Hi Derin,
as far as I can see your description is correct. Note: in your screenshots the base is shown in a different slice (but I believe that you probably scrolled through the image to make sure no skull is included in a different slice).
Actually in this situation, the long runs should not need editing, if the brainmask.mgz in the base is accurate. It is mapped to the longitudinals and used as a brainmask there.
Have you tried editing the brainmask in the longitudinal directory (or if done in the cross sectional you can simply copy it over as it is in the same space). Then pass -long .... and -autorecon2-pial -autorecon3? Not sure what this does or if it works, but it's worth a try. If it does not work, I guess we need to look at this data, to see what is going on.
Currently I am working on testing out the 5.0 fix and some other possible improvements...
Best, Martin
On Fri, 2010-09-03 at 13:54 -0500, Derin Cobia wrote:
Based on our understanding of the longitudinal pipeline for 4.5, image edits for the -long runs come mostly from the template/base subj (with an optional flag for CPs to be copied from the template; http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg13256.html, http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12895.html). In addition, our assumption is that pial edits will come via the template, as the -long brainmask, is a result of masking the -long T1.mgz by the template brainmask.mgz (which itself is the norm_template.mgz, a combination of every time point's norm.mgz [which is pre-edit stage]).
We've run into an issue where our -long runs are still in need of pial editing, despite edits having been done to both the cross sectional and template runs (see attached). However, it's also our understanding that we should not edit the -long runs and try to re-run (using -autorecon2-pial -autorecon3), as this will pollute the correction for intrasubject variation (per communication from Martin). How would you recommend to proceed? Thanks.
-Derin
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