Multi‐atlas thalamic nuclei segmentation on standard <scp>T1</scp>‐weighed <scp>MRI</scp> with application to normal aging

Pfefferbaum, Adolf; Sullivan, Edith V.; Zahr, Natalie M.; Pohl, Kilian M.; Saranathan, Manojkumar

doi:10.1002/hbm.26088

Cited by 13 publications

(6 citation statements)

References 62 publications

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“…The joint fusion algorithm used in HIPS-THOMAS (cf. majority voting in T1w-THOMAS), also likely contributed to increased label accuracy (Bernstein et al, 2021; Pfefferbaum et al, 2023). HIPS is computationally efficient, does not add much complexity to the image analysis pipeline of THOMAS, and does not require separate training for the different scenarios of scanner manufacturers and field strengths, as required by CNN-based methods.…”

Section: Discussionmentioning

confidence: 99%

“…While WMn-THOMAS has been used in several studies examining the role of thalamic nuclei in alcohol use disorder and multiple sclerosis (Zahr et al, 2020; Su et al, 2020), WMn-MPRAGE sequences are neither part of commonly used clinical protocols nor available in existing data repositories like ADNI or OASIS. To segment conventional MPRAGE T1w data, THOMAS was recently modified to use mutual information (MI) instead of cross-correlation (CC) as the nonlinear registration metric (Bernstein et al, 2021; Pfefferbaum et al, 2023) and a majority voting algorithm for label fusion (which we call T1w-THOMAS). While this method achieved good accuracy compared to WMn-MPRAGE for larger nuclei such as the mediodorsal or pulvinar, it was less accurate for segmentation of the smaller centromedian and habenular nuclei.…”

Section: Introductionmentioning

confidence: 99%

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Robust thalamic nuclei segmentation from T1-weighted MRI using polynomial intensity transformation

Vidal,

Danet,

Péran

et al. 2024

Preprint

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Accurate segmentation of thalamic nuclei, crucial for understanding their role in healthy cognition and in pathologies, is challenging to achieve on standard T1-weighted (T1w) magnetic resonance imaging (MRI) due to poor image contrast. White-matter-nulled (WMn) MRI sequences improve intrathalamic contrast but are not part of clinical protocols or extant databases. In this study, we introduce histogram-based polynomial synthesis (HIPS), a fast preprocessing transform step that synthesizes WMn-like image contrast from standard T1w MRI using a polynomial approximation for intensity transformation. HIPS was incorporated into Thalamus Optimized Multi-Atlas Segmentation (THOMAS) pipeline, a method developed and optimized for WMn MRI. HIPS-THOMAS was compared to a convolutional neural network (CNN)-based segmentation method and THOMAS modified for T1w images (T1w-THOMAS). The robustness and accuracy of the three methods were tested across different image contrasts (MPRAGE, SPGR, and MP2RAGE), scanner manufacturers (PHILIPS, GE, and Siemens), and field strengths (3T and 7T). HIPS-transformed images improved intra-thalamic contrast and thalamic boundaries, and HIPS-THOMAS yielded significantly higher mean Dice coefficients and reduced volume errors compared to both the CNN method and T1w-THOMAS. Finally, all three methods were compared using the frequently travelling human phantom MRI dataset for inter- and intra-scanner variability, with HIPS displaying the least inter-scanner variability and performing comparably with T1w-THOMAS for intra-scanner variability. In conclusion, our findings highlight the efficacy and robustness of HIPS in enhancing thalamic nuclei segmentation from standard T1w MRI.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Robust thalamic nuclei segmentation from T1-weighted MRI using polynomial intensity transformation

Vidal,

Danet,

Péran

et al. 2024

Preprint

Self Cite

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“…To segment the thalamic nuclei on our precision mapping participant, we used the hips_thomas.csh function from the version 2. 1 that has been validated for use of T1 acquisition only (Pfefferbaum et al, 2023) and that is available on docker (https://github.com/thalamicseg/hipsthomasdocker). We used the average T1 acquisition that has been produced for the registration of all functional data.…”

Section: Thalamus Segmentationmentioning

confidence: 99%

The brainstem’s red nucleus was evolutionarily upgraded to support goal-directed action

