Hello Antonin, Apologies, I forgot to send them. This is the email and the vertex coordinates. For vertex, it shows N/A hence, not sure what value i need to enter in the vertex section of edit coordinates in the reposition surface tool. Thank you Best, Paul
On Tue, Jan 10, 2017 at 4:54 PM, Antonin Skoch <a...@ikem.cz> wrote: > 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, > 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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