The WU-Minn Human Connectome Project: An overview

In the paper

“Figure 9 displays results from the language processing task developed by Binder et al. (2011), with the specific contrast being story processing versus math. These data are acquired in approximately 8 minutes, and show robust group level activation in anterior and inferior temporal regions, as well as ventral prefrontal regions typically associated with various components of language processing.”

What the sources say

• Supported

  The Results (FMRI Results: MCW Cohort) describe Story-versus-Math activation in the anterior and inferior temporal cortex, including the temporal pole and inferior temporal gyrus. The same section reports activation in the ventral inferior frontal gyrus and ventromedial prefrontal cortex. (LLM, conf=0.94)

  cites Binder et al. (2011) source

In the paper

“A four-question satisfaction survey administered at the end of testing shows that participants report a very high level of satisfaction with their experiences.”

In the paper

“In general, the participants studied to date (through April, 2013) have tolerated the entire experience very well, including the extended time in a customized scanner with a reduced bore diameter (see below).”

In the paper

“Relative to a standard commercial Skyra, the customized hardware includes a gradient coil and gradient power amplifiers that together increase the maximum gradient strength from 40 mT/m to 100 mT/m on the WU-Minn 3T.”

In the paper

“Many practical issues have been resolved to allow recruitment and visits to occur at a pace sufficient to study 1200 subjects over 3 years at a single imaging site, as discussed below.”

In the paper

“Preliminary analyses based on a finalized set of acquisition and preprocessing protocols demonstrate the exceptionally high quality of the data from each modality.”

In the paper

“To date, no participants who have passed the initial telephone screening have been subsequently excluded during the SSAGA.”

In the paper

“A two-year effort to develop and refine the scanning protocols for the 3T Connectome Scanner has yielded important advances in each of the four MR-based imaging modalities (Ugurbil et al., 2013).”

What the sources say

• Not checked yetcites Ugurbil et al., 2013 source

In the paper

“The majority of participants rate their experience as a 9 or 10 (out of 10) overall (Supplemental Table S4).”

In the paper

“Complete or near-complete scans for all modalities were obtained from 68 of these subjects (see Supplemental Table S3).”

In the paper

“As a consequence, all scans have gradient distortions larger than in a conventional scanner.”

In the paper

“Fortunately, our preliminary analyses indicate that head motion is relatively low in the majority of HCP subjects.”

In the paper

“Combined with the spatial resolution of 1.25 mm isotropic, this yields exceptional data quality for in vivo whole brain diffusion imaging at 3T (Sotiropoulos et al., 2013c; Ugurbil et al., 2013).”

What the sources say

• Not checked yetcites Sotiropoulos et al., 2013c
• Not checked yetcites Ugurbil et al., 2013 source

In the paper

“The most significant pulse sequence development for the HCP was the implementation and optimization of slice-accelerated multiband (MB) acquisitions for fMRI and dMRI (Larkman et al., 2001; Moeller et al., 2008; Feinberg et al., 2010; Moeller et al., 2010; Setsompop et al., 2012; Ugurbil et al., 2013).”

What the sources say

• Not checked yetcites Larkman et al., 2001 source
• Not checked yetcites Moeller et al., 2008
• Not checked yetcites Feinberg et al., 2010 source

In the paper

“Initial pilot studies have focused on fMRI and have produced high quality images at higher spatial resolutions (~ 1mm) than the 2mm isotropic voxels used for fMRI data acquired in HCP subjects at 3T.”

In the paper

“Despite this, early results (see Ugurbil et al 2013) indicate that ~ 1mm isotropic resolutions over the whole brain are feasible with a TR of around 2 s.”

What the sources say

• Not checked yetcites Ugurbil et al 2013 source

In the paper

“This illustrates the high quality of the structural images themselves and of the cortical segmentation, including regions where cortex is notably thin, such as the calcarine sulcus (red arrow) and precentral sulcus (black arrow).”

In the paper

“The resulting preprocessing pipelines provide substantial improvements used for each of the MRI modalities, including structural MRI, fMRI (both rfMRI and tfMRI), and dMRI.”

In the paper

“The resulting resting-state network timeseries show exceptionally clean power spectra (Smith et al., 2013).”

What the sources say

• Not checked yetcites Smith et al., 2013 source

In the paper

“The fine detail in the cerebellum is also notable, as most lamellae and even many individual folia are discernible.”

In the paper

“The differences in shape maps for identical twins (A1 vs A2; B1 vs B2) are comparable to those between unrelated individuals (either ‘A’ subject vs either ‘B’ subject).”

In the paper

“The symmetry in the pattern of myelin content between the two hemispheres can be appreciated by comparing the location of corresponding vertices in the two hemispheres, which were selected to be centered on myelin hotspots in the left hemisphere (black circles) and are approximately centered on corresponding hotspots in the right hemisphere (blue dots).”

In the paper

“In general, the myelin maps for this and the other HCP subjects are higher in quality than those originally reported (Glasser et al., 2011), thanks to the higher spatial resolution (0.7 vs 1 mm isotropic voxels) coupled with several algorithmic improvements (Glasser et al., 2013a,b).”

