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help > Adding MCALT Atlases to WFU_PickAtlas Toolbox in SPM12
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Apr 2, 2020 10:04 PM | Alexandria Jensen - University of Colorado Denver Anschutz Medical Campus
Adding MCALT Atlases to WFU_PickAtlas Toolbox in SPM12
Hello,
I am attempting to add the atlases from the NITRC MCALT download into the WFU_PickAtlas Toolbox for SPM12. I have followed the developer's manual instructions from the toolbox but, when I try to access the atlases, I get the following error:
I have tried nearly everything I can think of to fix this error but nothing is working unfortunately. Any assistance would be greatly appreciated!
Alexandria Jensen
I am attempting to add the atlases from the NITRC MCALT download into the WFU_PickAtlas Toolbox for SPM12. I have followed the developer's manual instructions from the toolbox but, when I try to access the atlases, I get the following error:
ans
=
struct with
fields:
atlasname:
'MCALT HUMAN ATLAS'
subdir: 'MCALT_atlas_templates'
lookupfile: 'master_lookup.txt'
dispimage: 'MCALT_T1.nii'
licensefile: ''
conversionfile: ''
conversion: []
subdir: 'MCALT_atlas_templates'
lookupfile: 'master_lookup.txt'
dispimage: 'MCALT_T1.nii'
licensefile: ''
conversionfile: ''
conversion: []
Unrecognized
function or variable 'Region'.
Error in
wfu_get_atlas_list>lookup (line 117)
if ~(isempty(Region))
if ~(isempty(Region))
Error in
wfu_get_atlas_list (line 31)
[A] = lookup(atlas_path, T, I, O, N);
[A] = lookup(atlas_path, T, I, O, N);
Error in
wfu_pickatlas>Initialize (line 214)
[Atlas]=wfu_get_atlas_list(handles.data.SelectedAtlasType.subdir, ...
[Atlas]=wfu_get_atlas_list(handles.data.SelectedAtlasType.subdir, ...
Error in
wfu_pickatlas (line 55)
Initialize(fig, [], handles, varargin{:})
Initialize(fig, [], handles, varargin{:})
Error in spm
(line 946)
evalin('base',xTB(i).prog);
evalin('base',xTB(i).prog);
Error while
evaluating UIControl Callback.
I have tried nearly everything I can think of to fix this error but nothing is working unfortunately. Any assistance would be greatly appreciated!
Alexandria Jensen
Apr 3, 2020 01:04 PM | Christopher Schwarz - Mayo Clinic
RE: Adding MCALT Atlases to WFU_PickAtlas Toolbox in SPM12
I've never used that toolbox; you may need to get support from its
authors.
Based on the error message my guess is it is not reading the atlas region names correctly. There is no master_lookup.txt in MCALT, so this should probably be changed to MCALT_ADIR122.txt. Once that's done, I have no idea whether that file is in the format that WFU_PickAtlas expects to read (probably, it's not, and you will have to convert it somehow).
Good luck,
Chris Schwarz
Based on the error message my guess is it is not reading the atlas region names correctly. There is no master_lookup.txt in MCALT, so this should probably be changed to MCALT_ADIR122.txt. Once that's done, I have no idea whether that file is in the format that WFU_PickAtlas expects to read (probably, it's not, and you will have to convert it somehow).
Good luck,
Chris Schwarz
Apr 3, 2020 05:04 PM | Alexandria Jensen - University of Colorado Denver Anschutz Medical Campus
RE: Adding MCALT Atlases to WFU_PickAtlas Toolbox in SPM12
Thank you for your response. I am agnostic to the use of the Wake
Forest Pick Atlas toolbox and am open to using whichever method you
suggest to bring in the atlases into SPM of FSL. My ultimate goal
is to make masks for certain ROIs within the atlases to use in a
grey matter volumetric analysis.
Apr 12, 2020 06:04 PM | Christopher Schwarz - Mayo Clinic
RE: Adding MCALT Atlases to WFU_PickAtlas Toolbox in SPM12
Alexandria,
Today's 1.4 release now includes code that transforms the atlases into the space of your input image and computes regional GM volumes and TIV measurements.
Best regards,
Chris
Today's 1.4 release now includes code that transforms the atlases into the space of your input image and computes regional GM volumes and TIV measurements.
Best regards,
Chris