All CSF measurements for all methods in each subject.

<p>One slice from subject 8 from A) the HR T₁-weighted image (downsampled images have the same in-plane resolution); B) 3D T₁-weighted FSL HR; C) 3D T₁-weighted SPM HR; D) postprocessed CSF LR; E) postprocessed CSF HR. No image is presented for FreeSurfer, because FreeSurfer uses the determinant of the transformation matrix to estimate ICV rather than distinguishing the skull from peripheral CSF.</p

Precision of BPV and ICV for CSF LR, CSF HR and automated segmentation methods with downsampled data.

<p>Precision of BPV and ICV for CSF LR, CSF HR and automated segmentation methods with downsampled data.</p

All BPV measurements for all methods in each subject.

<p>CSF LR = CSF low resolution MRI scan; CSF HR = CSF high resolution MRI scan.</p

The ICV derived from the CSF MRI sequence.

<p>Example of the ICV in an axial (A), saggital (B) and coronal (C) slice. The mask resulting from the BET application to the CSF data is shown in red. The raw CSF data is shown in gray-scale in the background.</p

Bland Altman plots for the comparison of ICV between the CSF MRI sequences and the 3D T₁-based brain segmentation methods.

<p>The dashed lines represent the limits of agreement (mean difference ±1.96*SD of the differences). CSF LR = CSF low resolution MRI scan; CSF HR = CSF high resolution MRI scan; FS = FreeSurfer.</p

All ICV measurements for all methods in each subject.

<p>CSF LR = CSF low resolution MRI scan; CSF HR = CSF high resolution MRI scan.</p

The CSF MRI sequence.

<p>After presaturation and T_s the signal strength depends on T₁ decay to ensure an equal magnetization at the start of each MLEV-T₂ preparation. The MLEV-T₂ preparation with a varying amount of refocusing pulses allows the mapping of T₂ decay. Variation of time T_s in combination with a fixed number of refocusing pulses allow the mapping of T₁ decay. A short T_s is used to determine signal decay. Multi-slice echo planar imaging is used for the readout at each effective echo time.</p

Spatial activation maps and time courses of the GE and SE HRF upon short visual stimulation.

<p>A) Percent signal change (PSC) map of the visual cortex V1 for the GE (top) and SE (bottom) HRF data with isotropic voxel sizes of 1 mm and 2 mm, respectively. As expected the SE contrast shows reduced sensitivity. B) Closer examination of the cortical surface and pial vasculature on the 0.5 mm T2*-weighted anatomical scan. The cortical surface (white) was manually delineated in 3D and from this surface the cortical depth profiles were computed: black; 0–1 mm, red; 1–2 mm, and green; 2–3 mm. The high-resolution T2*-weighted scan was also used to identify the larger pial draining veins, which were excluded from the GE BOLD analysis. C) GE HRFs across cortical depth (0–1, 1–2, and 2–3 mm) and the SE HRF for a representative subject (subject 4 as indicated in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054560#pone-0054560-t001" target="_blank">Table 1</a>). As the GE and SE BOLD do not measure from the exact same vasculature there should be no exact spatial match in their activation patterns from the functional localizer. We therefore focused on the temporal evolution of the estimated HRFs, with the following parameters of interest: onset time, time-to-peak (TTP), full-width-at-half-maximum (FWHM), and maximum percent signal change (PSC). Onset times of the SE and GE HRF in deep gray matter (>1 mm cortical depth) are very comparable while the FWHM and TTP are increased for the GE HRF for all cortical depths indicating that the earlier part of deep gray matter GE HRF is weighted toward microvascular dynamics. Shaded areas denote the standard error of the mean (SEM). The black bar indicates the stimulus onset and duration (250 ms).</p

Bland Altman plots for the comparison of BPV between the CSF MRI sequences and the 3D T₁-based brain segmentation methods.

<p>The dashed lines represent the limits of agreement (mean difference ±1.96*SD of the differences). CSF LR = CSF low resolution MRI scan; CSF HR = CSF high resolution MRI scan; FS = FreeSurfer.</p

Correlation between the CSF MRI sequences and the HR 3D T₁-based brain segmentation methods.

<p>Correlation between the CSF MRI sequences and the HR 3D T₁-based brain segmentation methods.</p