Morphologist-UI is a user-friendly interface to the Morphologist pipeline. It is based on the same processing chain, and offers interactive visualization using anatomist.
It is a simplified intercace, providing only the default parameters settings. For the sake of simplicity, there are no buttons, parameters, or other tuning which may affect processing: it is designed for “standard” processing.
Users distributions are available on http://brainvisa.info
The normalization step may make use of external software, that has to be installed separately. If none is installed, the normalization defaults to the AimsMIRegister (mutual informaton) method, which is not the best tested one and might suffer from robustness issues. If installed and configured (see configuration options), the following software may be used instead, in that order:
- SPM (FIL, UK). It needs to be installed separately and setup in Morphologist configuration. SPM8 or SPM12 are supported, both with either the regular matlab version or the standalone compiled one.
- FSL flirt (FMRIB, UK). It needs to be installed separately and setup in Morphologist configuration.
- Baladin (Inria, France). You will probably not use it, since this software is not freely available.
Run the executable script morphologist in the bin/ directory of the BrainVisa/Morphologist distribution.
It can also be found in BrainVISA processes, in the Morphologist toolbox.
There are actually three configuration sets in Morphologist-UI.
These configuration options are linked to the “study” directory: a study contains all needed configuration, and two different studies may have completely different configurations.
So, see the next section, Study.
A study is both the working data directory and all configuration settings needed to run the processings.
Configuration options include:
Subjects may be added or removed from a study.
New subjects will be imported (copied into the study directory).
This option enables to create a complete study from a directory tree containing organized data. It may be a BrainVisa database directory, or a directory with a different organization (well, this is not supported yet, actually...).
With BrainVisa databases, subjects may be either used in-place (reusing the existing database directory to work in it and share data with BrainVisa/Morphologist), or by copying raw T1 images in a new study directory.
Process several or all subjects. Run in parallel using Soma-Workflow. Results appear in the display window at the time they are available.
Processing steps currently running are visible in the subjects state (right panel in the interface). It is also always possible to monitor the workflow execution via the soma_workglow_gui program.
Morphologist-UI is a very simplified interface for running Morphologist analyses, and provides no options or tuning in processing steps. When things go wrong on some images, the simplified user interface will not allow users to fix problems and re-run the processings with modified settings.
At least not for now.
In this case, users should use the older (and complete) BrainVisa toolbox to overcome problems: as it is compatible, and provides many processing options, it is possible to run specific steps with modified settings using BrainVisa.
This is a first release of Morphologist-UI. It currently supports the main segmentation steps, sulci extraction, and sulcal morphometric measurements extraction. The morphometric step is whole brain, and there is currently no choice and no statistical analysis provided.
In the future, Morphologist-UI will be extended for inter-subject statistical analysis on sulcal morphometric features.
Other improvements in specialized steps visualization windows are planed, especially for processing parameters edition, and manual correction of processed data, as in BrainVisa editors.