1. Participants and data acquisition
1.1. Primary and test-retest datasets (HCP)
Structural, diffusion, and resting-state functional MRI data were obtained from the HCP repository (https://humanconnectome.org). Two datasets have been employed for the present work: the first dataset (primary dataset) consisted of 210 healthy participants (males = 92, females = 118, age range 22–36 years), and the second dataset (test-retest dataset) included 44 participants with available test-retest MRI scans (males = 13; females = 31; age range: 22–36 years). Data have been acquired by the Washington University, University of Minnesota and Oxford University (WU-Minn) HCP consortium. Participants recruitment procedures, informed consent, and sharing of de-identified data were approved by the Washington University in St. Louis Institutional Review Board (IRB) 115
For MRI data acquisition, a custom-made Siemens 3T “Connectome Skyra” (Siemens, Erlangen, Germany), provided with a Siemens SC72 gradient coil and maximum gradient amplitude (Gmax) of 100 mT/m (initially 70 mT/m and 84 mT/m in the pilot phase 116.
For high-resolution T1-weighted MPRAGE scan acquisition, the following parameters were used: voxel size = 0.7 mm, TR = 2400 ms, TE = 2.14 ms 115.
Multi-shell diffusion-weighted imaging (DWI) data (b-values: 1000, 2000, 3000 mm/s2) were acquired using a single-shot 2D spin-echo multiband Echo Planar Imaging (EPI) sequence. DWI volumes were acquired with 90 directions per shell in addition to 18 non-diffusion-weighted (b = 0 mm/s2) volumes, and a spatial isotropic resolution of 1.25 mm 54
Resting-state functional MRI data (rs-fMRI) were acquired with a gradient-echo EPI sequence, using the following parameters: voxel size = 2mm isotropic, TR = 720 ms, TE = 33.1 ms, 1200 frames, ~ 15 min/run. While data were acquired separately on different days along two different sessions, each session consisting of a left-to-right (LR) and a right-to-left (RL) phase encoding acquisition 55,115,116, the present work features LR and RL acquisitions of the first session only.
1.2. Validation dataset (LEMON)
High-quality structural, diffusion, and rs-fMRI data of 213 healthy subjects (males = 138, females = 75, age range 20–70 years) were retrieved from the Leipzig Study for Mind-Body-Emotion Interactions (LEMON) dataset (http://fcon_1000.projects.nitrc.org/indi/retro/MPI_LEMON.html). The study was carried out in accordance with the Declaration of Helsinki and the study protocol was approved by the ethics committee at the medical faculty of the University of Leipzig. A 3T scanner (MAGNETOM Verio, Siemens Healthcare GmbH, Erlangen, Germany) equipped with a 32-channel head coil was employed for MRI data acquisition.
The parameters of the MP2RAGE sequence used for structural T1w data acquisition were: voxel size = 1 mm, TR = 5000 ms, TE = 2.92 ms. DWI data (single shell, b = 1000 s/mm2) were acquired using a multi-band accelerated sequence with spatial isotropic resolution = 1.7 mm, and 60 diffusion-encoding directions plus 7 non-diffusion-weighted (b = 0 s/mm2) volumes. For rs-fMRI data, a gradient-echo EPI was acquired with the following parameters: phase encoding = AP, voxel size = 2.3 mm isotropic, TR = 1400 ms, TE = 30 ms, 15.30 min/run 46.
2. Data preprocessing
2.1. Structural preprocessing
Skull-stripped T1 weighted images provided by the HCP were segmented into cortical and subcortical gray matter (GM), white matter (WM), and cerebrospinal fluid (CSF) using FAST and FIRST FSL’s tools 117,118. A 5-tissue-type (5TT) image, which was required later for diffusion signal modeling, was obtained from structural segmented images. For the HCP dataset, the already available MNI-space transformations included in the minimal preprocessing pipeline were employed (FLIRT 12 degrees of freedom affine; FNIRT nonlinear registration) 119. For the LEMON dataset, T1-weighted volumes were also non-linearly registered to the 1-mm resolution MNI 152 asymmetric template using a FLIRT 12 degrees of freedom affine transform and FNIRT non-linear registration 120–122 and direct and inverse transformations were saved; a visual quality check as in Benhajali et al. 2020 was performed to ensure proper alignment of major sulcal and gyral structures.
