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Author Topic:   vmp -> smp - drawing depth?
RSL
Junior Member
posted 09 October 2010 22:57     Click Here to See the Profile for RSL     Edit/Delete Message   Reply w/Quote
Dear Experts,
I have a vmp file and would like to overlay it on an (old) inflated surface. There is lots of activation in visual cortex in the vmp. However, when I load the mesh and overlay the vmp via (>meshes: surface maps->create smp) there appears a hole at the occipital pole - presumably because the inflated brain was slightly larger. Is there an easy way to either inflate the vmp a bit - or change the drawing depth?
Best, Ralf

JochenWeber
Administrator
posted 10 October 2010 03:58     Click Here to See the Profile for JochenWeber     Edit/Delete Message   Reply w/Quote
Dear Ralf,

First of all, to get a reasonably accurate display of the VMP on the surface, you need a (more or less) folded surface.

In case you only have the smoothed (inflated) surface, you should be able to change the sampling depth in the Mesh -> Create MTC dialog (where you set the range from which the VTC data is sampled). However, this will be only a rough estimate of the actual map that you would have gotten otherwise (and this should be noted).

Is there any way you can locate or re-create the folded surface?

/jochen

RSL
Junior Member
posted 10 October 2010 04:06     Click Here to See the Profile for RSL     Edit/Delete Message   Reply w/Quote
Hi Jochen,
thanks, that way it gets better.
Yes, I also have the folded (uninflated) version available. If I create the the vmp>smp on that one, it also is a little 'off' at the occipital pole. Is there anything I could improve here?

Best, Ralf.

JochenWeber
Administrator
posted 10 October 2010 15:57     Click Here to See the Profile for JochenWeber     Edit/Delete Message   Reply w/Quote
Hey Ralf,

Am I correct in assuming that the folded mesh you have corresponds to the anatomical/functional data in the VMR/VTC? If so, I'm not sure where the spatial mismatch (results being "off") comes from...

If you think that the entire mesh is shifted and/or has the wrong size, you could try to apply a global transformation (from the Mesh menu).

Could you be a bit more specific about what you mean by "a little off at the occipital pole"? If there are "holes" (missing data), this might be due to the fact that the underlying VTC/VMP has a too small bounding box (in which case you might have to re-create the VTCs from the FMRs using a larger bounding box). You can check this as the source of the problem by using the Selection tool in the surface module and click on one of the "empty" patches and note the coordinate in the status bar of BrainVoyager QX. Then use the File -> VTC properties dialog to check whether this coordinate is covered by the bounding box of your data...

Can't think of anything else at the moment...

/jochen

RSL
Junior Member
posted 06 November 2010 17:38     Click Here to See the Profile for RSL     Edit/Delete Message   Reply w/Quote
Hi Jochen,
the whole story is this: I have - because I didn't do classical GLM analysis but some other stuff - only the vmp-file containing values I'd like to visualize. The vmp is in TAL-Space and overlaying it on the Talairach-VMRs works fine. Now, to create nice figures, I'd like to illustrate my results on an inflated surface brain. To do so I loaded a single-subjects mesh and simply used the ">surface maps>create smp"-button, which pulls the vmps from the volumes-menu over to the meshes-window. However, this procedure doesn't allow me to tweak the sampling depth... As a result, although there are significant values at the occipital pole in with vmr/vmp, there is a hole at the occipital pole of the mesh/smp illustration. Is there any way how I may change the sampling depth when I create the smp from the vmp?

Thanks a lot,
Ralf.

JochenWeber
Administrator
posted 06 November 2010 19:09     Click Here to See the Profile for JochenWeber     Edit/Delete Message   Reply w/Quote
Hey Ralf,

The options you configure in the Meshes -> Mesh Time Courses... dialog on the "Create MTC from VTC" tab will also be used when you press the "Create SMP" button on the overlay SMPs dialog!

So, just load the VMP and SRF, then configure the sampling depths and then use the Create SMP function

Cheers,
/jochen

RSL
Junior Member
posted 08 November 2010 00:01     Click Here to See the Profile for RSL     Edit/Delete Message   Reply w/Quote
Dear Jochen,
that is exactly what I was looking for.
Thanks a lot, Ralf.

jakiman
Member
posted 24 August 2011 11:15     Click Here to See the Profile for jakiman     Edit/Delete Message   Reply w/Quote
Hey y'all!

Actually I am wondering what the range of "Create MTC options: Sampling VTC along mesh vertex normals" means. Does this compute an orthogonal vector inward and outward of my surface (the linked original surface, respectively) and then averages the values? Does this take the peak statistical value? I already searched the user's guide and the Getting Started Guide (as the last named describes the surface module)...

Glad for any help!

Cheers...

jakiman
Member
posted 31 August 2011 15:28     Click Here to See the Profile for jakiman     Edit/Delete Message   Reply w/Quote
...? Nobody knows what BV does?

JochenWeber
Administrator
posted 31 August 2011 20:18     Click Here to See the Profile for JochenWeber     Edit/Delete Message   Reply w/Quote
Well, I think it samples along the "normal vector" (using the coordinates of the vertices + from/to * normal vector, in 1mm steps) and then averages the data...

/jochen

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