1709
Comment:
|
3045
|
Deletions are marked like this. | Additions are marked like this. |
Line 1: | Line 1: |
Keep up to date with this [:ImagingComputingDevelopments:list of latest software developments] | = Neuroimaging software = You might want to [:ScientificComputing:read this overview of scientific computing] and keep up to date with this [:ImagingComputingDevelopments:list of latest developments] |
Line 3: | Line 4: |
= Major neuroimaging software packages installed at the CBU = | Try the [:StudentForum:student forum for helpful tips] |
Line 5: | Line 6: |
Most imagers at the CBU use [:SpmInformation:SPM], the dominant software analysis package from the FIL in London. However, [:FslInformation:FSL] ("fossil") - a powerful and fast collection of tools from FMRIB, Oxford, also has a following. | == Major neuroimaging software packages installed at the CBU == Most imagers at the CBU use [:SpmInformation:SPM, the dominant software analysis package from the FIL in London], which has consistently been on the cutting edge of new methods. It runs under [:LearningMatlab:a language called Matlab] allowing you to browse the source and write your own components relatively easily. |
Line 7: | Line 9: |
For some applications (particularly flat mapping, or performing grey & white matter segmentation for MEG analysis) you might wish to use [:FreeSurferAnalysis:Freesurfer]. | [:FslInformation:FSL] ("fossil") - a powerful and fast collection of open source tools from FMRIB, Oxford also has many strengths and has a substantial following. For some applications (particularly generating inflated brains, flat mapping, or performing grey & white matter segmentation for MEG analysis) you might wish to use [:FreeSurferAnalysis:Freesurfer]. |
Line 11: | Line 15: |
There are some old licenses for Brain Voyager around. This point-and-click commercial package has many impressive features. It seems we might have [:BrainVisaInformation:Brain Visa] installed but I think it is probably an old version. If you find out, please put the latest information here! |
|
Line 13: | Line 21: |
= Smaller tools = | == Smaller tools == |
Line 16: | Line 24: |
= Extensions to SPM/Matlab = * [:AutomaticAnalysisIntroduction:aa] - a system to automate SPM analyses, allowing the easy application of a set of pre-defined analysis recipes |
== Extensions to SPM/Matlab == * [:AutomaticAnalysisIntroduction:aa - automatic analysis] - a system to automate SPM analyses, allowing the easy application of a set of pre-defined analysis recipes |
Line 21: | Line 29: |
= Other tools you might find useful = = Useful tools in Linux = |
* LoadShare - our tool for balancing SPM jobs across machines * SpmBatchPrintContrasts - for printing contrasts automatically * DisplaySlices program for displaying multiple images slices in SPM == Beyond fMRI == * AnalyzingDiffusion * UsingFreesurfer '''Scripts''' = General software = == Programming == * LearningUnix * LearningMatlab * LearningPython * ImageDataFormats == Other tools you might find useful == * ["UsingVNC Using VNC at the CBU"] - gives you a graphical desktop on the linux machines from your desk * [:CbuSoftware:An archive of other software that you might find useful] == Useful tools in Linux == |
Line 29: | Line 50: |
# kghostview - ps / psf / eps viewer useful for SPM postscript files | * kghostview - ps / psf / eps viewer useful for SPM postscript files |
Neuroimaging software
You might want to [:ScientificComputing:read this overview of scientific computing] and keep up to date with this [:ImagingComputingDevelopments:list of latest developments]
Try the [:StudentForum:student forum for helpful tips]
Major neuroimaging software packages installed at the CBU
Most imagers at the CBU use [:SpmInformation:SPM, the dominant software analysis package from the FIL in London], which has consistently been on the cutting edge of new methods. It runs under [:LearningMatlab:a language called Matlab] allowing you to browse the source and write your own components relatively easily.
[:FslInformation:FSL] ("fossil") - a powerful and fast collection of open source tools from FMRIB, Oxford also has many strengths and has a substantial following.
For some applications (particularly generating inflated brains, flat mapping, or performing grey & white matter segmentation for MEG analysis) you might wish to use [:FreeSurferAnalysis:Freesurfer].
[:AfniInformation:Afni] is also installed.
There are some old licenses for Brain Voyager around. This point-and-click commercial package has many impressive features.
It seems we might have [:BrainVisaInformation:Brain Visa] installed but I think it is probably an old version. If you find out, please put the latest information here!
There is [:AvailableSoftware:a list of the people responsible for maintaining our neuroimaging (fMRI & MEG) software].
Smaller tools
[:MriCro:MriCro and its successor MriCron] are a pair of very useful tools for viewing structural or functional images, producing 3D renderings of activation, and examining anatomical templates.
Extensions to SPM/Matlab
[:AutomaticAnalysisIntroduction:aa - automatic analysis] - a system to automate SPM analyses, allowing the easy application of a set of pre-defined analysis recipes
MarsBar - a useful toolbox for performing region-of-interest (ROI) analyses
[:DataDiagnostics:tsdiffana] - data diagnostics utility, good for checking the quality of your fMRI data
SnpmInformation - for doing non-parametric statistics in SPM
LoadShare - our tool for balancing SPM jobs across machines
SpmBatchPrintContrasts - for printing contrasts automatically
DisplaySlices program for displaying multiple images slices in SPM
Beyond fMRI
Scripts
General software
Programming
Other tools you might find useful
- ["UsingVNC Using VNC at the CBU"] - gives you a graphical desktop on the linux machines from your desk
[:CbuSoftware:An archive of other software that you might find useful]
Useful tools in Linux
- gimp - Graphics viewing and editing program; the Linux version of Photoshop
- acrobat - PDF viewer.
- mozilla - web browser
- nedit, gedit, emacs - text editors
- kghostview - ps / psf / eps viewer useful for SPM postscript files