Skull-stripped T1 weighted images provided by the HCP were segmented into cortical and subcortical gray matter (GM), white matter (WM), and cerebrospinal fluid (CSF) using FAST and FIRST FSL’s tools 117,118. A 5-tissue-type (5TT) image, which was required later for diffusion signal modeling, was obtained from structural segmented images. For the HCP dataset, the already available MNI-space transformations included in the minimal preprocessing pipeline were employed (FLIRT 12 degrees of freedom affine; FNIRT nonlinear registration) 119. For the LEMON dataset, T1-weighted volumes were also non-linearly registered to the 1-mm resolution MNI 152 asymmetric template using a FLIRT 12 degrees of freedom affine transform and FNIRT non-linear registration 120–122 and direct and inverse transformations were saved; a visual quality check as in Benhajali et al. 2020 was performed to ensure proper alignment of major sulcal and gyral structures.
2.2. DWI preprocessing
The DWI scans of the two datasets underwent different preprocessing pipelines: namely, the HCP datasets were available in a minimally preprocessed form, while the LEMON DWI scans were available only in raw form and were preprocessed entirely with a dedicated pipeline included in the MRtrix3 software 124. We decided to keep the preprocessing pipelines different, as in our previous work 44, to further highlight the reproducibility of our findings.
The minimal preprocessing pipeline of the HCP data includes eddy currents, EPI distortion and motion correction, and cross-modal linear registration of structural and DWI images 125.
The LEMON DWI scans were preprocessed following the subsequent steps: 1) denoising using Marchenko-Pastur principal component analysis (MP-PCA) 126, 2) removal of Gibbs ringing artifacts 127, 3) eddy currents, distortion (by exploiting the available reverse-phase encoding scans) and motion correction using EDDY and TOPUP FSL’s tools 118,128,129 and 4) bias field correction using the N4 algorithm 130.
2.3. Resting-state fMRI preprocessing
Both HCP and LEMON rs-fMRI data were obtained in preprocessed and denoised form, though the featured preprocessing steps are different between the two datasets. As mentioned above, we decided to use the already preprocessed functional volumes, considering the different acquisition features of the two datasets and further highlighting the robustness of the derived findings.
The HCP data minimal preprocessing pipeline included the following steps: 1) artifact and motion correction; 2) registration to 2-mm resolution MNI 152 standard space, 3) high pass temporal filtering (> 2000 s full width at half maximum) 125, 4) denoising, which features ICA-based artifact identification (ICA-FIX) 131 as well as regression of artifacts and motion-related parameters 55. In addition to the minimal preprocessing, data were band-pass filtered (0.01–0.09 Hz), and the global WM and CSF signal was regressed out to improve ICA-based denoising further 132.
The LEMON dataset processing pipeline included the following steps: 1) removal of the first 5 volumes to allow for signal equilibration, 2) motion and distortion correction, 3) outlier and artifact detection (rapidart) and denoising using component-based noise correction (aCompCor), 4) mean-centering and variance normalization of the time series and 5) spatial normalization to 2-mm resolution MNI 152 standard space 46,133.
To minimize BOLD partial volume sampling from the white matter, both HCP and LEMON rs-fMRI time series were additionally smoothed through convolution with a relatively large Gaussian kernel (6mm full width at half maximum) in line with the reference tw-dFC work 43. All the additional preprocessing was carried out using CONN toolbox 134.
2.4. Bundle-specific tractography and tw-dFC
Diffusion signal modeling was performed on the preprocessed DWI data using the constrained spherical deconvolution (CSD) framework, which estimates white matter Fiber Orientation Distribution (FOD) function from the diffusion-weighted deconvolution signal using a single fiber response function as reference 135. For HCP DWI data (multi-shell), a multi-shell multi-tissue (MSMT) CSD signal modeling algorithm was applied to estimate separate response functions in WM, GM, and CSF 136. For LEMON DWI data (single-shell), a single-shell 3-tissue (SS3T) CSD signal modeling was applied, despite the very low b-value, to keep the processing as consistent as possible between the two datasets, since it is necessary for the following automatic tract extraction step. In addition, it has been suggested to outperform the tensor model for tract reconstruction even at very low b values 137. SS3T-CSD is a variant of the MSMT model optimized for RF estimation in single-shell datasets and was performed using MRtrix3Tissue 138, a fork of MRtrix3 software (https://3tissue.github.io).
