (maybe ones that did not need edits) separately with 3 time > points in the base and test for differences. > > The re-creation of the base is the biggest problem in unbiased longitudinal > processing, but necessary to ensure all time points undergo exactly the same > treatment. > > Best, Martin > >> On Oct 8, 2015, at 4:40 PM, Adam, Ruth <ruth.a...@med.uni-muenchen.de >> <mailto:ruth.a...@med.uni-muenchen.de>> wrote: >> >> Dear all, >> >> We have run recon-all longitudinal stream on two time points and now have an >> additional time point we would like to integrate. >> Since edits and analysis were already done using the 2 time points template, >> we would like to avoid creation of a new template (by combining all time >> points) and instead register the third time point to the pre-existing >> template. >> What is the best way to do so? Is there a way to force recon-all to use a >> specific template? >> >> Many thanks! >> >> Best, >> ruthi
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