Thanks Donna! You gave me enough information for me to figure out the problem in several directions.
I let you know later if I solved the issue. Many thanks! Cheers! João V. Dornas > On Mar 21, 2016, at 19:43, Donna Dierker <donna.dier...@sbcglobal.net> wrote: > >> On Mar 21, 2016, at 12:44 PM, João Vicente Dornas <joaodor...@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 <roohy...@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 <joaodor...@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@brainvis.wustl.edu >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>> >>> >>> _______________________________________________ >>> caret-users mailing list >>> caret-users@brainvis.wustl.edu >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> _______________________________________________ >> caret-users mailing list >> caret-users@brainvis.wustl.edu >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
