help > loading MNI images onto freesurfer images
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Nov 12, 2018  01:11 AM | Luca Fornia - University of Milan
loading MNI images onto freesurfer images
Dear all,
I have fMRI activation coming from SPM.
I want to overlap the activation onto the FSaverage template using Surf Ice. The picture seems consitent with the others template MNI152.
However, as you suggest, analyse data with SPM and use FSaverage as a template could create some mismatch.
To overcame as possible tha gap between template, i follow your instructions "Loading MNI images onto FreeSurger images". All the conversion process run correctly. However, when I try to visualize with the Surf Ice the converted fMRI data onto the FSaverage I get an error:
GIFTI OVERLAY HAS A DIFFERENT NUMBER OF VERTICIES THAN THE BACKGROUND MESH. I can visualize the converted data just on the lh.pial.surf.gii file, that I actually is not reason why I converted the file.
Do you any suggestions?
All the best
Luca
Nov 12, 2018  04:11 AM | Chris Rorden
RE: loading MNI images onto freesurfer images
Can you explain which approach you are using
  • If you attempt to load the SPM NIfTI file directly you will need to use the BrainMesh_ICBM152.gii template, as FreeSurfer FSaverage images are in a different space.
  • If you convert the SPM NIfTI file to a mesh, you will also end up with results better aligned to the BrainMesh_ICBM152.gii.
  • You could also warp the SPM NIfTI to freesurfer space. This uses Darren Price's mni2fs. If you follow this approach, you can either follow the steps on the Surfice wiki or Darren's quick start guide. I suspect you are using this approach. While this does put the images in FreeSurfer space, note that it asks whether you want to have the data mapped to the left hemisphere or right hemisphere. You would overlay these on the corresponding left (lh.pial) or right (rh.pial) hemisphere meshes, not the bilateral brain image. This would explain your issue, as you can not load the unilateral vertices on top of a bilateral mesh. If you want this, I suspect you could update Darren's code to support bilateral meshes (and you could issue a pull request to share your changes with the community).
Nov 12, 2018  04:11 AM | Luca Fornia - University of Milan
RE: loading MNI images onto freesurfer images
I m using the Darren Price's mni2fs. My fMRI activation is whole brain activation, howevere i specified during conversion that I want to select just the left hemisphere. The mismatch that I get is 175409 verticies vs 163842. The procedure I think is correct, but probably the FSaverage template could have less number of vertex respect to what set by default in the Darren script. what do you think?
Luca
Nov 12, 2018  05:11 AM | Chris Rorden
RE: loading MNI images onto freesurfer images
Precisely. If you use Darren's tools you should overlay the maps on the surfaces he provides.
Nov 12, 2018  06:11 AM | Luca Fornia - University of Milan
RE: loading MNI images onto freesurfer images
I attached a pdf with a brief example. On the left I'm trying to load the converted fMRI file onto the FSaverage (that is my goal!). See the error.
On the right side, the same fMRI converted file was suitable for a template coming from Darren's tool, but that actually is not the FSaverage. I'm a bit confusing, mni2fs convert fMRI activation from normal MNI152 to be compatible with FSaverage, but finally the converted file is not suitable for FSaverage due to a mismatch in vertex numbers. is it correct?
Moroever, if I load the original fMRI file (no mni2fs conversion) directly on the FSAverage, it looks quit precisely, more than the results on Darren's template. Please, you already face such kind of mismatch before, do you have any sugestions?
Thaks again
Luca
Attachment: example.pdf
Nov 12, 2018  06:11 AM | Chris Rorden
RE: loading MNI images onto freesurfer images
Exactly, your background image is FSaverage, but Darren's tool is computing the vertices for the meshes he provides in
 https://github.com/dprice80/mni2fs/tree/master/surf
If you use one of his images, for example rh.pial.surf.gii instead of FSaverage, it will work. Darren's template has a different number of vertices than FSaverage. Darren's code is open source, so feel free to modify it for your desired template.
Nov 12, 2018  07:11 AM | Luca Fornia - University of Milan
RE: loading MNI images onto freesurfer images
Thank you very much.
Luca