Participants
In this study, we used 11 independent datasets comprising 863 total participants after quality control. These datasets include (1) PIPD dataset99: 166 patients with PD and 60 HC individuals; (2) DBS-fMRI dataset: 14 patients with PD, with evaluations conducted both before and after DBS surgery, along with 25 HC individuals; (3) TMS dataset: 36 patients with PD; (4) DBS-SS dataset: 342 patients with PD; (5) DBS-ECoG dataset: 17 patients with PD who underwent STN-DBS surgery and DBS-evoked ECoG recording; (6) MRgFUS dataset: 10 patients with tremor-dominant PD; (7) aDBS dataset: 4 patients with PD; (8) LCT dataset: 21 patients with PD; (9) ET dataset100: 45 patients with ET and 45 HC individuals from the PIPD dataset; (10) dystonia dataset: 42 patients with dystonia and 21 HC individuals; and (11) ALS dataset: 30 patients with ALS and 30 HC individuals. PD was diagnosed according to the revised clinical diagnostic criteria of the International Movement Disorder Society (MDS, 2015 version) or the Chinese Parkinson’s Disease Diagnostic Criteria (2016 version). The following sections provide detailed descriptions for each dataset.
PIPD dataset
Patients
In total, 180 patients with PD were recruited from Henan Provincial People’s Hospital (HPPH), China. The inclusion criteria included being aged 18 years or above and a clinical diagnosis of PD. Exclusion criteria comprised the following: (1) MRI contraindications; (2) a history of neurological disorders aside from PD, including stroke, cerebrovascular disease, seizures and brain tumours; (3) previous invasive neurosurgeries such as DBS or ablation; and (4) average relative head motion larger than 0.2 mm during rsfMRI scanning. Four patients did not complete MRI scanning, and ten patients were excluded owing to excessive head motion. Ultimately, 166 patients were included in the analysis (64 women, 102 men; mean ± s.d. age = 61.8 ± 7.84 years; demographic and clinical details are provided in Extended Data Table 1).
HC participants
In total, 71 healthy participants aged 18 years or older, lacking neurological or psychiatric disorders, were enrolled. Exclusion criteria included MRI contraindications and an average relative head motion exceeding 0.2 mm. After excluding 11 participants owing to excessive head motion, the analysis included 60 HC participants (34 women, 26 men; mean ± s.d. age = 56.10 ± 6.64 years; Extended Data Table 1). The control group exhibited significantly different demographics from the PD group. We therefore sampled a subset of 65 patients with PD from the 166 patients to ensure demographic matching when performing case–control analyses (Extended Data Table 1). The experimental protocol was approved by the HPPH Institutional Review Board (IRB). Written informed consent was obtained from all of the participants.
MRI acquisition
The participants underwent one structural MRI scan lasting 8 min and 50 s, and five scans, each spanning 6 min and 14 s, resulting in a cumulative scan duration of 31 min and 10 s. MRI was performed using the Siemens 3 T Prisma MRI scanner equipped with a 64-channel head coil. The structural scans involved T1-weighted images acquired through a MP2RAGE sequence (TI1 = 755 ms, TI2 = 2500 ms, TE = 3.43 ms, TR = 5,000 ms, flip angle1 = 4°, flip angle2 = 5°, matrix size = 256 × 256, 208 sagittal slices, spatial resolution = 1 × 1 × 1 mm3). An acceleration factor of 3 (with 32 reference lines) was applied in the primary phase encoding direction, with online GRAPPA image reconstruction. rsfMRI data were acquired using a gradient-echo echo planar imaging (GE-EPI) sequence (TE = 35 ms, TR = 2,000 ms, flip angle = 80°, and 75 slices, spatial resolution = 2.2 × 2.2 × 2.2 mm3). During data acquisition, the participants were instructed to keep their eyes open, remain awake while keeping their body still and minimize head movement.
DBS-fMRI dataset
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