Emily S Finn1, Laurentius Huber2,3, David C Jangraw2, Peter J Molfese2, Peter A Bandettini2. 1. Section on Functional Imaging Methods, Laboratory of Brain and Cognition, National Institute of Mental Health, Bethesda, Maryland, USA. emily.finn@nih.gov. 2. Section on Functional Imaging Methods, Laboratory of Brain and Cognition, National Institute of Mental Health, Bethesda, Maryland, USA. 3. MR-Methods Group, Maastricht Brain Imaging Center, Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands.
Abstract
Working memory involves storing and/or manipulating previously encoded information over a short-term delay period, which is typically followed by a behavioral response based on the remembered information. Although working memory tasks often engage dorsolateral prefrontal cortex, few studies have investigated whether their subprocesses are localized to different cortical depths in this region, and none have done so in humans. Here we use high-resolution functional MRI to interrogate the layer specificity of neural activity during different periods of a delayed-response task in dorsolateral prefrontal cortex. We detect activity time courses that follow the hypothesized patterns: namely, superficial layers are preferentially active during the delay period, specifically in trials requiring manipulation (rather than mere maintenance) of information held in working memory, and deeper layers are preferentially active during the response. Results demonstrate that layer-specific functional MRI can be used in higher-order brain regions to noninvasively map cognitive processing in humans.
Working memory involves storing and/or manipulating previously encoded information over a short-term delay period, which is typically followed by a behavioral response based on the remembered information. Although working memory tasks often engage dorsolateral prefrontal cortex, few studies have investigated whether their subprocesses are localized to different cortical depths in this region, and none have done so in humans. Here we use high-resolution functional MRI to interrogate the layer specificity of neural activity during different periods of a delayed-response task in dorsolateral prefrontal cortex. We detect activity time courses that follow the hypothesized patterns: namely, superficial layers are preferentially active during the delay period, specifically in trials requiring manipulation (rather than mere maintenance) of information held in working memory, and deeper layers are preferentially active during the response. Results demonstrate that layer-specific functional MRI can be used in higher-order brain regions to noninvasively map cognitive processing in humans.
Working memory (WM) is the highly evolved mental capacity to store and
manipulate information for short-term use. It is often probed with delayed-response
tasks that require encoding a stimulus, sustaining a representation of the stimulus
over a delay, and finally making a memory-guided behavioral response.The dorsolateral prefrontal cortex (dlPFC) has been linked to WM processes in
both humans and non-human primates [1-4]. Like much of
the cerebral cortex, dlPFC gray matter is organized into layers with distinct
cytoarchitecture, connectivity and function. Early electrophysiological work in
non-human primates suggested that in delayed-response tasks, different task periods
are preferentially associated with activity in different cortical layers [5,6]. Specifically, delay-period activity is thought to be driven by
recurrently connected networks of pyramidal cells in layer III [3], while response-related activity takes place
predominantly in layer V [7] Two
recent studies in macaques, which overcame the challenge of separating activity
recorded from distinct cortical layers, provide direct evidence for this
dissociation [8,9]However, it remains unclear to what extent dlPFC exhibits homologous function
between monkeys and humans. While dlPFC often appears active during WM tasks in
human functional MRI studies, human dlPFC may not be strictly necessary for mere
maintenance of information—that is, for sustaining the representation of a
stimulus “as-is” without performing further operations on it. Instead,
dlPFC may be necessary only when the task calls for rule-based manipulation of
information stored in WM; for example, when items must be reordered or transformed
in some other way. Indeed, disrupting dlPFC activity with lesions [10,11] or repetitive transcranial magnetic stimulation (rTMS)
[12] impairs manipulation,
but leaves maintenance largely intact.To the extent that human dlPFC is specialized for manipulation rather than
pure maintenance, the laminar specificity of these operations is unknown. Following
an evolutionary progression, we hypothesize that manipulation in humans might
recruit the same local recurrent excitatory networks of layer III pyramidal cells as
maintenance does in non-human primates. This hypothesis is also supported by
converging evidence from schizophrenia, which is associated with reduced dendritic
spine density specifically in dlPFC layer III neurons [13,14] as
well as behavioral deficits in manipulation (over and above maintenance)[15]. On the other hand, activity
involved in response selection and action initiation may take place predominantly in
infragranular layers, as has been observed in non-human primates [16,17,9]. To date there is
no empirical evidence for such a dissociation in humans, largely because
conventional neuroimaging techniques lack the sensitivity and specificity to resolve
cortical layers.Recent methodological advances in fMRI, including higher field strengths
(i.e., 7 Tesla and above) combined with innovations in pulse sequences and contrast
mechanisms, now allow for non-invasive, reliable measurements of cortical
depth-dependent activity in humans. These advances have enabled layer-specific
imaging in several primary cortices, including visual [18-20], auditory [21],
and motor [22]. (Note that in the
context of fMRI, the term ‘layer’ refers to estimates of different
cortical depths, not necessarily to cortical layers as defined
cytoarchitectonically.) While simulations suggest that fMRI should in principle be
able to resolve laminar differences in more complex tasks [23], it is still unclear if these techniques are
sensitive and robust enough to be applied outside primary cortices.Here, by further developing layer-fMRI methods to move beyond unimodal
cortex[22] into higher-order
areas, we provide evidence for cortical depth-dependent processing during a
sophisticated cognitive task in one of the most highly evolved regions of human
association cortex. Specifically, we use simultaneously acquired blood oxygen
level-dependent (BOLD) and cerebral blood volume (CBV) images of human dlPFC during
a working memory task to show that during the delay period, manipulation evokes
greater activity than maintenance specifically in superficial layers, while during
the response period, activity is localized to deeper layers. These results deepen
our understanding of the laminar specificity of WM-based operations in humans, and
demonstrate the promise of high-resolution fMRI for mapping cognitive cortical
circuitry at the mesoscale.
RESULTS
Task paradigm
To test our hypotheses about layer-dependent activity during WM, we used
a well-validated task paradigm that dissociates maintenance from manipulation
during the delay period[24], and
added a second contrast to separate action from non-action during the response
period. See Fig. 1A for a schematic of the
task. All trials are matched for sensory input, with the only difference being
the nature of the mental activity during the delay for the first contrast, or
the presence or absence of action selection and execution during the response
period for the second contrast. (Note that an action-related signal can also be
isolated from the first contrast by examining activity at the time of the
response compared to all other timepoints; we exploit this in a second
acquisition protocol described further below.)
Fig. 1
Task, hypothesis and region of interest.
(A) Trial structure. Top panel: first contrast type, contrasting
manipulation (‘alphabetize’) versus maintenance
(‘remember’) during the delay period. Subjects see a string of
five random letters (e.g., ‘BDCEA’), then a cue instructing them
to either rearrange the letters in alphabetical order
(‘ALPABETIZE’, manipulation condition) or to simply remember them
in their original order (‘REMEMBER’, maintenance condition) over
the course of a delay period, during which they see only a fixation cross.
