in may cases it is very, VERY hard to paint the apropriate subset of nodes, if the geometry is truly complex.
one must use many little borders instead of one large one. even if you do get all the nodes painted, smoothing operations won't work out in these situtations. this isn;t a niave question, to which the standard solutions apply. I've spent probably hundreds of hours on this issue. it is very hard. It may well only come in in ex-vivo. caret has problems with painting by border enclusure, and with smoothing, when the geometry of the set of nodes is really complex, convex, concave, and folder UNDER itself (but still homeomophic to a sphere) I thought you guys probably knew that. On 21 July 2012 18:00, <[email protected]> wrote: > Send caret-users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://brainvis.wustl.edu/mailman/listinfo/caret-users > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of caret-users digest..." > > Today's Topics: > > 1. Re: part of a surface (Donna Dierker) > 2. Re: part of a surface (David Van Essen) > 3. Re: Freesurfer Surface and Volume are not in register when > shown in Caret (Pablo Polosecki) > 4. Re: Freesurfer Surface and Volume are not in register when > shown in Caret (David Van Essen) > > > ---------- Forwarded message ---------- > From: Donna Dierker <[email protected]> > To: "Caret, SureFit, and SuMS software users" < > [email protected]> > Cc: > Date: Fri, 20 Jul 2012 18:18:51 -0500 > Subject: Re: [caret-users] part of a surface > On Jul 20, 2012, at 5:06 PM, Colin Reveley wrote: > > > Is it possible to inflate just part of a surface? I doubt it. > > Inflate, I don't think so; smooth -- definitely. You can use paint to > select nodes, then constrain the smoothing that way. > > I don't have caret handy, but look at the options under Surface: Geometry. > > > > > I am experiencing my usual agony in smoothing the medial wall of my > surfaces. as you can see, the medial wall region is very complicated and > hard to make into a smooth sheet, with big convexities, big concavities, > and loads of smaller ones. > > > > Actually I can't even make a crossover free sphere from this one. > > > > yes, I can change my segmentation by hand. but at the risk of losing > accuracy. altering the segmentation is normally what I do. aside from being > a bit dodgy, it's also very laborious. > > > > another way is to smooth it piecemeal, but this example is probably too > far gone for that. > > > > can't I just suck those nodes out of there?! > > > > best, > > > > Colin > > <capture.jpg>_______________________________________________ > > caret-users mailing list > > [email protected] > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > ---------- Forwarded message ---------- > From: David Van Essen <[email protected]> > To: "Caret, SureFit, and SuMS software users" < > [email protected]> > Cc: > Date: Fri, 20 Jul 2012 18:20:54 -0500 > Subject: Re: [caret-users] part of a surface > Colin, > > First, assign your medial wall nodes to a paint (label) identity. If you > haven't done this already, it can be done using Draw Borders and filling in > the ROI, starting with a very inflated or spherical surface. If you have > crossovers in your medial wall, this might take some futzing and an extra > round, but I think it can be made to work. > > Then use Surface: Surface ROI: Node Selection: Paint, and select the > medial wall nodes, but starting with the midthickness configuration in the > main window. > Then use ROI Operation: Smoothing, and choose parameters that yield > adequate smoothing. > > If you have crossovers initially, you can probably re-inflate and > re-project to the sphere starting with the partially smoothed medial wall. > > Good luck. > > David > > > On Jul 20, 2012, at 5:06 PM, Colin Reveley wrote: > > > Is it possible to inflate just part of a surface? I doubt it. > > > > I am experiencing my usual agony in smoothing the medial wall of my > surfaces. as you can see, the medial wall region is very complicated and > hard to make into a smooth sheet, with big convexities, big concavities, > and loads of smaller ones. > > > > Actually I can't even make a crossover free sphere from this one. > > > > yes, I can change my segmentation by hand. but at the risk of losing > accuracy. altering the segmentation is normally what I do. aside from being > a bit dodgy, it's also very laborious. > > > > another way is to smooth it piecemeal, but this example is probably too > far gone