[f.ramezani]

Dear Brainsuite team,
How do you expand inner cortex (after doing topology correction)to outer boundary for making pial surface? I mean what’s the algorithm?

[yeunkim]

Hi,

The method for pial surface generation is described here:

http://brainsuite.org/processing/surfaceextraction/pial/

Please let us know if you have more questions.

Best,
Yeun

[f.ramezani]

Hi,
I would appreciate your help with a question; how can i obtain the volume after Pial surface stage or indeed obtaining the GM,CSF and WM labels after the topology correction and wisp removal stages? I’ve seen a contour view showing the inner and OUTER boundaries of the cortex in BrainSuite_Workshop_2017 file ( Pial surface title) but i can’t find if there are any features or output files in the app which contains the labels or volumes after Pial surface stage.
Looking forward to hearing from you.
Thank you

[Anand Joshi]

The white matter mask after topology correction is stored in subject.dewisp.mask.nii.gz files.
The WM GM and CSF tissue types are stored in subject.pvc.label.nii.gz. Since at MR resolution, most voxels contains a mixture of tissues. The partial tissue fractrions are stored in subject.pvc.frac.nii.gz. These are before topology correction, but depending on your application, these might serve the purpose. Please refer to the following link for more information.
http://brainsuite.org/processing/surfaceextraction/pvc/

[f.ramezani]

Yes i know these outputs, but they don’t contain the outer cortex; which is obtained by expanding the inner cortex( inner cortex is obtained by applying the topology correction ad wisp removal) in pial surface stage.

[Anand Joshi]

Hi BrainSuite does not currently store a mask corresponding to the pial surface, since at voxel resolution, such a mask does not retain sulcal depths in the pial surface. Can you please explain a bit more on what you are trying to do, so that we can see if there an output that will serve the purpose? thanks,

[f.ramezani]

Well i’m looking for the outer boundary of the cortex label which is obtained by expanding the inner cortex in pial surface stage.( In BrainSuite topology correction stage affects the inner boundary not the outer; so the outer boundary is defined in making the pial surface). Can you please have a look at BrainSuite_Workshop_2017_GUI_David_Shattuck file; pial surface part ? Am wondering how the volume is shown there after the pial surface.

[Anand Joshi]

Are you trying to visualize the cross section of surface and slices?
In order to see the pial surface on the cross section of the volume, you can load:
1. Load brain image and pial surfaces in BrainSuite.
2. Move the green cross hair to where you want to see the cross section in the image.
3. Go to surface view and press x, y or z depending on which cross section you want to see. You can try these keys multiple times to toggle cross sections.

As mentioned earlier, there is no volumetric mask for the pial surface since it is at much higher resolution than the WM surface. Can you please let me know what you want to do so that we can figure out how to best do it within BrainSuite.

[f.ramezani]

I’m looking for the volume of pial surface.I’ve seen the volume for pial surface in the workshop file which i mentioned. So I’m wondering how it’s done while there are no masks as you said.

[Anand Joshi]

I assume you are referring to BrainSuite_Workshop_2017_GUI_David_Shattuck.pdf, right?
You can obtain the screen shown in slide 45 by following the instructions above. If that is not what you are looking for, can you please let me know the slide number?

[f.ramezani]

Yes i see that’s it. Are there any options to correct the volume due to the surface?
Thank you for your respond.

[Author]

Posts