Cannot save ROI...

Questions about Anatomist manipulation

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BarrettVictor7
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Joined: Wed Mar 30, 2016 1:03 am

Cannot save ROI...

Postby BarrettVictor7 » Thu Apr 07, 2016 9:55 pm

Hello, this is my first post here.

Whenever I try to save an ROI on a cortical mesh in the 3D window, Anatomist crashes. I'm using a windows computer and everything else seems to be fine. Does anyone know what I am doing wrong?

-Barrett

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riviere
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Re: Cannot save ROI...

Postby riviere » Mon Apr 18, 2016 2:10 pm

Hi,
The latest Windows version of Anatomist has problems (apparently with Qt dialog boxes, such as file dialogs), as we have mentioned it on the download page (http://brainvisa.info/web/download.html). We have not found the cause of the problem so far, it started to happen after the build with very different settings (different build system, different compiler, different versions of many libraries including Qt) so we don't really know what could cause the problem. I admit that as we are not working on Windows, we cannot spend much time in investigating this problem, unfortunately.
When we find a solution, we will release an update, but for now it's not fixed.
Denis

BarrettVictor7
Posts: 4
Joined: Wed Mar 30, 2016 1:03 am

Re: Cannot save ROI...

Postby BarrettVictor7 » Tue May 31, 2016 9:26 pm

Thank you for your reply, Denis. I finally got it running on Linux and have no issues with saving the ROI now.

Regards,
Barrett

BarrettVictor7
Posts: 4
Joined: Wed Mar 30, 2016 1:03 am

Re: Cannot save ROI...

Postby BarrettVictor7 » Tue May 31, 2016 9:45 pm

I have another ROI question!

Now that I am able to save ROIs on a cortical mesh, I need to know how to quantify the size of the ROI (which would allow me to determine the surface area of the ROI).

This is where I am at currently:

1) I use the constraint editor and surface paint tools to draw a ROI on the cortical surface and I save the texture.
2) Then I use the "fusion" button to make a TEXTURED SURF.

This is where I am stuck. I read over the Anatomist manual but could not find any further info on quantifying the ROI (texture). I'm sure it's something simple I'm missing, but it is starting to bug me that I can't figure it out. If it helps in describing what I am trying to do, I am trying to use the same general anatomical labeling methods of Altarelli et al., (2014) "Planum Temporale Asymmetry in Developmental Dyslexia: Revisiting an Old Question"

Thank you so much in advance,
-Barrett

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riviere
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Re: Cannot save ROI...

Postby riviere » Fri Jun 03, 2016 5:08 pm

Hi,
Well, there is no builtin tool in Anatomist to display the area of a surface ROI, that's right. It's relatively easy to write a little python script to do it from the mesh and ROI texture files. We only have a tool to measure the surface of a mesh, and another one to extract a portion of mesh for a ROI, so combining them is quite easy.

Code: Select all

#!/usr/bin/env python

from soma import aims

mesh_filename = 'mesh.gii'
roi_tex_filename = 'roi_texture.gii'
label = 1

mesh = aims.read(mesh_filename)
tex = aims.read(roi_texture_filename)
# in case tex is not int16 type
texint = aims.TimeTexture(dtype='S16')
texint[0].assign(tex[0].data())
sub_mesh = aims.SurfaceManip.meshExtract(mesh, texint, label)
# you can write the extracted mesh to check if it is the one you needed
# aims.write(sub_mesh[0], '/tmp/sub_mesh.gii')
area = aims.SurfaceManip.meshArea(sub_mesh[0])
print 'ROI area:', area

Denis

BarrettVictor7
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Joined: Wed Mar 30, 2016 1:03 am

Re: Cannot save ROI...

Postby BarrettVictor7 » Tue Jun 07, 2016 11:49 pm

Hi Denis,
Thank you very much for your providing me with information about the python script to quantify surface area of the ROI texture file. I appreciate your prompt reply.

Regards,
-Barrett


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