for that. > > > > can't I just suck those nodes out of there?! > > > > best, > > > > Colin > > <capture.jpg>_______________________________________________ > > caret-users mailing list > > [email protected] > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > ---------- Forwarded message ---------- > From: Pablo Polosecki <[email protected]> > To: "Caret, SureFit, and SuMS software users" < > [email protected]> > Cc: > Date: Fri, 20 Jul 2012 19:27:48 -0400 > Subject: Re: [caret-users] Freesurfer Surface and Volume are not in > register when shown in Caret > Hi Donna, > > Your excerpts were really inspiring. Many many thanks. I got them > finally well-alligned. > One more question: My volumes and surfaces have a nominal resolution > of 1mm but they are actually .5mm (This means we scan at .5 mm > resolution but we have to trick FreeSurfer into thinking we scan at > 1mm because it doesn't display things correctly with other resolution > values). Does this matter for working in Caret and registering to F99? > Or do I have to rescale all my files back to .5mm? > > Thanks! > Pablo > > On Fri, Jul 20, 2012 at 5:12 PM, Donna Dierker <[email protected]> > wrote: > > Sorry I'm not as familiar with that script, but I am familiar with > scripts we use for importing human freesurfer files into Caret. Hopefully > these excerpts might help: > > > > #Find c_ras offset between FreeSurfer surface and volume and generate > matrix to transform surfaces > > MatrixX=`$FreeSurferInstallationDirectory/bin/mri_info --cras > $InputFreesurferSubjectDirectory/mri/orig.mgz | cut -f1 -d' '` > > MatrixY=`$FreeSurferInstallationDirectory/bin/mri_info --cras > $InputFreesurferSubjectDirectory/mri/orig.mgz | cut -f2 -d' '` > > MatrixZ=`$FreeSurferInstallationDirectory/bin/mri_info --cras > $InputFreesurferSubjectDirectory/mri/orig.mgz | cut -f3 -d' '` > > Matrix1=`echo "1 0 0 ""$MatrixX"` > > Matrix2=`echo "0 1 0 ""$MatrixY"` > > Matrix3=`echo "0 0 1 ""$MatrixZ"` > > Matrix4=`echo "0 0 0 1"` > > MatrixCRAS=`echo "$Matrix1"" ""$Matrix2"" ""$Matrix3"" ""$Matrix4"` > > > > for Surface in white pial ; do > > caret_command -surface-apply-transformation-matrix > $OutputRootDir/$Subject/$InitialMeshDirectory/$Subject.$Hemisphere."$Surface"_orig.initial_mesh.coord.gii > > > > $OutputRootDir/$Subject/$InitialMeshDirectory/$Subject.$Hemisphere.initial_mesh.topo.gii > $OutputRootDir/$Subject/$InitialMeshDirectory/$Subject.$Hemisphere."$Surface"_orig.initial_mesh.coord.gii > -matrix $MatrixCRAS > > done > > > > Also, it might matter which volume you use (e.g., orig.mgz vs others). > > > > > > On Jul 20, 2012, at 3:55 PM, Pablo Polosecki wrote: > > > >> Hi Donna, > >> > >> I tried converting to RAS (this converst the heder information, which > >> apparently Caret does use) and the data matrix. The problem is the > >> same: the axes are correct (i.e., R points to the right side, D is > >> dorsal, etc). However, the surface and the volume still don't match in > >> Caret just like before. The issue seems to be some sort of offset in > >> the center of coordinates (when I click on the surface, the > >> highlighted points seem to be on a sensible medio-lateral and > >> dorso-ventral position. The problem is that the highlighted voxel is > >> too posterior in the volume view). Does this make sense or hint to a > >> possible solution to you perhaps? Worst case scenario, I could eyeball > >> how big this translation offset is, open the volume in matlab and have > >> it translate the data matrix. That way, it would roughly look okay, > >> but perhaps there is a more graceful way of handling this. > >> Thank you again, > >> Pablo > >> > >> On Fri, Jul 20, 2012 at 3:14 PM, Donna Dierker < > [email protected]> wrote: > >>> Be aware that what AFNI/Caret calls LPI, Freesurfer calls RAS. ;-) > >>> > >>> Can you try having mri_convert write the volume out as RAS, instead of > >>> LPI? Freesurfer will read the header and do the right > flipping/rotating > >>> so that the surface aligns with it. Freesurfer did the right thing, > as it > >>> understands that label. But that understanding is not what other > software > >>> desires, in this case. (At least that's my read of your problem.) > >>> > >>> I think the axes don't need rotating anymore, but all three need > flipping. > >>> > >>>> Dear List, > >>>> > >>>> I successfully completed the FS-to-F99 tutorial and now I am trying to > >>>> reproduce the steps with my own FreeSurfer dataset. According to the > >>>> FS-to-F99 