help > Adding ICBM atlas to WFU pickatlas toolbox
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May 28, 2015  12:05 PM | Georgia O'Callaghan - Trinity College Dublin
Adding ICBM atlas to WFU pickatlas toolbox
Hi there!

I am a final year PhD student & I am currently doing VBM analysis. I wanted to add a white matter atlas to my WFU pickatlas toolbox but I am having a few problems!

I chose the ICBM DTI-81 atlas and downloaded it from here; 

i added it to the 'MNI_atlas_templates' folder & the information to the 'master_lookup.txt' file and, as a result, the atlas now appears in the main WFU pickatlas toolbox window in the drop down menus for atlases down at the bottom, beside the coordinates function. I can enter coordinates & press go & it will give me the subregion where those coordinates are located so it seems to be recognising the atlas here.

HOWEVER! I really wanted to use this atlas to create WM ROIs for a SVC analysis and the atlas is not appearing in the pink 'HUMAN ATLAS' tab on the left hand side of the window. Does anyone know why this might be the case? I tried adding the same files to the 'legacy' folder within 'MNI_atlas_templates' and I noticed that all of the other atlases have .mat files too - could the reason my atlas is not appearing be that I am lacking this file? There was no .mat file in the ICBM atlas I downloaded from the link above.

Or if anyone new of an alternative WM atlas I could use - I'm pretty much up for anything at this point!

Any help would be greatly appreciated,

Georgia O'Callaghan
PhD Candidate, Psychology
Trinity College Dublin
May 28, 2015  12:05 PM | Benjamin Wagner - UT Southwestern Medical Center
RE: Adding ICBM atlas to WFU pickatlas toolbox
Hi Georgia,
  Did you happen to follow the instructions and tips found in the Developer's Guide:  This describes all the ins and outs of adding an atlas to the pickatlas.

If you still have questions/problems after working through that please let me know.

Ben Wagner
May 29, 2015  08:05 AM | Georgia O'Callaghan - Trinity College Dublin
RE: Adding ICBM atlas to WFU pickatlas toolbox
Thanks - I had actually been looking at the 'users' manual & didn't realise that there was a separate developer's manual!

I have been following the steps from the developer's manual today and I am stuck on orientation - my atlas file is oriented such that the front of the brain is pointing towards the right and the MNI_T1.nii is facing the left!

Doing manual reorientation in 'display' in SPM12 doesn't work as I need to flip or invert the image rather that just rotate it (which results in the image being upside down!). I have also tried 'reorient' in the batch window & it says for a left-right orientation you enter the vector [-1 0 0 0; 0 1 0 0; 0 0 1 0; 0 0 0 1] but I want to orient it from right to left - any tips? (also when I try their left-right vector on a left facing image, e.g. the MNI_T1.nii, it looks exactly the same afterwards when I do a check reg?

I have attached the atlas I am trying to reorient - just in case you wanted to view it. 

Thank you in advance for your help!
Jun 20, 2017  02:06 PM | Andrew Merluzzi - University of Wisconsin - Madison
RE: Adding ICBM atlas to WFU pickatlas toolbo
Hi Georgia and company, hope all is well!

I'm having the exact same issue right now - my ICBM white matter template (nifti_MNI_ICBM_DTI_81_WMPM.nii) is in the opposite anterior/posterior orientation as the MNI_T1.nii. Did you ever figure out how to solve this problem a couple years ago? 

I'm also having trouble reslicing the ICBM image to match the T1 image in terms of dimensions. I've consulted the pickatlas developer's manual, and my two images are in different dimensions (see attached image for the matlab output). All that the manual says is: "If you receive a message similar to the one below, then you should reslice your images to the template. Be sure to use nearest neighbor interpolation in your reslice."

Maybe someone has solved these issues? Or figured out a better way to create ROI's using the ICBM white matter atlas than within the WFU-pickatlas? Any and all advice would be appreciated!

May 22, 2020  09:05 AM | Lukas Van Oudenhove
RE: Adding ICBM atlas to WFU pickatlas toolbox
Hi Ben & colleagues,

This thread and the developers manual are really helpful when adding custom atlases to WFU Pickatlas.

I am trying to add the new AAL3 atlas based on the steps in the developers manual, and my only problem is that the voxel size for my AAL3.nii file is [-2 2 2] compared to [2 2 2] for the MNI_T1 template file provided with Pickatlas, causing the dimensions to disagree.

This is probably easy to fix (does it have anything to do with flipping), but could you please point me to the right solution?

Thanks very much in advance!

Best wishes,