[caret-users] AAL 3D rendering

Donna Dierker donna.dierker at sbcglobal.net
Mon Mar 21 13:43:54 CDT 2016


On Mar 21, 2016, at 12:44 PM, João Vicente Dornas <joaodornas at gmail.com> wrote:

> Dear Rouhi,
> 
> thanks for the prompt response.
> 
> In fact, I did that already, but the Freesurfer oversample the image to 1 mm. 
> 
> I had two problems. In one attempt, when I use mri_vol2surf to create my labels/annotation files from AAL.nii my subcortical regions Pallidum and Hippocampus disappeared.
> 
> Later on I solved this problem, and I did the rendering, showing all 90 ROI colorful, but a few vertexes are empty, and therefore black on the top of the brain.

See this page:

http://brainvis.wustl.edu/help/pals_volume_normalization/

These were procedures for the PALS surfaces, but similar steps were used to get colin in various stereotaxic spaces.  I chose SPM2, because I guessed it was the best fit for AAL's MNI space.  Maybe the original (unwarped) colin would be better, but I'm not sure I can still find that.  These were in the caret distribution.

This figure illustrates how different mapping can be with different versions of MNI space:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2045137/figure/F1/

… due to methodological (warping) differences.

> I was wondering if there is somewhere a surface file for the Colin27 brain but sampled on 2mm MNI152, because my AAL volume is MNI152 2mm.

This surface should align with both 1mm and 2mm volumes in MNI space.  There are multiple vertices within each cubic 2mm voxel, so if you map the volume to the surface, many vertices will have the same value.

http://brainvis.wustl.edu/help/pals_volume_normalization/spm5_captures/

The second link shows the surface contours overlaid on the volume.  These captures show PALS subjects rather than colin, but they illustrate what the surface contour looks like on a 1mm T1.  If you downsampled the T1 to 2mm, it would just look blockier -- the alignment wouldn't change.

> Or maybe I could do the recon-all from Freesurfer on Colin27 T1 image but WITHOUT changing the dimensionality. I mean, without registration and spatial normalization to another space.

Yeah, I wonder if David has the original, unwarped colin surface.  I did look in two places I thought it might be, but no luck.

> Maybe I am doing something wrong. But so far I had the plots, but with these two drawbacks.
> 
> Do you know for instance a way to load the "spec" file from Colin from Caret on FreeView?

The only way I know is to export to GIFTI (surf.gii), which you can do in caret5 (File: Save Data File: Gifti Surface file) while the colin surface is loaded in the main window.  But the only specs I could find were all warps of some sort (afni, 711-2B, SPM99, SPM2).  The unwarped surface exists somewhere, I'm sure -- just don't know how to find it.

Joern Diedricksen may have it, as he was using the colin cerebellar surface for SUIT; however, I'm not sure he'd have if for the cerebral hemispheres. :(

> 
> thanks for the help,
> 
> 
> João V. Dornas
> 
> On Mar 21, 2016, at 17:36, Rouhollah Abdollahi <roohy466 at gmail.com> wrote:
> 
>> Dear Joao, 
>> 
>> The simple way is to do the segmentation with the Colin27 brain that will create all the surfaces in Freesurfer. The following link is the Colin27 brain:
>> 
>> http://packages.bic.mni.mcgill.ca/mni-models/colin27/mni_colin27_1998_nifti.zip
>> 
>> and if you know freesurfer do the recon-all then you have all surfaces that you want.
>> 
>> Best regards
>> Rouhi
>> 
>> 
>> 
>> Institut für Neurowissenschaften und Medizin (INM-3)
>> Forschungszentrum Jülich
>> Leo-Brandt-Straße
>> 52425 Jülich, Germany
>> Tel: +49 2461 61-9324
>> 
>> 
>> 
>> On Mon, Mar 21, 2016 at 4:51 PM, João V. Dornas <joaodornas at gmail.com> wrote:
>> Dear Friends,
>> 
>> I need a surface compatible with AAL volume with the dimensions from MNI152 2mm (91x109x91).
>> 
>> I learned that Caret has the “spec” files from Colin27, which was the brain reference for AAL.
>> 
>> Does someone knows a straightforward way to load this surface on FreeView from FreeSurfer ?
>> 
>> Thanks for the help,
>> 
>> -- 
>> João V. Dornas
>> Phd student in Neuroscience
>> Cognitive Biology Group, Institute of Biology
>> Otto von Guericke University, Magdeburg
>> Germany
>> 
>> 
>> _______________________________________________
>> caret-users mailing list
>> caret-users at brainvis.wustl.edu
>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>> 
>> 
>> _______________________________________________
>> caret-users mailing list
>> caret-users at brainvis.wustl.edu
>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
> _______________________________________________
> caret-users mailing list
> caret-users at brainvis.wustl.edu
> http://brainvis.wustl.edu/mailman/listinfo/caret-users




More information about the caret-users mailing list