What the sources say

• Not checked yetcites Glasser et al., 2011 source
• Not checked yetcites Glasser et al., 2013a,b

In the paper

“ICA component 1 covers higher-level visual areas.”

In the paper

“In contrast to Fig. 3, these correlations are estimated without regression of the mean gray timecourse. Hence, the anti-correlated regions (blue, purple) are smaller in extent, because the mean is not forced to be zero.”

In the paper

“Many of the regions that are strongly correlated (yellow, red) with the retrosplenial seed are poorly correlated or anti-correlated with the nearby seed in cingulate cortex (blue, purple; but note this is after regression of the mean gray-matter timecourse – see below).”

In the paper

“The signal-to-noise improves substantially by virtue of the large group size.”

In the paper

“The functional connectivity hotspots associated with this location are spatially more blurred than equivalent maps derived from single subject datasets, owing to the fact that shape-based inter-subject registration can be inaccurate in aligning functionally defined areas, especially in regions of high folding variability.”

In the paper

“As with the working memory task, we also see activation in these same regions in the majority of individual subjects.”

In the paper

“Figure 8 displays the results from the working memory task, a variant of the N-back task, with the specific contrast a high working memory load (“2-back”) versus a low working memory load (“0-back”). The data for this task are acquired in ~10 minutes and show robust mixed-effects group level activation in dorsal frontal-parietal and cingulate systems typically associated with working memory and”

In the paper

“Figure 6 shows representative fractional anisotropy and color-encoded principal diffusion direction images from the HCP dMRI data, compared with a more conventional 2mm data set (from a different subject). The improvement in anatomical detail is clearly visible.”

In the paper

“Further, we see significant activation in these same regions in the majority of individual subjects, a result important for the individual difference and genetic analysis goals of the HCP.”

In the paper

“The bottom row shows a spatially corresponding ICA component from a 100-component group-level ICA-based network decomposition (with 82 ‘signal’ components), carried out on 66 HCP subjects from the Q1 data release. The correspondence in spatial patterns between the rfMRI ICA component and the task-fMRI activation is striking.”

In the paper

“We also developed a novel algorithm that greatly improves the correction of susceptibility and eddy-current induced distortions and the effects of subject motion (Andersson et al., 2012; Sotiropoulos et al., 2013c).”

What the sources say

• Not checked yetcites Andersson et al., 2012
• Not checked yetcites Sotiropoulos et al., 2013c

In the paper

“The hour’s worth of rfMRI scanning accumulated per subject yields ~5,000 frames (TR’s) of data for each of the ~90,000 grayordinates that represent the anatomical substrate on which a dense functional connectome is generated.”

In the paper

“By encouraging all consortium members to challenge standard assumptions, then let the pilot data and results from proposed analyses drive the decision, many improvements have been realized.”

In the paper

“However, the SNR for subcortical regions is generally weaker than for cerebral and cerebellar cortical regions, in large part because of their buried location relative to the 32-channel head coil (Ugurbil et al, 2013).”

What the sources say

• Not checked yetcites Ugurbil et al, 2013 source

In the paper

“Consequently, a large number of subjects will be needed in order to identify relationships between brain circuit phenotype and genotype.”

In the paper

“Studying sibships that include twins offers multiple advantages. Most obviously, it enables systematic assessment of the heritability of neural circuits.”

In the paper

“Combined analyses of MZ and DZ pairs will allow estimation of the extent to which genotype, shared environment, and non-shared influences each contribute to variation in traits.”

In the paper

“These refinements have been consolidated into a set of well-defined preprocessing pipelines that consistently and reliably carry out distortion correction and spatial alignment for each of the four imaging modalities (Glasser et al., 2013b).”

What the sources say

• Not checked yetcites Glasser et al., 2013b

In the paper

“In general, multiband pulse sequences greatly increase the amount of data acquired per unit time, using a strategy of simultaneously exciting and acquiring multiple brain slices, which are then separated from one another during image reconstruction, based on the spatial sensitivity profiles of the multiple receive coils (32 channels for the HCP standard Siemens 3T head coil).”

In the paper

“Thus, the two hardware systems provide complementary platforms for exploring the possible improvements that are available for tractography.”

In the paper

“For the specific method and diffusion weighting (b values) chosen in the WU-Minn consortium, 100 mT/m maximal gradient strength provides much of the gain that would be available at 300 mT/m (Ugurbil et al. 2013); the relative merit of each depends on the method and b- values employed.”

What the sources say

• Not checked yetcites Ugurbil et al. 2013 source

In the paper

“Each scan is repeated along two phase encoding directions (L/R and R/L) to allow correction of susceptibility induced distortions.”

In the paper

“This in turn permits the acquisition of much higher resolution images.”

In the paper

“The only scans used for structural preprocessing pipelines and released to the community are those in which one or more good/excellent T1w and T2w scans were acquired in the same session (and accompanied by corresponding receive and transmit bias field maps that are used in preprocessing).”

