|
Size: 2323
Comment:
|
Size: 2928
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | Line 1: |
| [wiki:Self:FreeSurferWiki top] | [wiki:Self:Installation previous] | [wiki:Self:SetupConfiguration next] | |
| Line 2: | Line 3: |
| == To install FreeSurfer from tar files == | == FreeSurfer Linux Installation == |
| Line 4: | Line 5: |
| 1. Obtain a license key from http://surfer.nmr.mgh.harvard.edu/registration.html or from a previous installation. If you are using a previous installation, the license file should be freesurfer/.license. | 1. Obtain a license key from http://surfer.nmr.mgh.harvard.edu/registration.html or from a previous installation. If you are using a previous installation, the license file is found in the main freesurfer directory and is called '.license'. |
| Line 6: | Line 7: |
| 2. cd to the directory just above where you want FreeSurfer to be installed (the ParentDir). You will need about 1G of space on this disk partition. | 2. cd to the directory just above where you want !FreeSurfer to be installed (the ParentDir). You will need about 1G of space on this disk partition. |
| Line 8: | Line 9: |
| 3. Enter the command: | 3. Enter the command (replacing 'freesurfer.tar.gz' with the actual filename downloaded): |
| Line 10: | Line 11: |
| `tar xvfz DISTDIR/freesurfer.tar.gz` | `tar xvfz freesurfer.tar.gz` |
| Line 16: | Line 17: |
| `freesurfer.tar.gz` -- FreeSurfer tree[[BR]] | `freesurfer.tar.gz` -- !FreeSurfer tree[[BR]] |
| Line 18: | Line 19: |
| `bert.raw.tar.gz` -- FreeSurfer tutorial data[[BR]] `bert.func.tar.gz` -- FreeSurfer functional tutorial data[[BR]] `bert.recon.tar.gz` -- reconstructed FreeSurfer tutorial data[[BR]] |
`bert.raw.tar.gz` -- !FreeSurfer tutorial data[[BR]] `bert.func.tar.gz` -- !FreeSurfer functional tutorial data[[BR]] `bert.recon.tar.gz` -- reconstructed !FreeSurfer tutorial data[[BR]] |
| Line 26: | Line 27: |
| `tar xvfz DISTDIR/bert.recon.tar.gz` | `tar xvfz DISTDIR/bert.recon.tar.gz`[[BR]] |
| Line 33: | Line 34: |
| FreeSurfer uses some of the tools developed at the Montreal Neurological Institue (MNI) (http://www.bic.mni.mcgill.ca) to align antomical volumes (using minctracc) and to compute the Talairach transform (using mritotal). You must have the MNI tools installed to be able to access this functionality through FreeSurfer. | !FreeSurfer uses some of the tools developed at the Montreal Neurological Institue (MNI) (http://www.bic.mni.mcgill.ca) to align antomical volumes (using minctracc) and to compute the Talairach transform (using mritotal). You must have the MNI tools installed to be able to access this functionality through !FreeSurfer. |
| Line 35: | Line 36: |
| Refer to the file ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.README.txt for more information on building the MINC toolkit from the source code. | The [http://www.bic.mni.mcgill.ca/software/distribution MNI-BIC software distribution page] contains binaries for most platforms. Note: the Mac OS X FreeSurfer distribution contains the MINC toolkit in its installation. An alternative is to build the tools required by FreeSurfer from source. A special source code bundle with build scripts has been prepared by MGH for FreeSurfer users. Refer to the file ftp://surfer.nmr.mgh .harvard.edu/pub/dist/mni.srcbuild.README.txt for more information on building the MINC toolkit from the source code. |
[wiki:FreeSurferWiki top] | [wiki:Installation previous] | [wiki:SetupConfiguration next]
FreeSurfer Linux Installation
1. Obtain a license key from http://surfer.nmr.mgh.harvard.edu/registration.html or from a previous installation. If you are using a previous installation, the license file is found in the main freesurfer directory and is called '.license'.
2. cd to the directory just above where you want FreeSurfer to be installed (the ParentDir). You will need about 1G of space on this disk partition.
3. Enter the command (replacing 'freesurfer.tar.gz' with the actual filename downloaded):
tar xvfz freesurfer.tar.gz
This will create a directory called freesurfer, in which will be the following files:
INSTALL -- this fileBR license.freesurfer -- license agreementBR freesurfer.tar.gz -- FreeSurfer treeBR talairach.tar.gz -- MNI 305 talairach brainBR bert.raw.tar.gz -- FreeSurfer tutorial dataBR bert.func.tar.gz -- FreeSurfer functional tutorial dataBR bert.recon.tar.gz -- reconstructed FreeSurfer tutorial dataBR average7.tar.gz -- contains average labels for checking spherical morphBR
4. The default subjects directory (the directory in which your subjects' data will be placed) is freesurfer/subjects. You may wish set to up your installation differently, e.g. if you have a large external hard drive you want to use for subject data. See the [wiki:SetupConfiguration 'Setup and Configuration'] section for details. Regardless, cd into your subjects directory (the default is called 'subjects', located within the freesurfer installation directory) and enter the commands:
tar xvfz DISTDIR/average7.tar.gz BR tar xvfz DISTDIR/bert.recon.tar.gzBR tar xvfz DISTDIR/talairach.tar.gz
This will populate your subjects directory with 'average7', the sample data set 'bert', and the MINC atlas subject 'talairach'.
MINC installation
FreeSurfer uses some of the tools developed at the Montreal Neurological Institue (MNI) (http://www.bic.mni.mcgill.ca) to align antomical volumes (using minctracc) and to compute the Talairach transform (using mritotal). You must have the MNI tools installed to be able to access this functionality through FreeSurfer.
The [http://www.bic.mni.mcgill.ca/software/distribution MNI-BIC software distribution page] contains binaries for most platforms. Note: the Mac OS X FreeSurfer distribution contains the MINC toolkit in its installation.
An alternative is to build the tools required by FreeSurfer from source. A special source code bundle with build scripts has been prepared by MGH for FreeSurfer users. Refer to the file ftp://surfer.nmr.mgh .harvard.edu/pub/dist/mni.srcbuild.README.txt for more information on building the MINC toolkit from the source code.