Use AAL as atlas for data normalized in ICBM152_adult

[Rui Li]

Hi Frank,

I'm new to analyze neuroimaging, and my lab requires me to use dsi studio to turn dwi images into connectivity matrix using AAL as atlas. I tried these below on my own:

1. I copied AAL.* in atlas/dHCP_neonate to /atlas/ICBM152_adult and used the batch processing to generate FIB files choosing ICBM152_adult as template, but when I used Step T3: Fiber tracking & Visualization and choosing regions in AAL, the picture looked like the figure I provide below, that is the atlas space didn't cover the ICBM152_adult space. And I think this may be because the AAL atlas is normalized for the dHCP_neonate space.

2. I try to use command line to get connectivity matrix, but when I set the parameter --connectivity=AAL, one ERROR happened saying that AAL is not a built-in atlas, then I tried to directly use AAL.nii.gz by setting --connectivity=AAL.nii.gz, but this time annother ERROR happened saying AAL could not be used for fiber tracking and informed me that if the atlas is in MNI space, add "_mni" in the name, so I just simply turn AAL.* into AAL_mni.* and this time no ERROR happened. But I'm not sure whether this is right to change like this.

So, it will be grateful if you could inform me how to use command line to generate connectivity matrix using AAL as the atlas

Thanks!

Rui

[Frank Yeh]

I'm new to analyze neuroimaging, and my lab requires me to use dsi studio to turn dwi images into connectivity matrix using AAL as atlas. I tried these below on my own:

1. I copied AAL.* in atlas/dHCP_neonate to /atlas/ICBM152_adult and used the batch processing to generate FIB files choosing ICBM152_adult as template, but when I used Step T3: Fiber tracking & Visualization and choosing regions in AAL, the picture looked like the figure I provide below, that is the atlas space didn't cover the ICBM152_adult space. And I think this may be because the AAL atlas is normalized for the dHCP_neonate space.

The AAL in the dHCP_neonate cannot be used in the adult space. You may need to download the official AAL3 atlas and copy it to the ICBM152 folder

 

2. I try to use command line to get connectivity matrix, but when I set the parameter --connectivity=AAL, one ERROR happened saying that AAL is not a built-in atlas, then I tried to directly use AAL.nii.gz by setting --connectivity=AAL.nii.gz, but this time annother ERROR happened saying AAL could not be used for fiber tracking and informed me that if the atlas is in MNI space, add "_mni" in the name, so I just simply turn AAL.* into AAL_mni.* and this time no ERROR happened. But I'm not sure whether this is right to change like this.

Yes

Best regards,

Frank

So, it will be grateful if you could inform me how to use command line to generate connectivity matrix using AAL as the atlas

Thanks!

Rui

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[Rui Li]

I'm sorry, does 'Yes' mean that turning AAL.nii.gz into AAL_mni.nii.gz is right to use the atlas in dHCP_neonate for ICBM152_adult?

[Frank Yeh]

No. 

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[Rui Li]

Hi Frank, I followed your advice to use AAL3v1 as the atlas, but it did not work. The ERROR said "No strategy to align AAL3v1 with FIB. If AAL3v1 is in the MNI space, specify mni in the file name (e.g. region_mni.nii.gz). If not, use --other_slices to load the reference T1W/T2W to guide the registration.", what should I do?

Thank you.

[Frank Yeh]

Add mini to the file name.

Frank

To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/0fa511dc-fbfd-42ea-8e77-b903a6c6e882n%40googlegroups.com.