Overlay Preprocessed Images on AAL atlas

Submitted by joana on

Dear all,

I've  been using DPARSF v2.3 to extract AAL time courses from fMRI data. 

I have a couple of subjects that seem to show signal dropout in the frontal lobe.

I would like to overlay the AAL atlas on the preprocessed fMRI images of these subjects to see if the AALs' frontal labels are affected.

I tried to do this by overlaying the preprocessed fMRI images on the AAL template of DPARSF but the problem is they have different dimensions.

Could anyone tell me which is the best way to corregister the AAL template to the preprocessed fMRI images of DPARSF? 

Many Thanks,

joana

YAN Chao-Gan

Thu, 05/15/2014 - 18:53

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Hi Joana,

I am guessing you are using FSL view?

You have two ways:

1. Use MRIcroN or REST Slice Viewer to overlay the images, these images can be displayed even with different dimensions (they all are in MNI space).

2. Use REST->Utilities->Reslice Image to reslice the AAL template and you preprocessed functional image to the same resolution, and then you can use FSL view to overlay.

Best,

Chao-Gan

Thanks Chao-Gan.
I used MRIcroN to overlay the aal.nii atlas on the preprocessed images (normalized, smoothed, corrected for motion parameters, CSF and WM signals).

I saw that some of the aal labels were on top of small parts of the ventricles filled with CSF. Isn't this a problem for network analysis?

Kind regards,

Joana


2014-05-15 20:53 GMT+02:00 The R-fMRI Network <rfmri.org@gmail.com>:
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Commented by YAN Chao-Gan (YAN Chao-Gan)

Hi Joana,

I am guessing you are using FSL view?

You have two ways:

1. Use MRIcroN or REST Slice Viewer to overlay the images, these images can be displayed even with different dimensions (they all are in MNI space).

2. Use REST->Utilities->Reslice Image to reslice the AAL template and you preprocessed functional image to the same resolution, and then you can use FSL view to overlay.

Best,

Chao-Gan


Online version of this post: http://rfmri.org/comment/3087#comment-3087


Hi Joana,

Very sorry for the delayed response.

This is true. And some regions also overlap with white matter regions. Thus some researchers will first make a conjunction with a grey matter mask, and then use the revised AAL template to extract ROI time series.

Best,

Chao-Gan

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