Psychology Brain Imaging Cluster (PBIC) Software
The following image analysis software is installed and supported on the cluster machines:
- AFNI
Open a terminal, type afni to run
- AutoSeg
Open a terminal, type AutoSeg_2.4.1 - BXH/XCEDE tools
Creation tools, Conversion tools and QA tools for processing QA - CARET (Computerized Anatomical Reconstruction and Editing Toolkit)
Open a terminal, type caret5
- DTIPrep
Open a terminal, type DTIPrep1.1.1
- FiberViewer
Open a terminal, type FiberViewer
- FreeSurfer
Usage instructions - FSL
Open a terminal, type fsl to run the main menu, or Feat to run the FEAT GUI, Flirt the FLIRT GUI etc
- GingerALE Open a terminal, type GingerALE
- Insightsnap
Open a terminal, type itksnap
- Mango
Free Dicom viewer supported on Mac, Windows and Linux operating system. - Matlab
- We have a number of different versions of Matlab running on the cluster, which can be set using the command matlab_vset. To run open a terminal, type matlab to run. You will then be remotely logged into the cluster node that is least busy. You will need to re-enter your password and Matlab will automatically start.
- mri3dX
Open a terminal, type mri3dX or template - MRIcron
Open a terminal, type mricron - MRIcroGL
Open a terminal, type mricrogl - MRS Software
- Peate
Open a terminal, type peate
- Slicer3
Open a terminal, type Slicer3
- SPM5
Run matlab and in the matlab window type spm5 to run - SPM8
Run matlab and in the matlab window type spm8 to run - SPM12
Run matlab and in the matlab window type spm12 to run
- SPM-toolbar wfu_pickatlas
- Talairach Client
Open a terminal and type talairach - TrackVis and Diffusion Toolkit
The initial installation requires a license to be setup.
Once this has been done, open a terminal, type trackvis or dtk - xmedcon
Open a terminal, type xmedcon
Please e-mail pbic-computing@contacts.bham.ac.uk for further help or advice with using the PBIC cluster.