Result analysis

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4 Discussion

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RPD measures. These quality controls were estimated in occipital-temporal regions due to their prox-imity to lower regions such as the cerebellum, which show high inhomogeneity143,148,149.

The SNR was estimated not only in ROIs in the VOTC that were in the interest of the project to extract a T1 relaxation laminar profile (mFus, pFus and CoS) but it was also calculated in other regions of the VOTC (IOG, ITG, MTG, LOS and OTS), as well as for the early visual cortex (V1-V3) and middle temporal cortex (hMT). Lastly, SNR was estimated in the whole-brain WM, GM and in the mask resulting from the combination of the two tissues. This way, it was possible to compare the SNR in mFus, pFus and CoS with the SNR in other neighboring regions. Additionally, the SNR was estimated in the grey matter within these fifteen occipital-temporal regions due to our interest in constructing a pipeline to study the myelin distribution in cortical layers. Although the SNR does not have an expected range of values and depends on the T1 values, SNR estimates ranging from 1 to 4 have already been reported in the literature for the MP2RAGE sequence at 7T¹⁶⁷. The differences found between the oc-cipital-temporal regions and the whole-brain WM and GM tissues may be because GM and WM contain only one brain tissue, leading to a smaller standard deviation of the signal in these regions when com-pared to other ROIs that contain several tissues of different molecular compositions and consequently different contrast values. In fact, the comparison of the SNR for the whole ROI with the SNR of the grey matter within that ROI shows that the SNR range for the GM increases and approximates the SNR of the whole-brain GM, which may be due to the lower dispersion of values. Although there is no range of expected SNR values, it is possible to compare the SNRs of distinct regions and have in consideration the ranges of SNR already mentioned in the literature, for the same acquisition and magnetic field strength. Additionally, other variables should be taken into consideration such as the size of the ROIs, the different tissues that compose them and their ratios, and the T1 values. Therefore, the SNR estimates suggest that there is no pronounced noise introduced in regions closer to lower regions of the brain, such as the VOTC. Although the SNR range of UNIT1 differs from the SNR range of T1 map, the SNR values have a similar pattern.

Regarding the variability in a scan re-scan test, the voxel-wise RPD was estimated for each voxel as the absolute difference divided by the mean of the values, as calculated by Sherif et al. (2022). The voxel-wise RPD ranges from 0 to 202 % for UNIT1 images and T1 maps. Values above 100 % corre-spond to voxels where the absolute difference between the two intensities is greater than the mean. The number of voxels in these cases is residual and the majority of them correspond to RPDs of 200 %.

RPDs of 200 % correspond to voxels where the difference is twice the average and this case corresponds to having one of the two intensity values equal to zero. These cases are found in the periphery of the brain, which may be originated in numerical operations that used interpolations to estimate the voxel-wise RPD between images with different orientations. In order to study the RPD values in each ROI of the occipital-temporal cortex, the median in each of the ROIs was estimated since it is not distorted by outliers. Median estimates for RPD in UNIT1 range between 2.50 % and 8.20 %. RPD medians for the T1 map range from 3.90 % to 9.30 %. These values seem very promising when compared to the MPM protocol results presented by Sherif et al. (2022) showing 9 out of 10 ROIs with median coefficient of variation estimates below 51.33 % in MT maps. Our results show that there is a low variability between scan and rescan in the UNIT1 and T1 map for VOTC regions, which demonstrates a high reliability of the MP2RAGE acquisition sequence.

The results presented for SNR and RPD are considered very reasonable and demonstrate that MP2RAGE is a very reliable sequence with low noise propagation in VOTC regions. Despite the prox-imity of the occipito-temporal regions to lower regions of the brain that demonstrate high inhomogene-ity, it does not seem to impair the results obtained in the metrics estimated. A low variability between scans increases confidence in future results arising from group comparisons with MP2RAGE, allowing

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for gaining deeper insights intro microstructural tissue alterations, through much faster acquisitions compared to the MPM sequence.

4.1.2 Extraction of the T1 relaxation laminar profile

The quality assessment of UNIT1 images and T1 maps showed that quantitative MRI based on a MP2RAGE acquisition provides fully quantitative and reproducible high-resolution maps of T1 relaxa-tion of the hydrogen protons present in the tissues of the brain from which it is possible to infer the myelin concentration in a specific region. The study of the quality of UNIT1 and T1 maps suggests that the MP2RAGE sequence is more reliable when compared to the MPM protocol available at the ULiège Cyclotron Research Centre for the VOTC regions. For this reason, the MP2RAGE acquisition sequence was chosen to proceed with the construction of the pipeline that would extract a laminar T1 relaxation profile in VOTC regions. The pipeline was initially developed for the primary visual cortex since it is one of the largest regions from which more information can be extracted from, and it has been exten-sively studied ex vivo making it possible to compare our results to these studies. Afterwards, the pipeline was applied in mFus, pFus and CoS.

The comparison of UNIT1 to the bias-corrected UNIT1 shows that the inhomogeneity corrections are residual, which demonstrates that our acquisitions with MP2RAGE at ULiège CRC do not introduce much inhomogeneity. However, a successful bias correction is essential for an improvement of FreeSurfer’s segmentation performance.

Before creating the cortical layers, it was required a careful visual inspection of the grey matter segmentation by FreeSurfer since it would interfer with the layers output and as a consequence with the T1 relaxation laminar profile. Laynii permits the creation of equidistant or equivolume layers.