Krimmel,

Laumann,

Chauvin

et al. 2024

Preprint

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The red nucleus is a large brainstem structure that coordinates limb movement for locomotion in quadrupedal animals (Basile et al., 2021). The humans red nucleus has a different pattern of anatomical connectivity compared to quadrupeds, suggesting a unique purpose (Hatschek, 1907). Previously the function of the human red nucleus remained unclear at least partly due to methodological limitations with brainstem functional neuroimaging (Sclocco et al., 2018). Here, we used our most advanced resting-state functional connectivity (RSFC) based precision functional mapping (PFM) in highly sampled individuals (n = 5) and large group-averaged datasets (combined N ~ 45,000), to precisely examine red nucleus functional connectivity. Notably, red nucleus functional connectivity to motor-effector networks (somatomotor hand, foot, and mouth) was minimal. Instead, red nucleus functional connectivity along the central sulcus was specific to regions of the recently discovered somato-cognitive action network (SCAN; (Gordon et al., 2023)). Outside of primary motor cortex, red nucleus connectivity was strongest to the cingulo-opercular (CON) and salience networks, involved in action/cognitive control (Dosenbach et al., 2007; Newbold et al., 2021) and reward/motivated behavior (Seeley, 2019), respectively. Functional connectivity to these two networks was organized into discrete dorsal-medial and ventral-lateral zones. Red nucleus functional connectivity to the thalamus recapitulated known structural connectivity of the dento-rubral thalamic tract (DRTT) and could prove clinically useful in functionally targeting the ventral intermediate (VIM) nucleus. In total, our results indicate that far from being a 'motor' structure, the red nucleus is better understood as a brainstem nucleus for implementing goal-directed behavior, integrating behavioral valence and action plans.

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“…For the thalamic nuclei segmentation in our precision mapping participant, the hips_thomas.csh function from version 2.1 was utilized. This version has been validated exclusively for T1 acquisition [108][109][110] and is accessible through Docker (https://github.com/thalamicseg/thomas_new). The average T1 acquisition, generated for the registration of all functional data, was employed for this purpose.…”

Section: Thalamic Nuclei Segmentation Using Thomasmentioning

confidence: 99%

Disuse-driven plasticity in the human thalamus and putamen

Chauvin,

Newbold,

Nielsen

et al. 2023

Preprint

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Cortico-striato-thalamo-cortical loops have been heavily studied because of their importance in movement disorders such as Parkinson’s Disease and tremor. Capturing plasticity effect in this circuit has been mainly successful using animals or using invasive electrophysiology in patients. Given the importance of the striatum and thalamus for motor control and skill learning, the current study leverages on an arm immobilization paradigm in humans with neuroimaging to induce disuse and explore human subcortical motor circuits plasticity. We employed an experimental paradigm involving upper-extremity immobilization for two weeks with daily resting-state functional connectivity (FC) and motor task-related fMRI. This approach of dense sampling of individuals, i.e Precision Functional Mapping (PFM), offers individual-specific insights and provides enough data to address the issue of low signal to noise ratio in the subcortex. Previously, we identified increased FC between somatomotor cortex and the cingulo-opercular network and emergence of disuse pulses in the cortex during casting. We expand our prior investigation to include analysis adapted to the signal characteristic of subcortical regions to capture disuse-driven plasticity in human subcortical circuits. Subcortical nodes, particularly the central thalamus and posterior putamen, exhibited strengthened FC during disuse and spontaneous activity pulses. Motor task fMRI validated that subcortical disuse-driven plasticity effects spatially correspond to the upper extremity movement execution circuitry, emphasizing the role of these structures in motor control and adaptation. In conclusion, our study highlights the involvement of the cortico-striato-thalamo-cortical loops in human motor plasticity and discuss similarities in findings with two research fields: Parkinson Disease (PD), suggesting a novel interpretation of PD neuroimaging finding; and sleep, particularly plasticity and sleep pressure regulated by the thalamus.

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Multi‐atlas thalamic nuclei segmentation on standard T1‐weighed MRI with application to normal aging

Cited by 13 publications

References 62 publications

Robust thalamic nuclei segmentation from T1-weighted MRI using polynomial intensity transformation

Robust thalamic nuclei segmentation from T1-weighted MRI using polynomial intensity transformation

The brainstem’s red nucleus was evolutionarily upgraded to support goal-directed action

Disuse-driven plasticity in the human thalamus and putamen

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