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| = Analysis of MRI Data in FreeSurfer = |
= Analysis of MRI Data in !FreeSurfer = |
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* For the tutorial, see the FreeSurfer wiki ([http://surfer.nmr.mgh.harvard.edu/fswiki]). == Futher Help == |
* For the tutorial, see the !FreeSurfer wiki (http://surfer.nmr.mgh.harvard.edu/fswiki). == Further Help == |
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* This page outlines a basic pipeline for some types of FreeSurfer analysis (however, it is specifically designed not to work by default. You should educate yourself and make decisions based on your specific experiment). There are far too many features in FreeSurfer to cover all of them in our wiki, so do not think this page covers all of the details: DansStructuralPage. * This page explains how to create structural data for source analysis: [http://imaging.mrc-cbu.cam.ac.uk/imaging/DanStructurals] |
* This page outlines a basic pipeline for some types of !FreeSurfer analysis (however, it is specifically designed not to work by default. You should educate yourself and make decisions based on your specific experiment). There are far too many features in !FreeSurfer to cover all of them in our wiki, so do not think this page covers all of the details: DanStructurals. |
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* See chapter 13 of the manual |
Can be found toward the bottom of this page: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki |
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| !FreeSurfer has been developed at the Martinos Center (in Boston, US). Here is its home: http://www.nmr.mgh.harvard.edu/martinos/userInfo/data/sofFreeSurf.php | |
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| MNE has been developed at the Martinos Center (in Boston, US), primarily by Matti Hämäläinen. Here is its home: http://www.nmr.mgh.harvard.edu/martinos/userInfo/data/sofMNE.php | At the moment, we are using "!FreeSurfer 4.3.0". At the CBU, !FreeSurfer is installed here: |
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| At the moment, we are using "MNE 2.6.0". At the CBU, MNE is installed here: | {{{/imaging/local/linux/freesurfer_4.3.0}}} |
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| {{{/imaging/local/linux/mne_2.6.0}}} | To source the MNE tools type "freesurfer_4.3.0". Some of the tools will only be available on vncserver.glx sessions (or at a linux workstation). |
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| To source the MNE tools type "mne_setup_2.6.0". Some of the tools will only be available on vncserver.glx sessions (or at a linux workstation). | A previous version "!FreeSurfer 4.0.1" is available. |
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| The previous version "MNE 2.5.0" is available. | To source this version type "freesurfer_4.0.1". |
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| To source this version type "mne_2.5.0". | == Recent Updates == == 2009/04/15 Installed latest MNE == Type {{{ mne_setup_2.6.0 }}} to use it [DGW] == 2009/04/15 Installed latest Freesurfer == Type {{{ freesurfer_4.3.0 }}} to use it[DGW] == 2008/06/03 Added MNE Tutorial setup == I've added a separate mne_tutorial setup which locally sources mne in order to avoid aliasing commands with --digtrig STI101. This should only be used for the MNE Tutorial. Instead of typing {{{mne_setup_2.5}}}, as you would normally, type {{{mne_tutorial}}}. [DGW] |
Analysis of MRI Data in !FreeSurfer
Demos
For the tutorial, see the FreeSurfer wiki (http://surfer.nmr.mgh.harvard.edu/fswiki).
Further Help
- The most important source for help is the wiki mentioned above.
This page outlines a basic pipeline for some types of FreeSurfer analysis (however, it is specifically designed not to work by default. You should educate yourself and make decisions based on your specific experiment). There are far too many features in FreeSurfer to cover all of them in our wiki, so do not think this page covers all of the details: DanStructurals.
Some relevant papers
Can be found toward the bottom of this page: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki
The code
FreeSurfer has been developed at the Martinos Center (in Boston, US). Here is its home: http://www.nmr.mgh.harvard.edu/martinos/userInfo/data/sofFreeSurf.php
At the moment, we are using "FreeSurfer 4.3.0". At the CBU, FreeSurfer is installed here:
/imaging/local/linux/freesurfer_4.3.0
To source the MNE tools type "freesurfer_4.3.0". Some of the tools will only be available on vncserver.glx sessions (or at a linux workstation).
A previous version "FreeSurfer 4.0.1" is available.
To source this version type "freesurfer_4.0.1".
Recent Updates
2009/04/15 Installed latest MNE
Type
mne_setup_2.6.0
to use it [DGW]
2009/04/15 Installed latest Freesurfer
Type
freesurfer_4.3.0
to use it[DGW]
2008/06/03 Added MNE Tutorial setup
I've added a separate mne_tutorial setup which locally sources mne in order to avoid aliasing commands with --digtrig STI101. This should only be used for the MNE Tutorial.
Instead of typing mne_setup_2.5, as you would normally, type mne_tutorial.
[DGW]