Finally, a probe letter comes onscreen (e.g, ‘D?’), and subjects
make a response to indicate the alphabetical or ordinal position of the probed
letter. Bottom panel: second contrast type contrasting action versus non-action
during the response period. These trials are identical to the first until the
response period, at which point subjects see either a true probe requiring a
button press (e.g., ‘D?’, action condition), or a dummy probe
(i.e., ‘*?’, non-action condition), which indicates that no
response is required and they can forget the information associated with that
trial. Colored frames are for schematic purposes only and were not seen by
subjects. (B) Schematic of hypothesis. We hypothesized that (i) in superficial
layers, manipulation trials would evoke more activity than maintenance trials
specifically during the delay period due to recurrent excitation in layer III
(purple arrows), and (ii) in deeper layers, action trials would evoke more
activity than non-action trials due to action-selection and/or motor-related
functions in layer V (teal arrows). WM, white matter; CSF, cerebro-spinal fluid.
(C) Macroscale location of left dlPFC region of interest (MNI coordinates for
center of mass: [x = +49, y = −21, z = +23], computed via group analysis
of whole-brain functional localizer data (resulting in cluster displayed at
voxelwise p < 0.01). For single-subject layer ROIs, see Fig. S3.
Thus the main paradigm followed a 2×2×2 design, with trial
type (manipulation/maintenance versus action/non-action), period (delay versus
response), and cortical depth (superficial versus deep) as the three factors. We
hypothesized a triple dissociation between trial type, period, and cortical
depth, such that: (1) superficial layers would respond more strongly during the
delay period of manipulation trials (as
compared to the delay period of maintenance trials), and (2) deeper layers would
respond more strongly during the response period of
action trials (as compared to the response period of
non-action trials). See Fig. 1b for a
schematic of the hypothesis. The strength of this experimental design is that we
control for each layer’s timecourse of activity primarily by observing
the same layer in a different condition, rather than directly comparing activity
levels across layers; this avoids measurement biases associated with different
cortical depths.
Data acquisition
Functional data are from n = 15 unique subjects scanned in a combined
total of 20 imaging sessions. During each high-resolution functional run, we
simultaneously measured changes in cerebral blood volume (CBV) and
blood-oxygen-level dependent (BOLD) signal using the SS-SI-vascular space
occupancy (VASO) method [25]
with a 3D-EPI readout [26] on a
7 Tesla scanner. This method has been implemented to successfully demonstrate
layer-specific activity in human motor cortex with good sensitivity and
specificity [22]. The
conventional BOLD signal has poor spatial specificity at high resolutions, since
it tends to be dominated by large veins at the pial surface, and depends on
non-linear interactions between physiological variables that can differ across
cortical depths, making it difficult to quantitate. VASO, while it has a lower
contrast-to-noise ratio, is a more quantitative measurement that is less biased
toward superficial depths. In short, BOLD is more sensitive, while VASO is more
specific.We used two different acquisition protocols over the course of the
study. The first had a nominal voxel resolution of 0.9 × 0.9 ×
1.1mm (referred to as the “axial [readout] protocol”). These data
were used to quantitatively compare activity timecourses across two distinct
cortical depths (superficial versus deep) at the group level. Later, we
introduced a second, higher resolution protocol with nominal voxel resolution of
0.76 × 0.76 × 0.99mm (referred to as the “sagittal
[readout] protocol”). These data were used to visualize activity across
different layers in individual subjects. For both protocols, the field of view
was not the whole brain but rather a slab centered on a region of interest
within left dlPFC that was identified via on online functional localizer
conducted at the start of each imaging session. (Due to restrictions on its MRI
sequence parameter space, and the need to apply a slab-selective inversion
pulse, VASO is currently limited in the spatial coverage that can be achieved at
these resolutions.) See Methods and Fig. S1 for further
details of our data acquisition and analysis pipeline.
Location of region of interest
Prefrontal cortex is large, and quite variable across individuals in
terms of structure and functional anatomy. Unlike other cortical landmarks, such
as the ‘hand knob’ of the primary motor cortex, functional
subdivisions of prefrontal cortex are difficult to pinpoint in individual
subjects using macroscale anatomical features. Therefore, regions of interest
(ROIs) were selected for each subject on the basis of an online functional
localizer conducted just prior to the experimental task runs (see Methods). Given that imaging parameters
could only be optimized for one hemisphere at a time, we focused on left dlPFC
in all subjects, based on previous reports as well as our own pilot experiments
indicating that this task more strongly engages the left over the right
hemisphere. (Because our stimuli, being letters, were verbal in nature, this
lateralization may be due in part to a left-hemisphere dominance for
language.)Despite the variance in prefrontal cortex size and anatomy across
subjects, the ROI location was highly consistent with respect to the
subject-specific cortical folding structure that was visible in EPI space. In
all subjects, the ROI was located in the ventral portion of the middle frontal
gyrus corresponding approximately to Brodmann area 9/46[27]. To ensure that our ROI selection
procedure was robust, we conducted test-retest scans separated by several weeks
on two subjects. Results showed good overlap between ROIs derived from
independent experimental sessions (Fig. S2), indicating that the functional region in question
can be reliably localized within subjects. Fig.
1c shows the average ROI location across subjects computed from the
whole-brain functional localizer (though note that this figure is a post-hoc
visualization only; all analyses of the high-resolution experimental data were
conducted in single-subject space to preserve spatial specificity). See Supplementary Videos
1–6
for slice-by-slice visualizations of the selected ROI in six individual
subjects.For each subject, two layers, superficial and deep, were each drawn
manually within the selected ROI (see Fig. S3 for layer masks for all subjects scanned using the
axial readout protocol). To better specify the position of our
“superficial” and “deep” layers with respect to
cortical laminae defined cytoarchitectonically, we compared all available
MRI-based anatomical contrasts with an existing histological image (Fig. S4). The boundary
between our superficial and deeper layers fell approximately between layer III
and layer IV.
Task performance
Subjects performed well on the task (overall mean accuracy = 0.82, s.d.
= 0.13, range = 0.59 – 0.97; note that chance is approximately 0.2),
including both manipulation trials (mean (s.d.), range: 0.79 (0.13), 0.54
– 0.96) and maintenance trials (mean (s.d.), range: 0.88 (0.15), 0.53
– 1.0). Subjects were less accurate on manipulation compared to
maintenance trials (paired t-test, t14 = −3.28, p = 0.01),
which is expected given previous reports using this task[24].Overall mean reaction time (RT) was 2.37 s (s.d., range: 1.24, 1.05
– 5.17). Crucially, there was no difference between mean RT on
manipulation versus maintenance trials (paired t-test, t14 = 1.29, p
= 0.22). It is therefore unlikely that conditions differ in latency of peak
response-related activity, allowing us to directly compare timecourses without
deconvolution.
