Version 6.0 - ?h.white.preaparc vs. ?h.white for determining the need to edit brainmask.mgz, wm.mgz, add control points, etc.
Hi,
My main question to the 6.0 experts is:
Is the lh.white.preaparc close enough to the lh.white to determine whether editing is needed (brainmask.mgz, wm.mgz,control points) or do we need to run the full pipeline and get ?h.white?
Here's the reasoning behind this question. In previous versions of Freesurfer we have run -autorecon1 -autorecon2, then checked surfaces, made edits if needed, and then only after we were satisfied with the surfaces we ran -autorecon3. Primarily we have done this for 2 reason, first is to save processing time, on both the initial pass and running -autorecon2-cp or -autorecon2-wm. We also use this as a quality control method, in which ONLY subjects whose surfaces have been verified, have been through -autorecon3, those that haven't, don't have stats files, and thus can't get inadvertently included with finished data.
If ?h.white.preaparc doesn't topologically differ from the ?h.white could we use it for determining what edits to do?
if it does differ obviously we will have to run the whole pipeline.
Thank you in advance for your guidance.
Sincerely,
Mira
_______________________________________________
Mira Michelle Raman
Lead Scientific Programmer
The Center for Interdisciplinary Brain Sciences Research
Stanford University
401 Quarry Rd, Ste. 1356
The final white surface probably won't change much from the preaparc, so it could be used to find fairly large errors.
On 2/15/17 3:31 PM, Mira Michelle Raman wrote:
Hi,
My main question to the 6.0 experts is:
Is the lh.white.preaparc close enough to the lh.white to determine whether editing is needed (brainmask.mgz, wm.mgz,control points) or do we need to run the full pipeline and get ?h.white?
Here's the reasoning behind this question. In previous versions of Freesurfer we have run -autorecon1 -autorecon2, then checked surfaces, made edits if needed, and then only after we were satisfied with the surfaces we ran -autorecon3. Primarily we have done this for 2 reason, first is to save processing time, on both the initial pass and running -autorecon2-cp or -autorecon2-wm. We also use this as a quality control method, in which ONLY subjects whose surfaces have been verified, have been through -autorecon3, those that haven't, don't have stats files, and thus can't get inadvertently included with finished data.
If ?h.white.preaparc doesn't topologically differ from the ?h.white could we use it for determining what edits to do?
if it does differ obviously we will have to run the whole pipeline.
Thank you in advance for your guidance.
Sincerely,
Mira
Mira Michelle Raman
Lead Scientific Programmer
The Center for Interdisciplinary Brain Sciences Research
Stanford University
401 Quarry Rd, Ste. 1356
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas Greve -
Mira Michelle Raman