Dear Paul, I cannot see your attachment since I am only getting mail digest (without attachments) and the mail archive does not store attachments.
I do not know for which option of surface reposition your question refers to. But, I hope when you play with the tool, you will figure out, as I did. Also, what do you mean, what step you should start? In case of "volume based" reposition, when you click on "apply", you internally invoke customized mris_make_surfaces code on the surface you want to modify. The run takes several seconds and when it is finished, you will see the result of reposition. Then you inspect the surface and when you are satisfied, you save the modified surface (by the proper name, i.e. overwriting the original surface, you can save it by different name before using this tool to be able to get back). Then you should rerun remaining steps of recon-all, which for example in case of V6beta after repositioning pial surface means running recon-all -s my_subject -cortribbon -parcstats -cortparc2 -parcstats2 -cortparc3 -pctsurfcon -hyporelabel -aparc2aseg -apas2aseg -segstats -wmparc -balabels Antonin Thank you very much Antonin. I do appreciate it. Do I need to insert a vertex number or just the coordinates? Because when i clicked on the surface outside the pial (see screenshot) the vertex = N/A ( see screenshot). ALso, what step of recon-all should i start? (autorecon-2 or autorecon3)? Best, PaulOn Tue, Jan 10, 2017 at 3:52 PM, Antonin Skoch <a...@ikem.cz> wrote: > 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.html). > Use = directions and parameters to input. Thanks > Best, > Paul > > On 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 >
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