NITRC WFU_PickAtlas Forum: help

Brodmann area 12 not visible

Rasha Alharthi — Sat, 03 Aug 2024 9:10:26 GMT

I am encountering an issue with the WFU-PickAtlas tool while attempting to use it for ROI-to-ROI analysis in the CONN Toolbox. Specifically, when selecting Brodmann area 12 from the available regions of interest (ROIs), it does not appear in the display region. All other Brodmann areas are visible and display correctly.
Additional Question: Regarding the use of the dilate tool in PickAtlas, is it appropriate to use this tool? If so, how should it be applied, and what impact might it have on my results in CONN Toolbox? Could using the dilate tool negatively affect the accuracy or validity of my analysis?
As a beginner in this field, I would greatly appreciate any guidance or recommendations on how to resolve this issue.
Thank you, Rasha

Table Generation Statistics Meaning

cmvomo — Fri, 10 May 2024 0:37:41 GMT

Hi,
 
I'm using WFU to get average SUV in the putamen  (using smoothed 18FDG PET files as input).
 
To do so, I select the region (HUMAN ATLAS->brodmann areas+ -> I chose putamen both side), and use generate table to get the average SUV in that region for each participant. 
Everything works fine but I was wondering whether the value in the average column of the tbl file corresponds to the actual mean SUV ?
 
Thank's in advance

RE: Problem saving masks

lidizpe — Thu, 25 Apr 2024 13:44:15 GMT

Hi!!
Did you ever get the answer? I'm having the same problem when trying to dilate my mask.
 
Thanks,
Lidia

wfu_pickatlas dilation problem

lidizpe — Thu, 25 Apr 2024 9:57:02 GMT

RE: Cann't see WFU_PickAtlas in SPM-12 Toolbox

tabea_ja — Tue, 19 Mar 2024 14:05:11 GMT

Hello! Did you or anyone else already find a solution? I have the same problem. Thank you!

Update wfupickatlas AAL masks

Olivier Brown — Tue, 20 Jun 2023 16:13:03 GMT

Dear experts,
 
I am hoping to save some .nii masks from the wfupickatlas on SPM12. I use the human atlas (MNI), then select masks as part of the AAL template. 
 
The standard AAL template seems to be outdated here, as there are more recent versions of this atlas. Does anyone know how I can obtain the masks for the latest atlas? The AAL toolbox seems to be strictly used for identifying clusters, while I'm hoping to use the anatomical masks for ROI analyses.
 
-Olivier

RE: Cann't see WFU_PickAtlas in SPM-12 Toolbox

Behcet Ayyıldız — Fri, 17 Feb 2023 10:25:04 GMT

Hi Muhammed,

I hope you are doing well. I got the same problem. Although I set the path to the toolbox, I couldn't see it in SPM_12 GUI toolbox. On the other hand, I was able to manage to set it in my personal Mac computer but I couldn't do it for my Linux computer at work.
Could manage to fix this problem? If you could share me how to manage it?

thanks,
best

Cann't see WFU_PickAtlas in SPM-12 Toolbox

Muhammad Badarnee — Mon, 19 Dec 2022 3:28:28 GMT

Hello!

Although I added a path of the WFU_PickAtlas to Matlab (set path-->spm12-->toolbox), I still can't see it under the Toolbox in SPM-12. I also tried to add three paths (one for each subfolder-- pickatlas, results and a third path for tbx_commn) but unfortunately nothing happened. I'd appreciate it if anyone has any idea about how to deal with this issue.

Thanks,
Muhammad B.

RE: Error in adding AAL3 atlas to PickAtlas

jiaoguojuan — Fri, 22 Jul 2022 8:59:39 GMT

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

RE: Error in adding AAL3 atlas to PickAtlas

neda mohammadi — Sat, 11 Jun 2022 4:51:49 GMT

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.