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| [[http://marsbar.sourceforge.net|MarsBaR]] is a region of interest toolbox for SPM99, SPM2 and SPM5. It is installed at the CBU. | |
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| [http://marsbar.sourceforge.net MarsBaR] is a region of interest toolbox for SPM99, SPM2 and SPM5. It is installed at the CBU. | The development version supports SPM5. To use this, start SPM / matlab on a machine that will run SPM5 (see [[CbuComputingResources#Software|the CBU computing page]]). |
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| The development version supports SPM5. To use this, start SPM / matlab on a machine that will run SPM5 (see [wiki:CbuComputingResources#Software the CBU computing page]). | MarsBaR should be available via the toolboxes button (let MatthewBrett know if not). |
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| Then type this at the matlab prompt: | You can also make MarsBaR available by manually adding the path: To do this, type the following at the matlab prompt: |
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| addpath /imaging/local/spm/marsbar/marsbar-0.40 | addpath /imaging/local/spm/marsbar/marsbar-devel-0.41 |
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| to start MarsBaR. | |
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| to start MarsBaR. | ---- = Local help for MarsBaR = Some pages showing basic steps (with screenshots) exist. [[http://www.mrc-cbu.cam.ac.uk/people/jessica.grahn/marsbarcreateroi.html|Steps for creating ROIs from an SPM cluster, and exporting ROIs to nii or hdr/img.]] [[http://www.mrc-cbu.cam.ac.uk/people/jessica.grahn/marsbar.html|Steps for extracting signal from Regions of Interest, for import into Excel/SPSS/etc., to do second level analysis.]] ---- Here are some marsbar batch files (JessicaGrahn): [[attachment:marsbarbatch.m]] : this batch file takes a list of coordinates and makes sphere ROIs, saving them in MarsBar and .nii format. [[attachment:marsbarbatchextract.m]] : this batch takes all rois in a directory, and extracts data from all the con/beta images in another directory, saving the data to a text file. [[attachment:marsbarbatchconvert.m]] : this batch file converts rois to .nii format |
MarsBaR
MarsBaR is a region of interest toolbox for SPM99, SPM2 and SPM5. It is installed at the CBU.
The development version supports SPM5. To use this, start SPM / matlab on a machine that will run SPM5 (see the CBU computing page).
MarsBaR should be available via the toolboxes button (let MatthewBrett know if not).
You can also make MarsBaR available by manually adding the path:
To do this, type the following at the matlab prompt:
addpath /imaging/local/spm/marsbar/marsbar-devel-0.41 marsbar
to start MarsBaR.
Local help for MarsBaR
Some pages showing basic steps (with screenshots) exist.
Steps for creating ROIs from an SPM cluster, and exporting ROIs to nii or hdr/img.
Here are some marsbar batch files (JessicaGrahn):
marsbarbatch.m : this batch file takes a list of coordinates and makes sphere ROIs, saving them in MarsBar and .nii format.
marsbarbatchextract.m : this batch takes all rois in a directory, and extracts data from all the con/beta images in another directory, saving the data to a text file.
marsbarbatchconvert.m : this batch file converts rois to .nii format