A robust and unbiased reconstruction of the AF is of key importance for the good quality and generalizability of results. For bundle-specific tractography of the AF, TractSeg (https://github.com/MIC-DKFZ/TractSeg/), a convolutional neural network-based tract segmentation approach, was employed. The TractSeg algorithm directly segments white matter bundles for each subject from the FOD peaks; importantly, this method has been demonstrated to be less affected by the original data quality compared to other automatic tract segmentation algorithms 48, and was then preferred to grant high comparability of the results between the different data-quality HCP and LEMON datasets.
Participant-level binary tract masks and ending masks obtained from TractSeg were employed to guide tractography of the AF, which was performed on FODs using deterministic tractography (SD-STREAM algorithm) 139 with default tracking parameters up to a fixed number of 2000 streamlines.
For each participant of both HCP and LEMON datasets, tractograms of left and right AF were registered to the MNI 152 standard space by applying the aforementioned non-linear transformations (paragraph 2.1), to bring individual tractography and rsfMRI data in the same space for track-weighted dynamic functional connectivity (tw-dFC) analysis. Then, tractograms were combined with preprocessed rs-fMRI time series using MRtrx3’s tckdfc command to generate a 4-dimensional tw-dFC time series 43. Separate tw-dFC time series were obtained for the left and right AF, and the following parameters were used: spatial resolution: 2 mm2, sliding window shape: rectangular, sliding window length: ~40 s (55 time points for the HCP data, TR = 0.72 s; 29 time points for the LEMON data, TR = 1.4 s). The length of the sliding window was chosen in line with previous works to maximize the stability of the time-varying connectivity profiles 56,69,111,140. For the HCP data, tw-dFC derived from LR and RL phase encoding volumes were temporally concatenated for each participant. Estimation of tw-dFC of the AF is summarized in Fig. 1.
3. Group-level analysis
3.1. Group ICA-based parcellation
Bundle-specific tw-dFC volumes underwent a spatial group ICA framework implemented in the Group ICA of FMRI Toolbox (GIFT) 49,50. Group analysis was performed separately for the primary dataset (HCP) and the validation dataset (LEMON) and for the left and right AF. For each AF tract, a binary mask for group ICA was built after transforming all the subject bundle masks to template space by summing up all individual masks and applying a probability threshold of 25% (i.e., voxels that were part of the AF in at least 75% of participants were considered for group analysis). The pipeline for group ICA analysis involved 1) a first dimensionality reduction step in which a subject-level principal component analysis (PCA) was applied to tw-dFC data to obtain 50 principal components per subject; 2) a second step in which dimensionality-reduced data of all subjects were temporally concatenated and a secondary PCA dimensionality reduction was applied along directions of maximal group variability; 3) the proper group ICA step, in which a given number (k) of independent components (ICs) is obtained from low-dimensional data using the Infomax algorithm 141; 4) back reconstruction, to obtain subject-specific spatial maps and time courses for each components using the group information guided ICA (GIG-ICA) algorithm 142; 5) back-reconstructed individual components were then averaged and normalized to obtain group-level z-maps of each component.
3.2. Data-driven dimensionality selection
To select the most appropriate number of components (k) for AF parcellation given our data, the ICA pipeline was iterated for the left and right AF separately at different values of k, ranging from 2 to 5, and for each ICA solution and the following measures were calculated:
1) Between-subjects spatial similarity: the primary dataset (HCP, 210 subjects) was split into symmetrical, random halves (105 subjects each) and the group ICA pipeline was run on each split for all the k values; the average Pearson’s correlation coefficient between group spatial ICA maps of the first and second split was employed as a measure of split-half similarity;
2) Within-subject spatial similarity: the test-retest dataset (HCP, 44 subjects with test-retest diffusion and rsfMRI data) was employed. The group ICA pipeline was run separately on test and retest tw-dFC data for all the k values; the average Pearson’s correlation coefficient between group spatial ICA maps of the test and retest data was employed as a measure of test-retest similarity;
3) Within-cohorts spatial similarity: the primary dataset (HCP, 210 participant) and the validation dataset (LEMON, 213 participant) were considered. Group ICA was performed separately on each dataset for all the k values; the average Pearson’s correlation coefficient between group spatial ICA maps of the primary dataset and the validation dataset was employed as a measure of external validation.
