Analysis code for the Auditory and Visual Sensory Thalamic Localizer Task
Released under the GNU Public License version 3.
To use this code, see the script: main_TL_analysis.m.
It sets up the required variables as described in the comments, and calls the main function that performs the analysis: internal_TL_analysis.m.
Requirements:
- Path to the participant's Sensory Thalamic Localizer task log file from Presentation
- Participant's ID number
- Desired path for the MGN and LGN functionally-defined regions of interest (fROIs)
- Desired path for intermediates used, such as outputs from first-level modeling and contrasts
- Paths to each run of unsmoothed BOLD fMRI data, supplied in a cell array.
- Paths to each run of Smoothed BOLD fMRI data, supplied in a cell array.
- Paths to the motion parameters for each run, supplied in a cell array.
- Repetition time for the BOLD data, (TR) in seconds
- Path of the FreeSurfer segmentation/parcellation atlas (Desikan-Killiany) in MNI space, Atlas.wmparc.2.nii
- Participant's FreeSurfer thalamic segmentation, warped to MNI space.
See: https://freesurfer.net/fswiki/ThalamicNuclei
Iglesias JE, Insausti R, Lerma-Usabiaga G, Bocchetta M, Van Leemput K, Greve DN, van der Kouwe A; Alzheimer's Disease Neuroimaging Initiative; Fischl B, Caballero-Gaudes C, Paz-Alonso PM.
A probabilistic atlas of the human thalamic nuclei combining ex vivo MRI and histology. Neuroimage. 2018 Dec;183:314-326.
doi: 10.1016/j.neuroimage.2018.08.012. Epub 2018 Aug 17. PMID: 30121337; PMCID: PMC6215335.
Please note that the Presentation task must be set to either "fMRI" or "fMRI_emulation" mode.
fMRI mode should be used exclusively alongside an MRI scanner that can send volume acquisition pulses to the computer running Presentation.
fMRI_emulation mode should be used only for testing.
One can switch between modes by editing lines 13 and 14 of the thal.sce file.
One of these lines must have a comment character (#) preceding the line in order to deactivate it, which the other must not.
fMRI mode:
scenario_type = fMRI;
#scenario_type = fMRI_emulation;fMRI Emulation mode:
#scenario_type = fMRI;
scenario_type = fMRI_emulation;Please cite this code as follows:
John C. Williams, Philip N. Tubiolo, Srineil Nizambad, Yash Patel, Zu Jie Zheng, Eilon B. Silver-Frankel, Dathy T. Pham, Natalka K. Haubold, Sameera K. Abeykoon, Anissa Abi-Dargham, Guillermo Horga, Jared X. Van Snellenberg. (2024).
Auditory and visual sensory thalamic localizer task (Version <Release Version>) [Computer software].
Available from https://github.com/CNaP-Lab/Sensory-Thalamic-Localizer and http://www.neurobs.com/ex_files/expt_view?id=302.
Code authors:
John C. Williams, Srineil Nizambad, Philip N. Tubiolo, Yash Patel, and Jared X. Van Snellenberg
Department of Psychiatry and Behavioral Health
Department of Biomedcial Engineering
Renaissance School of Medicine
Stony Brook University
Task Presentation code additionally found here:
Neurobehavioral Systems Archives of Neurobehavioral Experiments and Stimuli
http://www.neurobs.com/ex_files/expt_view?id=302
Accompanies the following manuscript:
John C. Williams, Philip N. Tubiolo, Zu Jie Zheng, Eilon B. Silver-Frankel, Dathy T. Pham, Natalka K. Haubold, Sameera K. Abeykoon, Anissa Abi-Dargham, Guillermo Horga, and Jared X. Van Snellenberg. (2024).
Functional Localization of the Human Auditory and Visual Thalamus Using a Thalamic Localizer Functional Magnetic Resonance Imaging Task.
bioRxiv 2024.04.28.591516; doi: https://doi.org/10.1101/2024.04.28.591516