tutorial, I need to have my mri volume "into LPI > >>>> orientation" and "the surfaces and volume need to be in register". My > >>>> original volume is in LIA orientation and is in register with my > >>>> surface, in the sense that when I open both on FreeSurfer's tkmedit > >>>> they are well-aligned to each other (I don't know how to check that > >>>> they are in register otherwise). If I use this surface and volume on > >>>> FS-to-F99's Stage-1 script and open the resulting spec file with > >>>> Caret, the volume's axes are wrong and the points on the surface and > >>>> in the volume don't match (I see this by clicking on the surface and > >>>> looking what is then highlighted on the volume window). If I transform > >>>> the volume into LPI orientation (using FreeSurfer's mri_convert > >>>> command), the new volume has the desired orientation and, > >>>> interestingly, it is still well-aligned to the surface in FreeSurfer's > >>>> tkmedit. However, when I use this surface and volume on the FS-toF99's > >>>> Stage-1 script, the volume and the surface are still not well-aligned, > >>>> even though the axes labels are now correct. How could I fix things so > >>>> that my volume and surface are in register when shown in Caret? > >>>> > >>>> Thank you very much, > >>>> Pablo > >>>> _______________________________________________ > >>>> caret-users mailing list > >>>> [email protected] > >>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users > >>>> > >>> > >>> _______________________________________________ > >>> caret-users mailing list > >>> [email protected] > >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users > >> _______________________________________________ > >> caret-users mailing list > >> [email protected] > >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > _______________________________________________ > > caret-users mailing list > > [email protected] > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > ---------- Forwarded message ---------- > From: David Van Essen <[email protected]> > To: "Caret, SureFit, and SuMS software users" < > [email protected]> > Cc: > Date: Fri, 20 Jul 2012 20:25:22 -0500 > Subject: Re: [caret-users] Freesurfer Surface and Volume are not in > register when shown in Caret > Pablo, > > Registration to F99 should not be impacted by issues of scaling. (For > example, it doesn't affect our monkey-to-human registration despite large > scale differences.) But if you want to rescale just for the sake of > veridical representation, you can use > caret_command -surface-apply-transformation-matrix or Surface: Tranform: > Scale within Caret. > > David > > On Jul 20, 2012, at 6:27 PM, Pablo Polosecki wrote: > > > Hi Donna, > > > > Your excerpts were really inspiring. Many many thanks. I got them > > finally well-alligned. > > One more question: My volumes and surfaces have a nominal resolution > > of 1mm but they are actually .5mm (This means we scan at .5 mm > > resolution but we have to trick FreeSurfer into thinking we scan at > > 1mm because it doesn't display things correctly with other resolution > > values). Does this matter for working in Caret and registering to F99? > > Or do I have to rescale all my files back to .5mm? > > > > Thanks! > > Pablo > > > > On Fri, Jul 20, 2012 at 5:12 PM, Donna Dierker <[email protected]> > wrote: > >> Sorry I'm not as familiar with that script, but I am familiar with > scripts we use for importing human freesurfer files into Caret. Hopefully > these excerpts might help: > >> > >> #Find c_ras offset between FreeSurfer surface and volume and generate > matrix to transform surfaces > >> MatrixX=`$FreeSurferInstallationDirectory/bin/mri_info --cras > $InputFreesurferSubjectDirectory/mri/orig.mgz | cut -f1 -d' '` > >> MatrixY=`$FreeSurferInstallationDirectory/bin/mri_info --cras > $InputFreesurferSubjectDirectory/mri/orig.mgz | cut -f2 -d' '` > >> MatrixZ=`$FreeSurferInstallationDirectory/bin/mri_info --cras > $InputFreesurferSubjectDirectory/mri/orig.mgz | cut -f3 -d' '` > >> Matrix1=`echo "1 0 0 ""$MatrixX"` > >> Matrix2=`echo "0 1 0 ""$MatrixY"` > >> Matrix3=`echo "0 0 1 ""$MatrixZ"` > >> Matrix4=`echo "0 0 0 1"` > >> MatrixCRAS=`echo "$Matrix1"" ""$Matrix2"" ""$Matrix3"" ""$Matrix4"` > >> > >> for Surface in white pial ; do > >> caret_command -surface-apply-transformation-matrix > $OutputRootDir/$Subject/$InitialMeshDirectory/$Subject.$Hemisphere."$Surface"_orig.initial_mesh.coord.gii > >> > $OutputRootDir/$Subject/$InitialMeshDirectory/$Subject.