Activity timecourses
Using data from 15 experimental sessions (n = 13 unique subjects)
scanned with the axial protocol, we observed layer-dependent activity
timecourses that followed the hypothesized patterns: in superficial layers,
activity was higher in manipulation relative to maintenance trials during the
delay period, and in deeper layers, activity was higher in action versus
non-action trials during the response period. These patterns were visible in
both VASO and BOLD (Fig. 2, Fig. S5). Below we
summarize characteristics of these depth-dependent timecourses during the two
main periods of interest, delay and response.
Fig. 2
Different trial types evoke distinct spatiotemporal patterns of
activity.
(A) Left panel: mean VASO signal change (in units of mL/100 mL cerebral
blood volume [CBV]) in superficial layers (top) and deeper layers (bottom) for
the first contrast, manipulation trials (‘alpha’) versus
maintenance trials (‘rem’). Right panel: mean VASO signal change
in superficial layers (top) and deeper layers (bottom) for the second contrast,
action trials (‘act’) versus non-action trials
(‘non-act’). Lines represent mean and shaded area represents 95
percent confidence intervals for the mean (determined via bootstrapping with
1,000 iterations) across n = 15 sessions (13 unique subjects). See Figs. S6 and S7 for single-subject
timecourses, and Fig.
S5a for mean BOLD timecourses. (B) Two-way analyses of variance
(ANOVAs) with factors trial period (delay versus response) and trial type
(either manipulation [‘alpha’] versus maintenance
[‘rem’], or action versus non-action) in superficial (top) and
deeper (bottom) layers. Panels as in (A). Dots represent mean and error bars
reflect 95 percent confidence intervals for the mean. **, interaction
significant at p < 0.001 (p = 7.7e−5 and p = 0.002 for
superficial alphabetize-versus-remember contrast and deeper
action-versus-non-action contrast, respectively); *, interaction significant at
p < 0.01 (p = 0.004 for deeper alphabetize-versus-remember contrast);
n.s., interaction not significant (p = 0.68 for superficial
action-versus-non-action contrast).
Delay-related activity.
In superficial layers (Fig. 2a,
top row), delay-period activity was uniformly high during manipulation
trials. This is evident in trials labeled ‘alpha’,
‘action’ and ‘non-action’ (recall that both
action and non-action trials call for alphabetizing, and they are
indistinguishable from one another until the probe appears). Superficial
delay-related activity was higher during manipulation than maintenance,
although results from the more-sensitive BOLD contrast indicated that
maintenance alone was also sufficient to evoke above-baseline activity
(Fig. S5). In
addition to the group-level results shown in Fig. 2, this effect was clearly visible in single-subject data
(Fig. S6).In contrast to superficial layers, deeper layers were markedly less
active during the delay period (Fig.
2a, bottom row; although note that the BOLD data in particular
suggest that their activity is still slightly above baseline during this
period, Fig. S5).
Thus, it seems that delay-related activity occurs predominantly, if not
exclusively, in superficial layers, and particularly when task demands call
for manipulation of information stored in WM rather than mere
maintenance.
Response-related activity.
During the response period, we observe the opposite pattern:
activity in deeper layers is high, but only in trials requiring an action.
Deep-layer activity peaks at the time of the response, which is expected at
approximately 6-7 seconds after the probe comes onscreen (reflecting
behavioral and hemodynamic delay). As expected, this peak is present in
action but not non-action trials (Fig.
2a, bottom right). Again, this effect was also visible in most
individual subjects (Fig.
S7).As for superficial layers, their activity is, if anything,
suppressed at the response peak in both trial types (Fig. 2a, top right). This confirms our prediction
that the response period is preferentially associated with activity in
deeper cortical layers.These same patterns were visible to some degree in the BOLD contrast
(Fig. S5),
although the strong superficial bias of BOLD make it difficult to draw firm
conclusions from these data. (For example, the apparent difference between
action and non-action trials in superficial layers visible in Fig. S5a, top right
is likely an artifact of draining veins from the deeper layers, since this
difference is not present at all in the VASO data shown in Fig. 2a, top right.) Due to the higher spatial
specificity and more quantitative nature of VASO, we performed all
statistical comparisons using this contrast as described in the following
section.
Quantification of differential activity
To quantitatively compare activity within cortical depths, we performed
a series of two-way, repeated-measures analyses of variance (ANOVAs) using
representative signals from each trial type during each trial period. In each
ANOVA, the two factors were trial type (either ‘alphabetize’ and
‘remember’, or ‘action’ and
‘non-action’) and trial period (delay and response), with subject
as the repeated measure.For superficial layers, we found a significant interaction between trial
type (manipulation versus maintenance, or ‘alphabetize’ versus
‘remember’) and trial period (F(1,14) = 34.7, p =
7.7e−5), such that activity was higher in manipulation
trials, but only during the delay period (Fig.
2b, top left). As expected, the contrast between the second condition
pair (action versus non-action) revealed a main effect of period (F(1,14) =
123.0, p = 2.6e−8), such that activity was higher during the
delay than during the response, but no interaction between period and trial type
(F(1,14) = 0.19, p = 0.68; Fig. 2b, top
right).For deeper layers, as predicted, we found the opposite pattern of
results. There was a significant interaction between trial type (action versus
non-action) and trial period (F(1,14) = 26.0, p = 0.002), such that activity was
higher in action trials during the response (Fig.
2b, bottom right). The contrast between the manipulation and
maintenance conditions indicated an interaction such that activity was higher
during the response than during the delay, but only in manipulation trials
(F(1,14) = 13.4, p = 0.004; Fig. 2b, bottom
left).Another way to assess relevant differences is to subtract the average
timecourse within each depth between the trial types of interest. Results
indicate that for superficial layers, the difference between manipulation and
maintenance peaks during the delay period (Fig.
3a, top and Fig.
S5b, top), while for deeper layers, the difference between action and
non-action trials peaks at the time of the response (Fig. 3a, bottom and Fig. S5b, bottom).
Fig. 3
Activity contrasts across layers and conditions of interest.
(A) Top: Superficial-layer VASO activity during maintenance
(‘rem’) trials subtracted from activity during manipulation
(‘alpha’) trials [purple line]. The largest difference can be seen
during the delay period. Bottom: Deeper-layer VASO activity during non-action
(‘non-act’) trials subtracted from activity during action
(‘act’) trials [teal line]. The largest difference can be seen
during the response period. Lines represent mean and shaded area represents 95
percent confidence intervals for the mean (determined via bootstrapping with
1,000 iterations) across n = 15 sessions (13 unique subjects; same data as in
Fig. 2). See Fig. S5b for subtractions
based on mean BOLD activity timecourses. (B) Two-way ANOVAs with factors layer
(superficial versus deeper) and contrast (manipulation – maintenance
[‘alpha – rem’, purple lines] versus action –
non-action [teal lines]), for each trial period (delay and response). Dots
represent mean and error bars reflect 95 percent confidence intervals for the
mean (determined via bootstrapping with 1,000 iterations) across n = 15 sessions
(13 unique subjects). **, interaction significant at p < 0.001 (p =
6.9e−6 and p = 3.0e−4 for the delay
period [left] and response period [right], respectively).