In the paper

“Obtaining higher resolution than conventional 1mm isotropic voxels is important because many HCP analyses rely on cortical surfaces that are as accurate as possible.”

In the paper

“The functional contrast to noise at such high resolutions is not compromised, despite the ~ 8 times smaller voxel size, because of the aforementioned increases in image SNR and BOLD based contrast (Ugurbil et al., 2013).”

What the sources say

• Not checked yetcites Ugurbil et al., 2013 source

In the paper

“The acquisition of such high resolution images will result in lower temporal resolution than the 2 mm isotropic resolution 3T data, because the many more slices needed to cover the entire brain results in a substantial increase in the TR.”

In the paper

“This is consistent with previous research suggesting that cortical folding patterns are only modestly heritable (Botteron et al., 2008)”

What the sources say

• Not checked yetcites Botteron et al., 2008

In the paper

“Accurate interhemispheric registration facilitates a variety of cross-hemisphere comparisons, such as the correspondence of myelin maps in the left and right hemispheres in individual subjects.”

In the paper

“Neurobiologically relevant fluctuations, which ideally should be the only signals used to drive functional connectivity analyses, represent only a small fraction (~4%) of the total temporal variance in the minimally preprocessed datasets (Glasser et al., 2013b; Marcus et al., 2013).”

What the sources say

• Not checked yetcites Glasser et al., 2013b
• Not checked yetcites Marcus et al., 2013 source

In the paper

“This is followed by registration to the Conte69 atlas, which brings the left and right hemispheres into precise geographic alignment using interhemispheric landmark-constrained registration (Van Essen et al., 2012).”

What the sources say

• Not checked yetcites Van Essen et al., 2012

In the paper

“Cortical myelin maps are another useful type of data that can be extracted from structural images by computing the ratio of the T1w and T2w image values at each voxel and mapping this ratio to the cortical surface (Glasser and Van Essen, 2011).”

What the sources say

• Not checked yetcites Glasser and Van Essen, 2011 source

In the paper

“For example, combining data across multiple receive coils using a sensitivity-encoding method (SENSE-1) increases the dynamic range of the signal relative to the conventional root-sum-of-squares approach (Lenglet et al., 2012; Sotiropoulos et al., 2012; Sotiropoulos et al., 2013c).”

What the sources say

• Not checked yetcites Lenglet et al., 2012 source
• Not checked yetcites Sotiropoulos et al., 2012 source
• Not checked yetcites Sotiropoulos et al., 2013c

In the paper

“ICA provides a powerful alternative approach to subdividing the brain into regions that functionally have a high degree of independence, but are not constrained to be topologically contiguous or non-overlapping.”

In the paper

“For example, a notable bias, present for clear geometric reasons, is that current tractography approaches are much more likely to trace to gyral crowns than to sulcal depths (Van Essen et al., 2013).”

What the sources say

• Not checked yetcites Van Essen et al., 2013

In the paper

“Taken together, these data illustrate our ability to acquire high quality tfMRI data from a range of paradigms.”

In the paper

“While containing a wealth of information, dMRI connectomes will inevitably contain biases and errors resulting from limitations of the technique.”

In the paper

“HCP has developed novel fiber reconstruction algorithms that are optimized for multi-shell data (Jbabdi et al. 2012).”

What the sources say

• Not checked yetcites Jbabdi et al. 2012 source

In the paper

“However, given the strong correlations in time (owing to the slow hemodynamic response function) and in space (neighboring grayordinates tend to be highly correlated), the actual amount of information is presumably much smaller, perhaps by around two orders of magnitude.”

In the paper

“The released HCP data are not considered de-identified, insofar as certain combinations of HCP Restricted Data (available through a separate process) might allow identification of individuals as discussed below.”

In the paper

“Because HCP participants come from families with twins and non-twin siblings, there is a risk that combinations of information about an individual (e.g., age by year; body weight and height; handedness) might lead to inadvertent identification, particularly by other family members, if these combinations were publicly released.”

In the paper

“Hence, for both modalities, the effective spatial resolution does not always achieve that implied by the size of the acquired voxels.”

In the paper

“If spatial correlations typically extend over ~50 – 100 grayordinates (e.g., patches ~15 – 20 mm in diameter), this would also suggest about 107 information bits per subject.”

In the paper

“At a macroscopic level, we know that individual cortical areas vary in surface area by two-fold or more across individuals (cf. Van Essen et al., 2012b)”

What the sources say

• Not checked yetcites Van Essen et al., 2012b

In the paper

“Hence, high sensitivity to sequence variants is critical for being able to characterize individual genomic differences and to relate these differences to phenotypes of interest.”

In the paper

“However, the level of nucleotide diversity across individuals is remarkably low (only about 1 part in 1000; Jorde and Wooding, 2004; Tishkoff and Kidd, 2004).”

What the sources say

• Not checked yetcites Jorde and Wooding, 2004
• Not checked yetcites Tishkoff and Kidd, 2004