4) Similarity to “static” functional connectivity-based ICA: we benchmarked our results against a recently developed algorithm that involves mapping of the function signal from fMRI to tractography-derived priors of white matter anatomy, the “Functionnectome” 41. In a recent implementation, this method has been extended to resting-state functional connectivity 42 Here, we employed the participant-level tractograms of left and right AF to derive group-level AF tractography priors. Then, we applied the Functionnectome algorithm to map the functional signal from individual BOLD volumes on these priors. The resulting 4-dimensional volumes underwent group ICA with the same parameters as for tw-dFC data. The group-ICA results for each value of k were compared using the average Pearson’s correlation coefficient.
5) Functional correlation between component time series: to investigate the temporal independence of time series at each value of k, we employed the back-reconstructed time series for all subjects of the main dataset. Pearson’s correlation was calculated pairwise for each pair of components on each individual and then averaged across the entire dataset. For values of k > 2, the average between pairwise correlation values was considered.
The optimal number of components was decided based on a consensus approach between all these metrics: the value k for which most metrics showed the highest value.
3.3. Component-driven AF parcellation
To derive a parcellation of the AF from the component maps, we applied a k-means clustering procedure in the component space. Briefly, after selecting an optimal number of components according to the measures described above, each voxel in the AF was clustered according to its similarity in weight in each component z-map. The ideal number of clusters (c) was determined using the silhouette coefficient 143.
3.4. Meta-analytic functional decoding
To provide a functional characterization for the white matter clusters derived from AF parcellation, we employed a custom meta-analytic approach, specifically designed to account both for the discrete nature of binary clusters and the white matter nature of the underlying spatial maps. Meta-analytic decoding was based on the Neuroquery database, which contains predictive activation maps estimated from over 7547 neuroscience terms 47.
Initially, we generated voxel-wise inverse distance maps from each cluster centroid to transform binary cluster maps into a continuous distribution of values reflecting the extent of each voxel belonging to each cluster. This process was carried out separately for the left and right AF clusters. Within voxel-wise distance maps, the value of each voxel indicates its proximity to cluster centroids, with higher values signifying closer distances. In an initial screening of terms from the Neuroquery database, these inverse distance maps underwent a masking procedure using a mean GM mask. Subsequently, the masked maps were utilized as inputs for the Neuroquery image search tool (https://github.com/neuroquery/neuroquery_image_search), retrieving the top 20 most correlated terms to each cluster distance map, resulting in a total of 120 neuroscience terms (2 hemispheres x 3 clusters x 20 terms). To this initial selection, a first screening procedure was applied by discarding duplicate terms and terms referring to anatomy or localization (e.g. “left”, “right”, “cortex”, “hemisphere” “pfc”). A template tractogram was obtained for left and right AF by summing all the subject-specific AF tractograms in standard space. Subsequently, the unthresholded statistical maps corresponding to each of the remaining terms were retrieved and converted to track-weighted predictive term maps using the left and right template tractograms 144 via MRtrix3’s tckmap command employing the option -scalar_map to provide the statistical maps as input 51,52.
Finally, pairwise Pearson’s correlation was employed to quantify the similarity between each cluster distance map and the resulting track-weighted term maps. To address the spatial autocorrelation (SA) properties of arcuate maps, statistical significance was assessed using a permutational approach described in Burt et al. (2020). This approach involved the generation of SA-preserving surrogated maps through 1000 permutations. The resulting p-values underwent correction for multiple comparisons using the Benjamini-Hochberg method. The effect sizes of correlations were assessed by computing the R2 determination coefficient.