As a final quantification step, we statistically compared these
differential activity levels by performing ANOVAs on representative signals from
each period (delay and response) in each differential time course
(manipulation–maintenance and action–non-action), again with
subject as the repeated measure (Fig. 3b).
While directly comparing superficial and deeper layers should be done with
caution as results can be biased by cross-depth differences in baselines, scale
factors and vascular cross-talk, in this case we use a difference-of-differences
approach that helps mitigate some of these concerns. Results confirm that during
both trial periods, there is an interaction between layer and condition pair
such that during the delay period, superficial layers are more sensitive to the
manipulation–maintenance contrast (F(1,14) = 92.7, p =
6.9e−6; Fig. 3b,
left), while during the response period, deeper layers are more sensitive to the
action–non-action contrast (F(1,14) = 30.5, p = 0.0003; Fig. 3b, right).
Visualization of depth-dependent activity
To better visualize the depth-dependent distribution of activity
associated with different periods within the trial, we used a second,
higher-resolution imaging protocol in which the field of view was a sagittal
slab centered on dlPFC with in-plane resolution of 0.76 × 0.76mm. In
these experiments, the task consisted exclusively of manipulation/maintenance
trials, all requiring an active response (i.e., the first contrast type shown in
Fig. 1a, top). Functional signals
during manipulation and maintenance trials were investigated across cortical
depths.We detected layer-dependent activity in all individual subjects imaged
using this protocol (n = 5; Fig. 4).
Manipulation evoked more activity than maintenance predominantly in superficial
layers (green stripes), while signal associated with response (as compared to
baseline; red stripes) was predominantly localized to deeper layers. These
patterns were visible in both the BOLD (Fig.
4a) and VASO (Fig. 4b) contrasts
(though note the different thresholds). Layer ROIs for each subject are shown in
Fig. 4c, and a discussion of the
observed variance in functional response across the cortical surface (i.e.,
across columns) is given in Fig. S8.
Fig. 4
Single-subject layer-dependent activity profiles.
Results from five subjects scanned using the sagittal protocol. Activity
is shown in both functional contrasts, BOLD (A) and VASO (B). Signal changes for
delay and response periods are smoothed within layers. No smoothing was applied
across layers. Note the different color scales for BOLD and VASO. Color
intensity indicates percent signal change. Red/orange reflects increased signal
during the response period compared to baseline (inter-trial interval). Green
represents increased signal during the delay period for manipulation compared to
maintenance trials. Inset line graphs show the corresponding layer activity
profiles plotted across cortical depth. In VASO insets (B), note that the red
line is always above the green line in the deeper layers (red shading), while
the green line is always above the red line in the superficial layers (green
shading), meaning that the task used here engages the layer superficial and
deeper layers differently. This is consistent across subjects. Estimates of
layers (cortical depths) for each subject are shown in (C). Insets in (C) are
subject-specific layer profiles distribution of the T1-weighted EPI signal. The
black arrow indicates the location of a myelin-related signal dip, which can be
taken as a landmark for the transition region between cytoarchitectonic layer
III and layer V (see Fig.
S4). Error bars in average profiles (bottom row) reflect standard
error of the mean across subjects.
DISCUSSION
While working memory has been known to engage dlPFC for decades, the degree
to which its sub-processes were layer-specific had been hypothesized [3] but demonstrated only a handful of
times in non-human primates [9,8]. Furthermore, the extent of
functional homology in this region between humans and non-human primates was
unclear. Here, we interrogate layer-specific functionality directly and
non-invasively in humans, shedding new light on the laminar specificity of WM
processes in dlPFC. By developing and optimizing state-of-the-art techniques in
high-resolution fMRI for cognitive brain areas, and using a task design for which we
had hypotheses about the location, magnitude and timing of neural activity, we were
able to detect timecourses at different cortical depths that followed the expected
patterns. Namely, we observed delay-related manipulation activity that was
predominantly localized to superficial layers, and response-related activity that
was predominantly localized to deeper layers.We interpret the observed laminar specificity of distinct working memory
processes in light of what is known about underlying neural circuitry. First,
superficial activity during the delay period may at least partially reflect
recurrent excitatory connections. While in early parts of the cortical hierarchy,
superficial layers give rise to feedforward connections, at the highest levels
(i.e., PFC), laminar projections become more complex. Layer III expands and is the
focus of extensive local, recurrent excitatory connections [28], as well as long-range recurrent connections
with other regions that may be involved in storing items in working memory, e.g.,
parietal association cortex [7,29] Recurrent excitation among these
cells is a feature of their unique molecular profile, notably their preferential
expression of n-methyl-d-aspartate (NMDA) receptors and specifically the NR2B
subunit, whose slower kinetics allow for persistent firing over long delays; this
has been predicted by computational models [30] and confirmed experimentally in primates [31]. While our findings suggest that
superficial layers are active specifically when the task calls for manipulating and
not just storing information, with our current task design, we cannot fully rule out
the possibility that superficial-layer activity depends somewhat on task difficulty
or engagement more generally. In future work, designs that parametrically vary load
under both manipulation and maintenance conditions will help define the precise
functional role of superficial-layer cells in dlPFC.Second, response-period activity in deeper layers likely reflects functions
related to response selection, action execution, or both. In our task paradigm, a
response could not be selected until the probe appeared onscreen. This is in keeping
with typical delayed-response paradigms used in human neuroimaging, but different
from those used with non-human primates, which are based on oculomotor responses to
a single remembered item, meaning the animal can predict the upcoming response
during the delay period. Human neuroimaging studies suggest a role for dlPFC in
selecting and planning an appropriate task response [32-34], even in the absence of a working memory requirement [35]; this activity scales with factors
affecting response selection even while eventual motor output is held constant
[36], seeming to indicate
response selection as the dominant process taking place in dlPFC. On the other hand,
non-human primate electrophysiological studies, most notably those featuring laminar
specificity [9,8], report deeper-layer activity that appears to
track action execution (i.e., saccades) more directly. This activity might reflect
one or a number of processes related to motor execution, such as initiating an
action, suppressing prepotent responses, or a feedback mechanism such as corollary
discharge. While dlPFC does not project directly to primary motor cortex (M1), it
may influence motor behavior polysynaptically via higher-order cortical motor areas
[37,38] or the striatum [39,40].
