NITRC Mayo Clinic Adult Lifespan Template and Atlases Forum: help

RE: Adding MCALT Atlases to WFU_PickAtlas Toolbox in SPM12

Christopher Schwarz — Sun, 12 Apr 2020 18:06:03 GMT

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

RE: how to compute the Grey matter volumes using MCALT atlas

Christopher Schwarz — Sun, 12 Apr 2020 18:04:45 GMT

Kate,
Today's 1.4 release now includes code that computes regional GM volumes and TIV measurements.
Best regards,
Chris

RE: Adding MCALT Atlases to WFU_PickAtlas Toolbox in SPM12

Alexandria Jensen — Fri, 03 Apr 2020 17:20:27 GMT

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.

RE: Adding MCALT Atlases to WFU_PickAtlas Toolbox in SPM12

Christopher Schwarz — Fri, 03 Apr 2020 13:49:18 GMT

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

Adding MCALT Atlases to WFU_PickAtlas Toolbox in SPM12

Alexandria Jensen — Thu, 02 Apr 2020 22:50:24 GMT

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:[code][color=#993300]ans =[/color][/code][code][color=#993300]struct with fields:[/color][/code][code][color=#993300]atlasname: 'MCALT HUMAN ATLAS'[/color]
[color=#993300]subdir: 'MCALT_atlas_templates'[/color]
[color=#993300]lookupfile: 'master_lookup.txt'[/color]
[color=#993300]dispimage: 'MCALT_T1.nii'[/color]
[color=#993300]licensefile: ''[/color]
[color=#993300]conversionfile: ''[/color]
[color=#993300]conversion: [][/color][/code][code][color=#993300]Unrecognized function or variable 'Region'.[/color][/code][code][color=#993300]Error in wfu_get_atlas_list>lookup (line 117)[/color]
[color=#993300]if ~(isempty(Region))[/color][/code][code][color=#993300]Error in wfu_get_atlas_list (line 31)[/color]
[color=#993300][A] = lookup(atlas_path, T, I, O, N);[/color][/code][code][color=#993300]Error in wfu_pickatlas>Initialize (line 214)[/color]
[color=#993300][Atlas]=wfu_get_atlas_list(handles.data.SelectedAtlasType.subdir, ...[/color][/code][code][color=#993300]Error in wfu_pickatlas (line 55)[/color]
[color=#993300]Initialize(fig, [], handles, varargin{:})[/color][/code][code][color=#993300]Error in spm (line 946)[/color]
[color=#993300]evalin('base',xTB(i).prog);[/color][/code][code][color=#993300]Error while evaluating UIControl Callback.[/color][/code]
[color=#000000]<span style="caret-color: #993300;">I have tried nearly everything I can think of to fix this error but nothing is working unfortunately. Any assistance would be greatly appreciated!</span>[/color]

[color=#000000]<span style="caret-color: #993300;">Alexandria Jensen</span>[/color]

RE: how to compute the Grey matter volumes using MCALT atlas

Kate Marvel — Thu, 30 Jan 2020 17:58:45 GMT

Thanks Dr Schwarz for the information.

Kate

RE: how to compute the Grey matter volumes using MCALT atlas

Christopher Schwarz — Wed, 29 Jan 2020 15:18:51 GMT

Kate,
If you have already transformed the atlases into the native space, then GM volumes are computed by summing the voxels in the c1*.nii segmentation maps within each atlas region. You then multiply by the volume of each voxel to convert the units mm^3. Sorry, I do not have code that I can provide for this, but it seems like you have already done the parts of it that are relatively more difficult. Eventually I plan to include code to compute GM volumes but this is not available yet and I do not have an ETA.
Best regards,
Chris

how to compute the Grey matter volumes using MCALT atlas

Kate Marvel — Tue, 28 Jan 2020 16:57:18 GMT

Dear Prof Schwarz,

Please can you help me with the script for computing the grey matter volumes for specific regions of interest found in MCALT atlas.

I have done the following steps:

1./ Segmented and normalized the images to the MCALT space using the matlab script you provided with the atlas (Thank you very much).

2./ The grey matter probability maps are smoothen using 6mm FWHM gaussian kernel.

3./ I have transformed the MCALT atlas into the native space of the image by using normalization parameters for transforming the image to MCALT space.

Kate

RE: Co-registration in V1.3

Kate Marvel — Tue, 28 Jan 2020 16:43:46 GMT

Thank you very much Prof Schwarz. It works now after making the string in single quotes.

kate

RE: Co-registration in V1.3

Christopher Schwarz — Fri, 03 Jan 2020 17:57:20 GMT

FYI in the next release I will update the function to detect string-type inputs and convert them to char-type to avoid this error.