Dear Paul,
I could chime in with my current limited experiences with this tool (using V6beta version of freeview). Maybe they could be helpful for you.
Most straigthforward is using "edit coordinate":
Select the surface you want to edit. Select tools-reposition surface - edit coordinate. With shift + left mouse button click on the surface to pick particular vertex. Manually enter new coordinates of the vertex. Save surface to store edits. This is prohibitively time consuming in case of large error, so it is usable only in case of small errors.
However, you can try to use combination of "edit coordinate" and "smooth". By smoothing you can nudge some area of adjacent vertices to desired position.
I was partially successful also with using reposition surface - volume based - coordinate: With shift + left mouse button select particular vertex In "volumes", load volume according to what you want to reposition the surface. With shift + ctrl + left mouse button click at the coordinate you want to reposition the surface to. Save surface to store edits.
Regarding the parameters: The "size" textfield determine the extent of the vertex neighbourhood which would be repositioned. Do not use too large value since then the behaviour is unpredictable, in my case the maximal resonable value is around 5. I am not sure about "sigma" parameter, maybe it has to do something with the smoothing (of the underlying volume?), however in my case altering this parameter did not change behaviour much. Also, the "gradient direction" in my case did not change much, in many cases it produced identical result regardless of the gradient direction selected.
In most cases, I was not satisfied with the result of the reposition, the particular vertex moved to desired position, however position of adjacent vertices did not make sense, mostly the surface got very jagged and irregular, with worsening of the position in areas where the position was good previously, etc. However, subsequent using of "smooth" usually improved the shape and after many iterations I finally arrived to desired shape of surface.
I also tried to study the relevant source code to learn the behavior of this tool and the significance of the parameters, but it is very complicated to me to comprehend (so far..).
Note that after using this tool you should rerun remaining code of recon-all
ReconAllDevTable https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable (for development version) would tell you which particular steps should be rerun. Please note that in case of rerun of recon-all from start you will lose all modifications of surfaces you achieved using this tool.
And, particularly, many surface errors can be corrected by editing the volume (particularly wm.mgz, brainmask.mgz, aseg.mgz) or adding control points to the white matter. Large errors of ?h.white (and subsequently ?h.pial) can be caused of wrongly corrected topological defect (which you can diagnose by inspecting ?h.orig.nofix and ?h.orig). In that case editing of wm.mgz or aseg.mgz would help to correct the issue. I also came across the error when ?h.white was cut off the particular gyrus near midline, which was caused by erroneous labeling of cortex in aseg.mgz (gyrus was attributed to contralateral hemisphere). Editing of aseg.mgz by assignment of the gyrus to correct hemisphere corrected the error.
Also, altering several of global parameters of mris_make_surfaces, as listed for example here
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg37990.html
could help you to get satisfactory results (however, the altering of these parameters should be done in my opinion for all subjects in the study to avoid bias).
Regards,
Antonin Thanks bruce for your response. Since there is no documentation, how can i use it because I seen trends on the forum where it was suggested to use reposition surface ( e.g. https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-October/026117.ht...). Use = directions and parameters to input. Thanks Best, PaulOn Tue, Jan 10, 2017 at 12:42 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
Hi Paul
sorry, this is something that Ruopeng put together for me to mess around with - there isn't any documentation
cheers Bruce
On Tue, 10 Jan 2017, miracle ozzoude wrote:
Hello Freesurfer, I would like to learn how to use the reposition surface
tool in freeview. Specifically, what parameters to enter in the gui (see screenshots). Is there any documentation on how to use it if not, can someone with experience work me through it. Thank you. best, Paul