Like most delayed-response human fMRI paradigms, our task timing and temporal
resolution do not allow us to separate response selection from action initiation
itself, meaning future work will be necessary to dissociate these two processes and
the extent to which they account for the layer-specific response profiles observed
here.Of note, schizophrenia is associated with altered genetics [7], morphology [14,13]
and function [41] in this very dlPFC
circuitry. Decreased delay-related activity in superficial layers, as well as
disinhibition in deeper layers, may underlie the deficits in working memory and
other cognitive functions seen in these patients. We expect that future studies
using layer-fMRI in populations with or at risk for schizophrenia will shed new
light on the spatiotemporal dynamics of cognitive dysfunction in this illness.From a methodological perspective, here we used advanced contrast mechanisms
and balanced task design to offset differences in vascular physiology across
cortical depths, which can introduce substantial biases and limit the
interpretability of layer fMRI [42].
In contrast to gradient-echo BOLD (GE-BOLD), CBV-weighted fMRI signal acquired with
VASO allows appropriate separation of microvascular responses at a layer-dependent
level [43,44]. We avoid biases of different hemodynamic response
functions (HRFs) across cortical depths [45,46] by refraining
from using statistical general linear model (GLM) deconvolution with predefined
HRFs, and by restricting our interpreting to quantitative signal differences that
are obtained at the same latency within identical task blocks. Additionally, we
collected conventional GE-BOLD fMRI concomitantly with VASO data. The
near-simultaneous acquisition of BOLD and VASO data allowed us to obtain a clean
BOLD-corrected, CBV-weighed VASO signal. The higher sensitivity of BOLD compared to
VASO was helpful in selecting the correct ROI, while the higher spatial specificity
of VASO was helpful for interpreting signal across cortical depths.These methodological advances have exciting implications for non-invasive,
in vivo mapping of input-output and feedforward-feedback
connections in the human neocortex. Outstanding challenges include expanding spatial
coverage without sacrificing resolution, which would allow for functional
connectivity analyses to infer information flow between far-flung cortical areas.
For example, simultaneous imaging of dlPFC, premotor and primary motor cortices
would help characterize inter-region interactions during response selection and
execution, while expanding coverage to parietal and sensory areas as well as
neighboring prefrontal areas would help characterize interactions that support
stimulus perception, information storage and manipulation during the encoding and
delay periods.Looking beyond working memory, these tools provide a starting point for
future work mapping layer-specific connections within high-order association cortex,
and between high-order and unimodal cortex, in the context of cognitive
neuroscience. Many influential theories of brain function that posit top-down and
bottom-up signals with origins and destinations in distinct cortical
layers—e.g., predictive coding and related frameworks—may now be
directly tested in humans[47]. This
opens the door to investigating computational mechanisms behind any number of
neuropsychological phenomena, such as selective attention, hallucinations and
delusions, and even consciousness itself, to name a few[48]. We expect that the ever-advancing tools of
high-resolution fMRI will ultimately transform our understanding of cognition in the
awake, behaving human brain.
METHODS
Please refer to the Life Sciences Reporting Summary, published alongside the
online version of this paper, to access a subset of this information in a
standardized format.
Subjects
Seventeen healthy volunteers participated after granting informed
consent under an NIH Combined Neuroscience Institutional Review Board-approved
protocol (93-M-0170, ClinicalTrials.gov identifier: )) in
accordance with the Belmont Report and US federal regulations that protect human
subjects. Data from two subjects were excluded due to technical difficulties or
experimenter error: in one subject, no clear activation was visible within the
field of view (meaning the region of interest was likely outside the field of
view), and in the second subject, an incorrect version of the task was used,
resulting in altered event timings that made this subject’s data
incompatible with the rest of the dataset. Of the remaining 15 subjects (age
20-47 years at the time of the experiment) whose data entered into the analyses
presented here, eight were male and seven were non-pregnant females.The functional data presented here come from a total 40 hours of scan
time collected in 20 two-hour scan sessions. Two different functional
acquisition protocols were used over the course of the study: an “axial
[readout] protocol” (n = 15 sessions) and a “sagittal [readout]
protocol” (n = 5 sessions); these are described further in their
respectively titled sections below. Of the 15 unique subjects, n = 8 were
scanned only once using the axial protocol; n = 3 were scanned once using the
axial protocol and once using the sagittal protocol; n = 2 were scanned only
once using the sagittal protocol, and n = 2 were scanned twice on the axial
protocol. Some overlap of subjects was by design, allowing us to assess
test-retest reliability of our ROI location (see Fig. S2). No statistical
methods were used to pre-determine sample sizes, but our sample size is
consistent with or larger than those reported in previous layer fMRI studies
[22,21,43,44,19,20].All fifteen subjects were invited for a separate scan session to obtain
high-resolution reference anatomical T1-weighted data with an
MPRAGE-based sequence. Five additional two-hour scan sessions were used as pilot
experiments to optimize the task design and investigate motion limitations and
sequence artifacts; data from these sessions are not shown.The task was created using PsychoPy2 software [49]. For the axial readout protocol (TR = 2
s, described below), each trial consisted of the following epochs (example,
duration): letter string presentation (BDCAE, 2.5 s), fixation cross (+, 1.5 s),
instruction cue (ALPHABETIZE or REMEMBER, 1 s), delay period with fixation cross
(+, 9 s), probe (D? or *?, 2 s), inter-trial interval with fixation cross (+, 16
s). Subjects could register a response at any time following the appearance of
the probe and before the start of the next trial (i.e., anytime during the
inter-trial interval). Each trial thus lasted 32 s, and each run consisted of 20
trials plus brief (8 s) additional fixations at the beginning and end of the
run, for a total of 10:56 min:sec per run. Runs alternated between two contrast
types: (1) manipulation versus maintenance (consisting of a mix of ALPHABETIZE
and REMEMBER trials, all requiring action), and (2) action versus non-action
(consisting of a mix of action and non-action trials, all ALPHABETIZE). Within
each run, the 10 trials of each type were presented in a fixed pseudorandom
order that was the same for all runs, to facilitate averaging.For the higher-resolution sagittal readout protocol (described below),
all runs were of the first contrast type (manipulation versus maintenance), and
trial epoch timings were adjusted to match the longer TR (2.5 s) by scaling the
duration of each epoch by a multiplier of 1.25. Each trial thus lasted 40 s, and
the duration of these runs was 13:40 min:sec. All other parameters, including
the pseudorandom order, were kept the same as above.Prior to the start of the experimental runs, we ran a 6-minute
functional localizer that was conducted at standard resolution and analyzed in
real time, allowing us to functionally define a region of interest within left
dlPFC in each individual subject while the subject was in the scanner. This
localizer consisted entirely of ALPHABETIZE trials and slightly altered timing.
The length of all trial epochs was as described above except the inter-trial
interval, which was shortened to 5 s to create a 10-s on, 10-s off paradigm.
Delay-related activity (including cue plus delay-related fixation) was
considered signal, while all other trial epochs were treated as baseline. The
location of peak activity from the real-time general linear model (GLM) analysis
was used to position the coverage of the subsequent sub-millimeter
experiments.
