scaling head size of user supplied brain structures in AtlasViewer
A participant brought up a question in our 2020 course on this topic that you can see here
The basic question is as follows:
We would like to use AtlasViewer to reconstruct an image of brain activation – I have found infant MRI Atlases of the brain and the head from 10.5 month old infants (on John Richard’s Neurodevelopmental MRI Database). Our question is, would it be possible to use the head measurement data that we have recorded (circumference, LPA to RPA) if we are missing the Cz to Nz distance? I.e. will AtlasViewer automatically adjust the Cz to Nz distance to fit our parameters? If not, will we just use all 3 default parameters in AtlasViewer? And will these be for an adult head?
For sure AtlasViewer allows you to provide head circumference, Nz-Iz distance, and A1-A2 distance to scale the Colin brain atlas to fit your give subject's head size. In theory, you can also do this for a head MRI structure that you provide yourself. So, for instance, if you provide an infant MRI atlas for a 10.5 month old that you got from John Richard, then you should be able to re-scale the head size to fit head circumference, Nz-Iz distance, and A1-A2 distance that you provide. BUT, this needs to be tested. We have never done this.
It would be great if you can try this out and report here how it works. This would be a great topic for a future webinar and we would be happy to work with you to make sure this can work. Keep us posted in this thread. Thanks
Thank-you for your response on this matter. I'm currently in the process of trying this out, but I'm running into an error fairly early on when importing the MRI anatomy into AtlasViewer. I select my files for brain (file name: ANTS10-5Months3T_brain_atlas.nii) and head (file name:ANTS10-5Months3T_head.nii), and when I press submit this runs for a little while but then produces an error in MATLAB when downsampling plial surface (see attached image).
Any advice on what might be causing this error?
hi! i've used John Richard's atlases before and thought i'd leave this info here in case it is helpful.
Re: using John's atlases in AtlasViewer, you should use the “…head.nii.gz” and a “…head_brain.nii.gz” files in the "head" folder. John wrote that "this brain was extracted from the head with fsl bet2 and other methods. This head and brain are in the same coordinate space, same dimensions, etc."
Not sure if this is causing your error, but figured I would share to make sure you're using the correct files.
@afiske I approved the post... curious about that... I thought I turned off moderation.
I now see your post above.
Re point 2, I think you have to re-do the analysis in homer3 to get the new group results file... but hopefully that is doesn't require much manual effort. You should be able to use the same processing stream and set it running.
Re point 3, we do really want anatomical labels for imported MRIs... many people ask for this. Hopefully it is something we can get to in the future.