Because ¹H-MRS requires large voxel volumes, a single voxel may contain a mixture of tissue types making partial volume correction necessary. Partial volumes of brain matter (BM) and cerebral spinal fluid (CSF) can be calculated via biexponential fitting of T2 relaxation of the unsuppressed water signal to obtain amplitudes of BM and CSF components at TE=0ms⁽¹⁾. Alternatively, segmentation of a high-resolution structural image can be used to determine gray matter (GM), white matter (WM) and CSF fractions within the voxel, assuming no head movement between voxel positioning and single voxel spectroscopy (SVS) acquisition. We aimed to compare these two methods and to determine whether large differences in CSF fraction between the two methods in 7-year-old children corresponded to substantial subject movement between acquisitions.

Participants were 113 7-year-old children from a neuroimaging follow-on study of the Children with HIV Early Antiretroviral Therapy (CHER) trial.

Scanning was performed on a 3T Allegra (Siemens, Erlangen, Germany). The protocol included a high-resolution T1-weighted 3D EPI-navigated⁽²⁾ multiecho magnetisation prepared rapid gradient echo (MEMPRAGE)⁽³⁾ (FOV 224x224 mm², TR 2530 ms, TI 1160 ms, TE’s 1.53/3.19/4.86/6.53 ms, bandwidth 650Hz/px, 144 sagittal slices, 1.3x1.0x1.0 mm³), followed by two 3D EPI-navigated DTI acquisitions⁽⁴⁾. SVS was obtained in the basal ganglia (BG), midfrontal gray matter (MFGM) and peritrigonal white matter (PWM), using an EPI volumetric navigated point-resolved spectroscopy (PRESS) sequence with real-time first-order shim and motion correction⁽⁵⁾ (TR 2000 ms, TE 30 ms, 64 measurements, vector size 512, spectral bandwidth 1000 Hz). Water unsuppressed ¹H MRS measurements were acquired at TE’s of 30ms, 50ms, 75ms, 100ms, 144ms, 500ms and 1000ms.

The voxel water signal S(TE) was quantified using LCModel and modeled in Matlab as a biexponential function of TE as follows:

$$S(TE)=S_{CSF}.exp\left(\frac{-TE}{T2_{CSF}}\right)\left[1-exp\left(-TR\frac{-TR}{T1_{CSF}}\right)\right]+S_{BM}.exp\left(\frac{-TE}{T2_{BM}}\right)\left[1-exp\left(-TR\frac{-TR}{T1_{BM}}\right)\right]$$

where S_CSF and S_BM are the fitted signals from CSF and BM, T2_CSF and T2_BM are the fitted T2 relaxation times, and T1_CSF and T1_BM are T1 times⁽¹⁾. The component with the longer T2 was assigned to CSF.

Percentage CSF (PV_CSF) in the voxel was estimated as:

$$PV_{CSF}=\frac{S_{CSF}}{S_{CSF}+S_{BM}\times0.75}\times 100$$

where SCSF and SBM are the signals from CSF and BM at TE=0, assuming that the signal from BM accounts for 75% of tissue volume, since BM is 75% water⁽¹⁾.

For each subject and region, the T1-weighted image was used to segment the SVS voxel into GM, WM and CSF in SPM12.

For cases where the difference between segmentation and biexponential methods was greater than 10% CSF, the displacement between the initial T1 image and the start of each SVS acquisition was calculated from motion parameters obtained by aligning the EPI navigator images from the preceding DTI and PRESS acquisitions in SPM12. For comparison, displacements were also calculated for 7 subjects where there was no difference in between the two methods.

BG: PV_CSF determined via segmentation was almost zero (<1%) for all but 2 subjects. Similarly, using the water signal T2 relaxation method a monoexponential fit (PV_CSF= 0), was appropriate in more than half of the subjects, although the upper range of PV_CSF calculated by this method was 95% (table 1).

PWM: PV_CSF from the segmentation method was <1% in all but 2 cases. Again the range was larger using the T2 relaxation method.

MFGM: There was a range of PV_CSF for both methods (figure 1), with a larger range for the T2 relaxation method.

The cumulative histogram of differences in PV_CSF between the two methods (figure 2), shows differences of less than 1% CSF for 3/4 of the subjects in the BG but for only 1/3 of subjects in the PWM and 1/4 in the MFGM.

Subjects with PV_CSF differences >10% CSF between methods showed a tendency for greater displacement between the T1 and SVS scans than those with no difference in PV_CSF between methods (mean displacement difference: BG 2.8mm, p=0.04; PWM 2.5mm, p=0.07; MFGM 1.43mm, p=0.2).

Agreement between the methods was best in the BG, since most PV_CSF were 0 for both methods. In the MFGM a number of points fell around the y=x line, indicating fair agreement for certain subjects. In the PWM, the biexponential method estimated consistently larger PV_CSF, since most of the CSF fractions calculated by the segmentation method were close to zero. In each region, there were some large discrepancies between methods that could not be fully explained by motion.There is most consistency between methods in regions where the PV_CSF is small, and less consistency where there are larger amounts of CSF. Inconsistencies may be due to segmentation inaccuracy in particular regions or subject motion.