Randomization and blinding
There were no experimental groups in this study; therefore, no
randomization of subjects was necessary. As stated in the “Task
paradigm” section above, within each run, the 20 trials (10 of each type)
were presented in a fixed pseudorandom order that was the same for all subjects
and all runs. This was done to facilitate averaging within subjects and to
ensure a relatively even distribution of each trial type across the beginning,
middle and end of runs (to mitigate concerns about signal drift that might
differentially affect one trial type or the other).Data collection and analysis were not performed blind to the conditions
of the experiments. Subjects were not told the purpose of the study or specific
hypotheses concerning differences between trial types and within-trial periods
ahead of time, but were debriefed following data collection upon request.
Experimental setup
All imaging was performed on a MAGNETOM 7T scanner (Siemens
Healthineers, Erlangen, Germany) with a
single-channel-transmit/32-channel-receive heal coil (Nova Medical, Wilmington,
MA, USA). Imaging sessions did not exceed 120 minutes. Imaging slice position
and slice angle were adjusted individually for every subject on the basis of the
functional localizer described above.A 3rd-order B0-shim was done with three iterations
using vendor-provided tools. The shim volume covered the entire imaging field of
view (FOV) and was extended down to the circle of Willis in order to obtain
sufficient B0-homogeneity to exceed the adiabaticity threshold of the
inversion pulse.Following the functional localizer, for the axial protocol, run type
alternated between the first contrast (alphabetize/remember) and the second
contrast (action/non-action). All subjects completed at least five runs (3 of
the alphabetize/remember contrast and 2 of the action/non-action) per imaging
session. Therefore there were 30 ‘alphabetize’, 30
‘remember’, 20 ‘action’ and 20
‘non-action’ trials per subject per session. (Note that
‘alphabetize’ and ‘action’ trials are technically
identical, although data were not pooled between these two conditions for
analysis purposes given that they were acquired in different runs.) When time
allowed (for n = 6 subject-sessions), a sixth run was acquired
(action/non-action contrast); these sessions thus comprised 30 of each trial
type.For the sagittal protocol, all runs were of the first contrast type
(alphabetize/remember), and also consisted of 10 trials of each type (20 total),
although note each trial was scaled to be longer in duration in order to match
the TR of this protocol. Most subjects scanned using this protocol (n = 3)
completed four total runs, or 80 total trials (40 ‘alphabetize and 40
‘remember’). One subject completed three total runs (60 total
trials/30 of each type) and one subject completed five runs (100 total trials/50
of each type).
Axial readout protocol
The protocol parameters were as follows: Readout type: 3D-EPI with one
segment per k-space plane [26],
in-plane resolution 0.91 × 0.91 mm2, slice thickness 1.1 mm,
FLASH GRAPPA 3, partial Fourier in the first phase encoding direction: 6/8, no
partial Fourier in the second phase encoding direction, TRVASO = 2000
ms, TRVASO+BOLD = 4000 ms, FOV read and phase = 150 mm, matrix size =
162, TE = 20 ms, read bandwidth = 1144 Hz/Px, phase echo spacing = 0.98.
Assuming a GM T2* = 28 ms, the expected
T2* blurring for EPI-readout results in a signal
leakage of 12% from one voxel into the neighboring voxels along the first
phase-encoding direction. A more detailed list of scan parameters used can be
found on GitHub: https://github.com/layerfMRI/Sequence_Github/blob/master/DLPFC_Emily/Emily_Intermediate_protocol.pdf.
Sagittal readout protocol
The protocol parameters are as follows: Readout type: 3D-EPI with one
segment per k-space plane [26],
in-plane resolution 0.75 × 0.75 mm2, slice thickness 0.99 mm,
FLASH GRAPPA 3, partial Fourier in the first phase encoding direction: 6/8, no
partial Fourier in the second phase encoding direction, TRVASO = 2500
ms, TRVASO+BOLD = 5000 ms, FOV read = 130 mm, FOV phase 98.8%, matrix
size = 172, TE = 27 ms, read bandwidth = 908 Hz/Px, phase echo spacing = 1.23
(limited by peripheral nerve stimulation thresholds). Assuming a GM
T2* = 28 ms, the expected T2* blurring for
EPI-readout results in a signal leakage of 14% from one voxel into the
neighboring voxels along the first phase-encoding direction. A more detailed
list of scan parameters used can be found on GitHub: https://github.com/layerfMRI/Sequence_Github/blob/master/DLPFC_Emily/DLPFC_high_res_076_0.76_1.pdf.
VASO-specific protocol parameters
Both readout protocols were acquired with the same VASO preparation
module. The protocol parameters were: Inversion pulse type: TR-FOCI pulse with a
bandwidth of 6.4 kHz, μ = 7, pulse duration: 10 ms, non-selective. The
phase skip of the adiabatic inversion pulse was adjusted to 30 deg to achieve an
inversion efficiency of 80%, shorter than the arterial arrival time in the dlPFC
[50]. The inversion time
was adjusted to match the blood-nulling time of 1100 ms as done in previous
studies [22]. To account for the
T1-decay during the 3D-EPI readout and potential related blurring
along the segment direction, a variable flip angle was chosen. The flip angle of
the first segment was adjusted to be 22 deg. The subsequent flip angles where
exponentially increasing, until last k-space segment was excited with a desired
flip angle of 90 deg.
Image reconstruction
Image reconstruction was done in the vendor-provided platform as done
previously [22]. GRAPPA 3 kernel
fitting was done on FLASH ACS data, using a 3 × 4 kernel, 48 reference
lines, and regularization parameter χ = 0.001. RF-channels were combined
with the sum-of-squares. To minimize resolutions losses in the phase-encoding
direction due to T2*-decay partial, Fourier reconstruction
was done with POCS using 8 iterations.
Anatomical reference data
In separate scan sessions, 0.7 mm resolution T1-maps where
collected covering the entire brain with an MP2RAGE sequence [51] for every subject. These data
were not used in the functional pipelines to analyze the layer-dependent
activity changes. Instead, these images were used to investigate the
reproducibility of location of activity across sessions (Figure S2) and across
subjects (Figure 1c).In four of the subjects that were invited for more than two 2-hour
sessions, slab-selective isotropic 0.5 mm and 0.4 mm resolution anatomical data
were collected with MP2RAGE and Multi-Echo FLASH, respectively. Those anatomical
data were not used in the pipeline for generating cortical profiles. They are
used to compare and validate the approximate position of the
cyto-architectonically defined cortical layers of individual subjects to the 20
reconstructed cortical depths, in which the functional data are processed (Fig. S4).
Functional image preprocessing
This section describes processing steps that were common to both the
axial and sagittal protocols. For a schematic overview of the analysis pipeline,
see Fig. S1.First, DICOM images were converted to NIFTI using the ISISCONV converter
(Fig. S1a). Motion
correction was performed using SPM software (Statistical Parametric Mapping;
SPM12) [52] and was done
separately for nulled and not-nulled frames (Fig. S1b). A
4th order spline function was used for spatial interpolation.
