Hello- I'm trying to add the AAL3 atlas to PickAtlas in order to use it for masking. I've followed the developer's manual to change the .txt files accordingly but MATLAB is throwing the following errors:

ans =

struct with fields:
atlasname: 'aal 3'
subdir: 'AAL3_atlas_templates'
lookupfile: 'master_lookup.txt'
dispimage: 'MNI_T1.nii'
licensefile: 'info.html'
conversionfile: 'atlas_space_conversions.txt'
conversion: [1×2 struct]

Unrecognized function or variable 'Region'.

Error in wfu_get_atlas_list>lookup (line 117)
if ~(isempty(Region))

Error in wfu_get_atlas_list (line 31)
[A] = lookup(atlas_path, T, I, O, N);

Error in wfu_pickatlas>Initialize (line 214)
[Atlas]=wfu_get_atlas_list(handles.data.SelectedAtlasType.subdir, ...

Error in wfu_pickatlas (line 55)
Initialize(fig, [], handles, varargin{:})

Error in spm (line 954)
evalin('base',xTB(i).prog);

Error while evaluating UIControl Callback.

I've attached a file of how I've changed the text files- I've tried everything I can think of, any help would be appreciated!

Thanks!

Update- I added tabs instead of spaces to the AAL3 .txt file and the error is removed. 

However, new problem- 

!!! DISABLING ATLAS due to mat/dim mismatch: aal3

Has anyone had success with using PickAtlas' MNI_T1 template with the AAL3 atlas? Or does the image need to be re-sliced/otherwise modified?

Also fixed- for anyone who it might help- co-reg (re-slice) the AAL3 nii image to the MNI template provided by PickAtlas (3x3x3mm)

Dear Breanne

I saw your question, and I want to know do you able to add the AAL3_170 to pickatlas?

Neda

Hi Neda-

yes I was able to after altering 2 issues. 1) the text file provided by AAL3 needed tabs instead of spaces between the brain region label and number (see other pickatlas text files for examples) to remove the MATLAB error and 2) the T1 image provided by pickatlas (or SPM) are 3x3x3mm voxels, where AAL3 provides nii files with 1 and 2mm. Here you can go to Co-reg (estimate & re-slice) and co-register the AAL3 .nii file with the T1 file from pickatlas (depending on what voxel size you want- you can co-reg to the 3mm T1, or co-reg the T1 to the AAL3 atlas image at 2 or 1 mm) . 

hope that helps,
Breanne

Thanks dear Breanne.


This error can occur when I call pickatlas:

ans =

struct with fields:
atlasname: 'aal3'
subdir: 'AAL3_atlas_templates'
lookupfile: 'master_lookup.txt'
dispimage: 'MNI_T1.nii'
licensefile: 'info.html'
conversionfile: 'atlas_space_conversions.txt'
conversion: []
Dot indexing is not supported for variables of this type.
Error in wfu_pickatlas>Initialize (line 331)
handles.AtlasMenuString=
wfu_implode({Atlas(1:end-1).Name},'|');
Error in wfu_pickatlas (line 55)
Initialize(fig, [], handles, varargin{:})
Error in spm (line 954)
evalin('base',xTB(i).prog);
Error while evaluating UIControl Callback.

Hi, thanks for your share, and I met some different problems, I add the name to master_lookup.txt, and take relevant files(AAL3v1.nii and AAL3v1.txt) into the MNI_atlas_templates, open the wfu_pickatlas in matlab, it could work, but the atlas that I want not appear, I don't know how to handle it, could you give me some suggestions