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, Paul
On 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 > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
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