Motion correction and registration across runs was done simultaneously. This
minimized the effect of spatial resolution loss to one single resampling step
[53]. Motion traces of
nulled and not-nulled were visually inspected to ensure good overlap for the two
contrasts (Fig.
S1b).Following these steps, frames were sorted into their respective
contrast: not-nulled (BOLD) or nulled (VASO; Fig. S1c). Note that BOLD
and VASO contrasts are kept separate from this point forward, and all analyses
below were performed for each contrast individually.Next, runs of the same contrast type were averaged (Fig. S1d), and within
these average runs, trials of the same type were averaged (Fig. S1e). Because all
runs have the same trial order, and all trials have the same epoch structure and
timing, runs and trials can be averaged without deconvolving the hemodynamic
response. This is an important feature of our experimental design, since
hemodynamic responses differ across cortical depths [46]. Following trial averaging, VASO data
were BOLD corrected using the dynamic division method (Fig. S1e). Thus, for each
contrast (BOLD and VASO), for the axial protocol, each subject had four average
trials: alphabetize, remember, action, and non-action. For the sagittal
protocol, each subject had two average trials: alphabetize and remember.In a parallel analysis, a region of interest (ROI) in the left dlPFC was
defined for each subject (Fig.
S1f, right). The approximate location of the ROI was taken from the
6-minute functional localizer (Fig. S1f, left) following GLM analysis with FSL FEAT (Version 5.98)
[54] . For the complete
FEAT design protocol, please see (https://github.com/layerfMRI/repository/tree/master/DLPFC_Emily/Featdesign).
The ROI was manually selected and drawn for every individual subject (see Fig. S3 for drawn ROIs in
every subject). Rather than only acquire an additional T1-weighted image for
anatomical reference, we used the functional EPI data itself to estimate the T1
contrast, and used this for manual delineation of two layers within this ROI,
one superficial and one deep (Fig. S1f, right). The advantage of this approach is that it avoids
the distortion correction and resampling steps necessary for registering EPI
images to a separately acquired T1 image, preserving spatial specificity. See
sections below for additional information about this layer-drawing procedure for
both the axial and sagittal protocols.
Layering and timecourse extraction for axial protocol
This section describes the steps applied to data acquired using the
axial protocol and shown in Figs. 2 and
3. The manual drawing of the layer
masks was done according to the following guidelines: a) layers were drawn as
connected collection of voxels without holes; b) the superficial layer was
positioned such that there was no partial voluming with CSF; c) the deeper layer
was positioned such that there was no partial voluming with WM; d) the
superficial and deeper layers were eroded until there was no residual overlap of
superficial and deeper layers; e.) the thickness of the superficial and deeper
layers were kept similar along the cortical ribbon; f) the thickness of the
superficial and deeper layers was chosen such that they fill as much of the
cortex as possible without violating the guidelines above; and g) for
consistency, the same person drew the layers for all subjects. The results of
all drawings are shown in Fig.
S3.Next, at each timepoint, signal was averaged across all voxels within
each layer to derive one average timecourse per layer in each of the four trial
types. Thus, each subject had eight timecourses: one per layer (superficial,
deeper) per trial type (alphabetize, remember, action, non-action; Fig. S2g).Before pooling data across subjects, BOLD timecourses were normalized
within subjects using the following steps. First, a per-layer
(y) mean baseline BOLD signal was calculated by averaging signal during
baseline timepoints across all four trial types (where “baseline
timepoints” include the first timepoint, which is before the appearance
of the stimulus, and the penultimate and ultimate timepoints, which are 18 and
22 seconds after the appearance of the probe, the point at which signal is
expected to have returned to at or near baseline). Next, the BOLD signal
s for layer y at timepoint
t was transformed to s’ as follows, to yield values
interpretable as percent signal change:Note that unlike BOLD, VASO is a quantitative measure that is
proportional to a physical unit (mL per 100 mL tissue volume), meaning units can
be directly interpreted and it is not necessary to convert to percent signal
change. VASO data were instead transformed as follows. First, to facilitate
interpretation, each subject’s VASO signal v at each
timepoint t was transformed from a negative to a positive
contrast as:Following this, VASO signals were normalized within subjects by
calculating a per-layer mean baseline VASO signal by averaging signal during baseline timepoints
(same timepoints as for BOLD above) across all four trial types. This mean
baseline signal was subtracted from each timepoint as follows:All of the subsequent statistical contrasts were performed directly on
these normalized signal timecourses. We refrained from using deconvolution or
inferential statistical models (e.g., general linear models) to measure
activation, to avoid biases of variable noise magnitudes and hemodynamical
response functions across cortical depths.For purposes of the two-way, repeated-measures analyses of variance
(ANOVAs) depicted in Figs. 2b, 3b and S5b, the representative
delay signal was the average of VASO measurements acquired at timepoints 4, 5
and 6 (corresponding to 12, 16 and 20 sec in trial time), and the representative
response signal was the average of VASO measurements acquired at timepoints 7
and 8 (corresponding to 24 and 28 sec in trial time). While the
repeated-measures ANOVA test is robust against violations of the assumption of
normality, it does assume sphericity, which refers to the condition where the
variances of the differences between all possible pairs of within-subject
conditions (i.e., levels of the independent variable) are equal. Because there
is currently no clear way to test for sphericity for the interaction term of a
two-way repeated measures ANOVA (our main term of interest), here, we report the
Greenhouse-Geisser-corrected p-value[55] for all tests, which is a conservative form of
correction that is recommended when nothing is known about the sphericity of the
data[56].
Layering for sagittal protocol
This section describes image processing for the single-subject
layer-dependent activity profiles acquired using the sagittal protocol and shown
in Fig. 4. Cortical depths were estimated
directly in EPI space without alignment to so-called anatomical space. This
minimizes the risk of resolution loss due to multiple spatial resampling steps
and avoids any potential errors in distortion correction and registration. An
anatomical reference contrast was calculated from the functional data by
calculating the inverse signal variability across nulled and not-nulled images,
divided by the mean signal. This measure is called here T1-EPI and
provides a good contrast between white matter (WM), gray matter (GM) and
cerebro-spinal fluid (CSF; see background images in Figure 4, S1 and S3). Borderlines between GM/WM and GM/CSF are manually drawn based
on this contrast. The manual drawing was done as described in previous
publications [57,22,58,59] according the
following guidelines: a) borderlines were drawn as continuous lines without
holes; b) the lines are drawn such that their curvature radius was kept smaller
than the cortical thickness; c) the position of the GM/CSF border was drawn
through voxels that were just above the GM, such that there was no GM partial
voluming; d) the position of the GM/WM border was drawn through voxels that were
just below the GM, such that there was no GM partial voluming—this means
that the position of the voxels that are half filled with GM are in the
respective upper-most and lower-most extracted layers. e) for consistency, the
same person drew the layers for all subjects.Manually drawn border lines are shown for all subjects in Figure 4c (bright yellow for GM/CSF and bright blue
for GM/WM). Twenty-one layers were calculated between these borderlines with the
LAYNII program LN_GROW_LAYERS (https://github.com/layerfMRI/LAYNII). In order to minimize
partial volume effects and allow the calculation of smooth layers, the layering
calculation was applied on a four-fold finer grid that the native functional
resolution. This means that the number of layers is higher than the number of
independent voxels sampled across the cortical depth. The number of layers
should not be confused with the effective resolution across cortical depths.