Nonetheless, so far there is not yet a type of cortical layers created with Laynii that is the best choice since both the equidistant and equivolume approches have disadvantages due to the computational and resolution limitations that still exist. In spite of the existing issues in creating layers, it would be interesting to study the myelin distribution on an smaller scale, which would require increasing the number of layers created and the resolution of the images.

The figures representing the VOTC with the regions of interest for the development of this pipeline show some separate clusters for the same ROI, such as pFus on the left hemisphere (Figure 3.19) spread through the VOTC. This can result in small clusters of cortical layers that do not encompass the entire cortex, resulting in a discrepant distribution of voxels across layers.

The T1 relaxation laminar profiles for V1 and mFus, pFus and CoS show a decrease in T1 values from the CSF neighbor layer to the WM neighbor layer, which suggests an increase in the amount of myelin from CSF to WM. The myelin distribution results are in agreement with both ex vivo and in vivo studies of the cortex demonstrating an increase in myelin density from the supragranular to the infra-granular layers13,20,173,174, which encourages future comparisons between populations.

Figure 4.1 and Figure 4.2 show the results of some in vivo and ex vivo studies of the primary visual cortex and of faces- and places- selective regions that corroborate our findings. Figure 4.1 com-pares the myelin distribution in V1 using myelin staining (Figure 4.1 a) and in vivo MRI (Figure 4.1 b), showing an increase of myelin density from the pial surface (CSF neighbor) to the closest layer to WM.

More myelin density is associated with a darker staining intensity for the ex vivo study, while for the in vivo is associated with an increase in R1 (1/T1). Figure 4.1 (b) also shows the laminar distribution of myelin in other cortical regions, which maintains the pattern of an increase in myelin density from the pial surface to the WM. Figure 4.2 presents some ex vivo and in vivo results showing the laminar dis-tribution of myelin in face-selective regions and place-selective regions. Optical density measurements

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of myelin staining (Figure 4.2 a) along the cortex show the increase in myelin density from the pial surface to the layer closest to the WM (Figure 4.2 b)¹³. This experience allowed them to confirm in vivo studies of myelin distribution changes throughout development (Figure 4.2 c)¹³. It was also possible to study in the adult population where myelin differences appear in the cortex of pFus and CoS, showing a higher myelin density for mFus in the intermediate layers (Figure 4.2 d)¹³.

In our results, comparing the laminar T1 profiles for mFus, pFus and CoS, it appears to exist a numerical difference in the T1 values of the middle layers between CoS and mFus in the left hemisphere.

However, visual comparison of the T1 laminar profiles obtained for the hemispheres suggests different results between hemispheres. Nonetheless, the T1 relaxation laminar profiles found suggest a numerical higher concentration of myelin for V1 compared to faces- and places- selective regions in the VOTC. It has been reported that V1 is a highly myelinated cortical region and presents high neuron densities²². Nonetheless, the causes for these myelination differences between cortical regions are still debated.

In conclusion, the study carried out here demonstrated that the MP2RAGE sequence, compared to the MPM sequence available at the Cyclotron Research Center (ULiège), provides myelin maps at faster acquisitions and introduces less noise and variability, allowing the study of the myelin laminar distribution in VOTC regions. The results obtained here agree with previous in vivo and ex vivo litera-ture, proving that MP2RAGE offers informative images of the composition of the human brain, in par-ticular of the myelin laminar distribution in the cortex. The pipeline developed during this dissertation with the three first scanned participants corresponds to the first stages of this project but in the future, comparative studies of the myelin laminar organization in VOTC regions between the blind and sighted populations will help in understanding the role of crossmodal plasticity due to blindness in reshaping the cortical microstructure.

Figure 4.1: Comparison of myelin distribution found in ex vivo and in vivo studies: (a) Myelo- and cytoarchitectonic images from myelin and Nissl staining in the primary visual cortex, taken from San Román and Bidmon (2018)¹⁷⁵. This figure shows an increase of myelin density from layer I (closer to the pial surface) to layer VI (closer to white matter); (b) Plot taken from

Marques et al. (2017)¹⁷⁴ showing the longitudinal relaxation rate (R1 = 1/T1) fitted results (solid line) for different depths (from white matter to pial surface) for different Brodmann regions: Br.2 somatosensory; Br.4 primary motor cortex; Br.17 primary visual cortex; Br. 41 auditory cortex; Br. 44 Broca's area and Br. 32 cingulate region. R1 shows an increase from the

pial surface to the white matter, suggesting an increase of myelin density towards white matter.

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Figure 4.2: Figures taken from Natu et al. (2019)¹³ showing the validation of in vivo data using adult postmortem myeloar-chitecture. (a) A sample histological section stained for myelin. Dashed red, midfusiform sulcus (MFS), fusiform gyrus (FG) and dashed green, collateral sulcus (CoS); (b) Measurements of optical density across cortical depths in 5 postmortem brains along the CoS and FG/MFS; (c) Development of T1 in grey matter as a function of cortical depth. T1 curves across

equidis-tant intracortical depths from the pial surface (pial) to grey matter (GM) and into adjacent white matter (WM) in bilateral mFus-faces (red) and bilateral CoS-places (green) across age groups; (d) In vivo measurement of relaxation rate (R1)

show-ing greater R1 in Right pFus-faces than CoS-places in middle and deep cortical layers across 27 adults.