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scaling head size of user supplied brain structures in AtlasViewer  

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David Boas
Posts: 21
(@dboas)
Eminent Member
Joined: 2 months ago

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

17 Replies
Abigail Fiske
Posts: 11
(@afiske)
Active Member
Joined: 2 months ago

Hi David,

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? 

Many Thanks,

Abi

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2 Replies
Jay Dubb
(@jdubb)
Joined: 1 month ago

New Member
Posts: 1

@afiske I would be happy to take a look at this if you share your folder (zipped) on google drive or dropbox. Is that something that you are allowed to share? I cannot tell very much from only looking at the error. 

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Abigail Fiske
(@afiske)
Joined: 2 months ago

Active Member
Posts: 11

@jdubb Thanks for your offer to help. Following our talk at the end of the course last week, I shared the zipped folder with you on Dropbox. You should have received an email notification, but maybe it went to spam?

Since then, I have tried two things that allowed me to open AtlasViewer and see the default head and brain, where before (as I showed you on Zoom) this was not there.

1. Reorganised the structure of the data folder so that each subject had their own folder

2. Moved this main folder from my external hard drive to the main computer

 

I then used Meredith's advice on the previous comment about checking I was using the correct files. When using the files Meredith suggested, I no longer receive the original error when downsampling pial surface. This means that I can now import the MRI atlas successfully.

BUT, I've now encountered some new problems.

1. Sensitivity map I've generated using 'Generate MC Input' seems to have holes in it (see attached) - this does not go away when changing to 'none' and then back to 'sensitivity'

2. When I go to the Image Recon GUI, I receive a message saying "groupResults not loaded, Cannot do image reconstruction". My groupResults.mat file is in the folder but not being recognised. Could this be because I generated the groupResults file in Homer2? If so, is there a way to convert this to Homer3 format so I don't have to completely redo my preprocessing?

3. When projecting probe to cortex, I see a message "Warning: No cortical anatomical labels provided for this anatomy". I assume this is because it is an external MRI (from the Neurodevelopmental Database). Is there a way to import anatomical labels? @meredith maybe you have experienced this before?

I am very grateful for any help you can offer, thank-you.

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Meredith Pecukonis
Posts: 5
(@meredith)
Active Member
Joined: 2 months ago

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.

 

 

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David Boas
Posts: 21
(@dboas)
Eminent Member
Joined: 2 months ago

@afiske, this is one of those errors that is resulting from the input files. We can only figure it out if we have the same input files. I hope you can share the files with @jdubb

Thanks

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1 Reply
Abigail Fiske
(@afiske)
Joined: 2 months ago

Active Member
Posts: 11

@dboas Thanks David. I shared the folder with Jay on Dropbox last Thursday after discussing this with him on Zoom following the course. I've written another comment to Jay in reply to this thread but it is 'awaiting moderation', I think because I have attached an image, and so may not be showing up. 

Thanks,

Abi

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David Boas
Posts: 21
(@dboas)
Eminent Member
Joined: 2 months ago

@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.

I will let @jdubb or @mayucel respond to you about point 1

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