Given the cortical thickness of 3.5-4 mm in dlPFC [60,61], the resolution of 0.76 mm in-plane and 0.99 mm slice
thickness is sufficient to sample 3-6 independent voxels across cortical depth.
This is enough to estimate activity in superficial and deeper layers (red-yellow
compared to blue-turquoise in Fig. 4c) with
Nyquist sampling. The number 21 was chosen based on previous experience in
finding a compromise between data size and smoothness (see Fig. S8 in [58] as well as [22,57]).For best visibility, functional signals were smoothed along the
tangential direction of the cortex (i.e., within “layers”) with a
Gaussian kernel of 0.76 mm. In order to maintain the spatial specificity across
layers, no smoothing was applied across cortical depths. This kind of layer
smoothing can improve the detectability of fMRI signal changes without unwanted
leakage of physiological noise above the cortical surface [62,22,58]. The
application of such layer smoothing is based on the assumption that neighboring
columnar structures are similarly engaged during the task. See Fig. S8 for a discussion
of variance in the functional response across columns. Note that the batch of
cortex investigated here is highly folded with respect to the external magnetic
field. This means that the BOLD signal change can be substantially variable
dependent on the columnar position along the sulcus[63,64].
Interpreting cortical depth-dependent results with respect to
cytoarchitectonic layers
In order to interpret the fMRI results according to known input-output
characteristics of different cortical layer groups II/III and V/VI, it is
helpful to approximate the location of functional activity with respect to
underlying layers as defined cytoarchitectonically. To confirm the approximate
borders and the different layers within these borders, we followed the approach
outlined in earlier work[65,66]. This is a three step
approach: First, we extracted layer signatures in high-resolution multi-modal
post-mortem histology data of an individual cadaver brain sample from the Ding
Atlas[67]. Second, we
identified the MR-sensitive features and landmarks[68] in anatomical MRI scans from a subject
from our study and estimated their relative position across the cortical
thickness. Third, we used these features as markers of the cytoarchitectonic
layers in the functional data from the same participant to confirm the relative
depth-position of the functional responses. With this procedure, we can attempt
to interpret the layer-origin of the functional signal solely based on the
relative depth of the cortical thickness. The results of this procedure are
shown in Fig. S4.Note that this approach of comparing fMRI data with histology data is
not conducted as part of the fMRI analysis pipeline. The time courses and layer
profiles shown here are solely extracted based on relative distance to the
GM/CSF and GM/WM borderlines. The comparison of the relative cortical depth in
fMRI data and histology data is based on the assumption that the relative
position of the cyto-architectonic layers and their relative thicknesses is the
same across subjects (see insets in Fig.
4C).
Spatial alignment across sessions (within-subject)
Note that all layer data are taken from individual sessions, and are
thus not susceptible to potential registration errors across days. However, it
is important to ensure that the location of activity is generally consistent
with a single subject across days and imaging sessions.To investigate this consistency in the two subjects on whom we collected
test-retest data (i.e., two imaging sessions separately by several days), each
session’s layer masks and the corresponding activation maps were
transformed into subject-specific anatomical reference spaces. Registration was
done with SyN in ANTs (Advanced Normalization Tools; [69]) with a spline interpolation. Since the
imaging coverage of the functional data is significantly smaller than the whole
brain, it was necessary to provide a manual starting point for the ANTs
registration to converge on reasonable registration quality. The initial manual
registration was done in ITK-SNAP. The registration from EPI-space to the
subject specific anatomical space was done by means of the similar T1
contrast of T1-EPI and the MP2RAGE UNI-DEN image. The same spatial
operation was applied to the layer masks and the functional activation maps. The
resulting activation patterns where compared across days in the anatomical space
of individual subjects (Fig.
S2). Note that the registration quality here did not need to achieve
accuracy levels at the sub-millimeter layer scale. Instead, the goal of this
analysis was to demonstrate that the process of ROI selection (several
millimeters large) was reproducible.
Spatial alignment across subjects (mean ROI location)
To verify placement of the ROI taken from the functional localizer, and
to create the group-level image shown in Fig.
1c, we processed data from the localizer run in AFNI[70], using the standard
“super-script” afni_proc.py. Each subject’s high-resolution
(T1-MPRAGE) whole-brain anatomical data were registered to the
MNI 152 template using a combined affine and nonlinear warp. To minimize
interpolation, this transformation was concatenated with both the affine
transform used to register the echo-planar images to the individual-subject
anatomical data, as well as the rigid (6 degrees of freedom) warp to account for
subject motion. Data were then smoothed using a 4mm (2 voxels) Gaussian kernel,
scaled to percent signal change, and submitted to a multiple regression. The
standard boxcar block design was convolved with the HRF along with six motion
parameters (3 translation, 3 rotation). Group analyses were conducted in
3dttest++, which yielded a cluster in left dlPFC with a whole-brain map at
voxelwise p < 0.01. This cluster represents the approximate location
where the higher-resolution layer slices were prescribed in the subsequent
experimental runs, and is included here for convenience as a post-hoc
visualization of the macroscale location of our region of interest.
DATA AVAILABILITY
Data are available via OpenNeuro at the following link: https://doi.org/10.18112/openneuro.ds002076.v1.0.1
CODE AVAILABILITY
All code is available in the following GitHub repository: https://github.com/layerfMRI/repository/tree/master/DLPFC_Emily
Authors: Daniel Sharoh; Tim van Mourik; Lauren J Bains; Katrien Segaert; Kirsten Weber; Peter Hagoort; David G Norris Journal: Proc Natl Acad Sci U S A Date: 2019-09-30 Impact factor: 11.205
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Authors: Nicole D Evangelista; Andrew O'Shea; Jessica N Kraft; Hanna K Hausman; Emanuel M Boutzoukas; Nicole R Nissim; Alejandro Albizu; Cheshire Hardcastle; Emily J Van Etten; Pradyumna K Bharadwaj; Samantha G Smith; Hyun Song; Georg A Hishaw; Steven DeKosky; Samuel Wu; Eric Porges; Gene E Alexander; Michael Marsiske; Ronald Cohen; Adam J Woods Journal: Cereb Cortex Date: 2021-02-05 Impact factor: 5.357