Dear Freesurfer experts,
We are about to do a mass reprocessing in our lab to update our FS 5.0 data to
the FS 5.1 and would like to do the following all in one run:
1) Preserve the wm and pial edits made in the 5.0 data in 5.1
From our understanding, using the command
--------------------------------------------
recon-all -all -s subjid
--------------------------------------------
will preserve our (wm and pial) edits when rerunning recon-all as long as
we do not use any -clear command. We've tested this command and it works.
However, we would also like to (go to #2)
2) Recreate the cerebellum in brainmask while preserving our edits.
We recently learned that the cerebellum should not be edited in
brainmask.mgz as this would affect the volumetric measurements of this region.
Since we are interested in this measurement, we want to recreate brainmask.mgz
when rerunning recon-all. I came across a post that suggested adding the option
-clean-bm and using brain.finalsurfs.manedit.mgz when rerunning reconall.
(http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20406.html). The
documentation on brain.finalsurfs.manedit.mgz suggests that this image
determines the final surfaces, regardless of what brainmask.mgz looks like,
which is why we could still use -cleanbm to recreate brainmask AND preserve our
edits.
However, when we ran the command
--------------------------------------------
recon-all -all -clean-bm -s subjid (with
brain.finalsurfs.manedit.mgz containing our edits in 5.0)
--------------------------------------------
the edits were only preserved in one subject that we tested. The edits did not
appear to be preserved at all in the other subjects. Does anyone have any
explanations for why edits were preserved in this subject but not the other
test subjects? Since running reconall takes a long time, we will really
appreciate it if there is a way to carry over the edits we made but also
recreate brainmask to get the cerebellum in one run. (Alternatively, we can add
voxels back to the cerebellum, but this method would be more time consuming.)
If brain.finalsurfs.manedit.mgz is indeed used to determine the final surface,
would be possible to make all edits in brain.finalsurfs.manedit.mgz instead of
brainmask.mgz? It seems more efficient and intuitive to make edits in one place.
We would like to move forward with our reprocessing and are looking forward to
your responses.
Best,
Vy T.U. Dinh
Research Assistant, Neurological Sciences
Rush University Medical Center
Phone: (312) 563-3853
Fax: (312) 563-4660
Email: vy_d...@rush.edu<mailto:vy_d...@rush.edu>
Vy T.U. Dinh
Research Assistant, Neurological Sciences
Rush University Medical Center
Phone: (312) 563-3853
Fax: (312) 563-4660
Email: vy_d...@rush.edu<mailto:vy_d...@rush.edu>
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