$Hemisphere.initial_mesh.topo.gii > $OutputRootDir/$Subject/$InitialMeshDirectory/$Subject.$Hemisphere."$Surface"_orig.initial_mesh.coord.gii > -matrix $MatrixCRAS > >> done > >> > >> Also, it might matter which volume you use (e.g., orig.mgz vs others). > >> > >> > >> On Jul 20, 2012, at 3:55 PM, Pablo Polosecki wrote: > >> > >>> Hi Donna, > >>> > >>> I tried converting to RAS (this converst the heder information, which > >>> apparently Caret does use) and the data matrix. The problem is the > >>> same: the axes are correct (i.e., R points to the right side, D is > >>> dorsal, etc). However, the surface and the volume still don't match in > >>> Caret just like before. The issue seems to be some sort of offset in > >>> the center of coordinates (when I click on the surface, the > >>> highlighted points seem to be on a sensible medio-lateral and > >>> dorso-ventral position. The problem is that the highlighted voxel is > >>> too posterior in the volume view). Does this make sense or hint to a > >>> possible solution to you perhaps? Worst case scenario, I could eyeball > >>> how big this translation offset is, open the volume in matlab and have > >>> it translate the data matrix. That way, it would roughly look okay, > >>> but perhaps there is a more graceful way of handling this. > >>> Thank you again, > >>> Pablo > >>> > >>> On Fri, Jul 20, 2012 at 3:14 PM, Donna Dierker < > [email protected]> wrote: > >>>> Be aware that what AFNI/Caret calls LPI, Freesurfer calls RAS. ;-) > >>>> > >>>> Can you try having mri_convert write the volume out as RAS, instead of > >>>> LPI? Freesurfer will read the header and do the right > flipping/rotating > >>>> so that the surface aligns with it. Freesurfer did the right thing, > as it > >>>> understands that label. But that understanding is not what other > software > >>>> desires, in this case. (At least that's my read of your problem.) > >>>> > >>>> I think the axes don't need rotating anymore, but all three need > flipping. > >>>> > >>>>> Dear List, > >>>>> > >>>>> I successfully completed the FS-to-F99 tutorial and now I am trying > to > >>>>> reproduce the steps with my own FreeSurfer dataset. According to the > >>>>> FS-to-F99 tutorial, I need to have my mri volume "into LPI > >>>>> orientation" and "the surfaces and volume need to be in register". My > >>>>> original volume is in LIA orientation and is in register with my > >>>>> surface, in the sense that when I open both on FreeSurfer's tkmedit > >>>>> they are well-aligned to each other (I don't know how to check that > >>>>> they are in register otherwise). If I use this surface and volume on > >>>>> FS-to-F99's Stage-1 script and open the resulting spec file with > >>>>> Caret, the volume's axes are wrong and the points on the surface and > >>>>> in the volume don't match (I see this by clicking on the surface and > >>>>> looking what is then highlighted on the volume window). If I > transform > >>>>> the volume into LPI orientation (using FreeSurfer's mri_convert > >>>>> command), the new volume has the desired orientation and, > >>>>> interestingly, it is still well-aligned to the surface in > FreeSurfer's > >>>>> tkmedit. However, when I use this surface and volume on the > FS-toF99's > >>>>> Stage-1 script, the volume and the surface are still not > well-aligned, > >>>>> even though the axes labels are now correct. How could I fix things > so > >>>>> that my volume and surface are in register when shown in Caret? > >>>>> > >>>>> Thank you very much, > >>>>> Pablo > >>>>> _______________________________________________ > >>>>> caret-users mailing list > >>>>> [email protected] > >>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users > >>>>> > >>>> > >>>> _______________________________________________ > >>>> caret-users mailing list > >>>> [email protected] > >>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users > >>> _______________________________________________ > >>> caret-users mailing list > >>> [email protected] > >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users > >> > >> > >> _______________________________________________ > >> caret-users mailing list > >> [email protected] > >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > > _______________________________________________ > > caret-users mailing list > > [email protected] > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > >
_______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
