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[idossha]

[LawsOfForm]

[idossha]

Hi @LawsOfForm ,

I cannot find your original post, I am assuming you removed it. If this is still relevant please let me know.

Best,
Ido

[LawsOfForm]

Hi Udo, I can still see my post but in any case I will add it again. Best, Filip
Subject: Question about Atlas File Integration in TI-Toolbox GUI

Dear TI-Toolbox team,

I recently installed the latest version of the TI-Toolbox and had great success running the pre-processing module via the Docker GUI.

I am now trying to use the Optimizer with a predefined atlas region. In the TI-Toolbox/resources/atlas folder, I can see several atlas files, including:

HarvardOxford-sub-maxprob-thr0-1mm.nii.gz

HOS-thr0-1mm.nii.gz

MNI_Glasser_HCP_v1.0.nii.gz

These are accompanied by corresponding .txt files.

However, when I select “Cortical” as the ROI Definition Method in the Optimizer tab, the “Atlas” dropdown menu remains empty and does not show these atlases as options.

Could you please advise:

Where should the atlas files be placed so they appear in the GUI dropdown?
Or is there an additional step I might be missing to enable them?
Thank you in advance for your support.

Best regards,
Filip

[idossha]

Hi @LawsOfForm,

I see the problem. Could you please convert this to its own discussion post and not a comment to the welcome message? I just want it to be available on the main discussion feed page.

Regarding the actual problem, the flex-search does not actual use those NIfTI files, those are used later in an optional MNI voxel analysis. The flex-search uses .annot files created during the preprocessing of the m2m folder We have recently refactor that preprocessing module, and may have introduced a potential bug as we did not set up a robust testing suite yet. In the meantime there are two ways around it,

1. Place a spherical target with appropriate size in your region of interest.
2. If the .annot files indeed were not created during preprocessing, you can manually generate them if you have a fully formed m2m folder. The command you can use is the following: subject_atlas -m "$m2m_folder" -a "$atlas" -o "$output_dir" Your outpur dir should be you m2m-subID/segmentation/. This should then be available to you for atlas based targeting in the flex-search.

##Update

I have identified the problem and have fixed it in the codebase. I have incorporated the changes in the current version (v2.2.4). For it to take effect, please log out of the TI-Toolbox and your next login will incorporate the update.

Now, every m2m step will automatically create the necessary .annot file. However, if you already have a number of head models and do not want to repeat that complete process, run this subject_atlas -m "$m2m_folder" -a "$atlas" -o "$output_dir" where Your outpur dir should be you m2m-subID/segmentation/ and atlas sould be either a2009s , DK40 , HCP_MMP1.

Let me know how it goes !

Ido