Tag Archives: 3D

Structural MRI artifacts

Magnetic resonance imaging (MRI) is a valuable and increasingly used method for studying brain anatomy as it allows large-scale, high-quality in vivo analyses. However, some artifacts might influence the digital results, and thus require cautious interpretation. In a recent review, these issues are addressed along with possible solutions. First, we need to keep in mind that the images acquired are not mere photographs of the brain, but reflect some biophysical properties of the tissues, by measuring the radio-frequency signals emitted by hydrogen atoms (present in water and fat) after being excited by magnetic waves. Thus, MRI is an indirect analysis of the brain anatomy and depends greatly on specific tissue properties. Second, researchers can choose from a variety of methods, depending on the aim of the survey. Macrostructure, i.e. the size and shape across voxels, can be studied through manual volumetry or automatic segmentation, voxel- or deformation-based morphometry, surface- based algorithms, or diffusion tractography. Microstructure, i.e. within-voxel contents, is usually analyzed through diffusion MRI, but also magnetization transfer imaging, or quantitative susceptibility mapping.

When making inferences on the biological significance of the outputs, the researcher must account for the possible digital artifacts. These can occur both during image acquisition and processing and can be subject-related and methodological-related. A common problem is subject motion, which might contaminate or influence the results, as the amount of motion varies with other factors influencing brain changes (age, sex, and disease status), or can even correlate with a specific effect being studied. For instance, motion induces gray matter reduction, which might be perceived as brain atrophy. Subject motion is unavoidable, but its influence can be reduced by using a motion detector during acquisition, or by estimating the amount of motion allowing statistical adjustments, also useful to  detect outliers. The difficulty in manipulating the magnetic and radio-frequency fields might also introduce deformation. The main magnetic field should be spatially uniform, but it is dispersed by brain tissue while concentrated by air. This can be partially compensated by applying additional fields. The radiofrequency field is not homogeneous, which affects MRI contrast and intensity. Combining multiple transmit coils might help reduce this caveat, although the contribution and sensitivity of each coil must be taken into account when processing the image.

A particular case that can affect estimates of cortical volume and thickness is the difficulty in discriminating the dura and gray matter due to the similar intensity and anatomical proximity. In this case,  MRI parameters can be manipulated in order to increase the contrast between these tissues, without reducing the contrast between gray and white matter. Individual variability in folding patterns is a further major issue in voxel-based morphometry studies because it complicates the mapping of correspondences between subjects. Registration might be enhanced by analyzing regions with larger variation to find possible anatomical alterations, aligning cortical folding patterns to locate corresponding areas, and mapping sulcal changes to improve sulci identification. Finally, researchers should continuously keep track of the constant advances and innovations in the field. The authors conclude acknowledging the importance of structural MRI when coupled with other biological information, like genetic expression (Allen Brain Atlas), cytoarchitecture (JuBrain), and cognitive associations (Neurosynth).

Sofia Pedro

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Which One? PLY vs. STL

3d-format As the use of virtual anatomy increases, awareness of different 3D mesh (digital model) formats is useful. Simply, a 3D mesh is the geometrical representation of an anatomical structure such as a cranium, endocast or tooth. Below, are the main differences, benefits, and uses of common PLY and STL 3D formats.

PLY (Stanford Polygon Format) is a 3D file format that was commonly developed from 3D surface scanners and photogrammetry software to allow the preservation of information on surface geometry while retaining information on RGB colour. STL (Stereolithography) is a 3D format commonly generated from software using only grayscale images such as raw CT (Computed Tomography) where RGB colour is not captured. 3D Printers only require preserved information on surface geometry, not colour, leaving STL to be a preferred format for 3D printing technologies.

Even though there is no discernible difference between the quality of the 3D mesh types, PLY format offers binary encoding of all information (including RGB colour). This results in a smaller file size, allowing less space occupied on a hard-drive or cloud-storage and faster loading of the 3D mesh into software programs as employed in 3D-geometric morphometrics.

Alannah Pearson


Non-human primate microCT dataset

Copes et al 2016A new dataset of non-human primate microCT scans is now available. The original specimens (59 species) belong to the Museum of Comparative Zoology at Harvard University. The dataset includes 431 skulls of adults and juveniles (and also some postcranial elements) with resolutions between 18 and 125 microns, depending on the size of the specimen. The scans can be freely downloaded, under registration, from the MorphoSource website, which is an open-access archive of 3D data. From the MorphoSource front page you can easily browse by Institutions, and access the specimens. In addition, the authors have also provided a dataset of landmark configurations digitized from the skull sample, available from Dryad Digital Repository.

Sofia Pedro