GENTOO:Install FreeSurfer
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Contents |
Install
View the contents of a distribution:
$ tar ztf freesurfer-Linux-rh9-dev-full.tar.gz # tar zxvf freesurfer-Linux-rh9-dev-full.tar.gz -C /usr/local
Configure
$ setenv FREESURFER_HOME /usr/local/freesurfer $ source $FREESURFER_HOME/SetUpFreeSurfer.csh
Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast SUBJECTS_DIR /usr/local/freesurfer/subjects FUNCTIONALS_DIR /usr/local/freesurfer/sessions MINC_BIN_DIR /usr/local/freesurfer/lib/mni/bin MINC_LIB_DIR /usr/local/freesurfer/lib/mni/lib PERL5LIB /usr/local/freesurfer/lib/mni/lib/perl5/5.8.0 GSL_DIR /usr/local/freesurfer/lib/gsl QTDIR /usr/local/freesurfer/lib/qt TCLLIBPATH /usr/local/freesurfer/lib/tcltktixblt/lib
Some of the MNI tools currently contain hard-coded paths to perl. To fix this situation, type:
$ fixup_mni_paths
Now the MNI tools will find the perl binary on your platform. You can confirm this by typing 'nu_correct', which should return version information (v1.10).
Install missing libraries
ldd bin/tkmedit
linux-gate.so.1 => (0xffffe000)
libtix8.1.8.3.so => not found
libtk8.4.so => not found
libtcl8.4.so => not found
libglut.so.3 => not found
libSM.so.6 => /usr/lib/libSM.so.6 (0xb7f41000)
libICE.so.6 => /usr/lib/libICE.so.6 (0xb7f28000)
libXmu.so.6 => /usr/lib/libXmu.so.6 (0xb7f13000)
libXi.so.6 => /usr/lib/libXi.so.6 (0xb7f0b000)
libGLU.so.1 => /usr/lib/libGLU.so.1 (0xb7e92000)
libGL.so.1 => /usr/lib/opengl/nvidia/lib/libGL.so.1 (0xb7e24000)
libX11.so.6 => /usr/lib/libX11.so.6 (0xb7d58000)
libgsl.so.0 => not found
libgslcblas.so.0 => not found
libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0xb7d38000)
libtiff.so.3 => /usr/lib/libtiff.so.3 (0xb7ce7000)
libz.so.1 => /lib/libz.so.1 (0xb7cd6000)
libm.so.6 => /lib/libm.so.6 (0xb7cb2000)
libcrypt.so.1 => /lib/libcrypt.so.1 (0xb7c84000)
libc.so.6 => /lib/libc.so.6 (0xb7b6c000)
libXt.so.6 => /usr/lib/libXt.so.6 (0xb7b19000)
libXext.so.6 => /usr/lib/libXext.so.6 (0xb7b0b000)
libstdc++.so.6 => /usr/lib/gcc/i686-pc-linux-gnu/3.4.4/libstdc++.so.6 (0xb7a3d000)
libgcc_s.so.1 => /usr/lib/gcc/i686-pc-linux-gnu/3.4.4/libgcc_s.so.1 (0xb7a33000)
libGLcore.so.1 => /usr/lib/opengl/nvidia/lib/libGLcore.so.1 (0xb7342000)
libnvidia-tls.so.1 => /usr/lib/opengl/nvidia/lib/libnvidia-tls.so.1 (0xb7340000)
libdl.so.2 => /lib/libdl.so.2 (0xb733c000)
/lib/ld-linux.so.2 (0xb7f5f000)
Install missing libraries
# emerge glut # gets libglut.so
Enter License
A license file is required to enable the tools. One can be obtained for free by registering at:
http://surfer.nmr.mgh.harvard.edu/registration.html
Upon receiving the license information by email, copy the three lines of the license information to a file named .license (thats DOT license) and copy that file to your $FREESURFER_HOME.
Test
$recon-all --help
will print text on the overall functionality of Freesurfer.
There is a sample subject, called 'bert', found in the freesurfer/subjects directory, which contains pre-processed data stored in .mgz files (not in COR formatted files, which is a deprecated format).
To view a volume, type:
$ tkmedit bert orig.mgz
To view the subcortical segmentation results, type:
$ tkmedit -segmentation mri/aseg.mgz \ $FREESURFER_HOME/FreeSurferColorLUT.txt bert norm.mgz
As you move the mouse over areas of the brain, the label info is found in the 'Sgmtn label' box.
To view a surface, type:
$ tksurfer bert rh pial
To increase brightness on that surface, in tksurfer:
$ View->Configure->Lighting->Brightness
To view cortical parcellation labels, in tksurfer:
$ File->Label->Import Annotation Browse to file rh.aparc.annot and select OK Redraw View icon is the one with the up/down arrows
To re-create all volume and surface files, on the command-line type:
$ recon-all -autorecon-all -subjid bert
Note that this operation may take 24 hours to complete. Consult recon-all --help for instructions on how to conduct multi-stage processing (eg. -autorecon1, -autorecon2 and -autorecon3).
Use
Given a subject having three sets of DICOMS (three runs of structural scans), do the following to setup a subject, where <subjid> is replaced with whatever name or id you want to give to that subject:
cd $SUBJECTS_DIR mksubjdirs <subjid> cd <subjid> cd mri/orig mkdir 001 mkdir 002 mkdir 003 cp -r <path_to_dicoms>/95555-2-*.dcm 001/ cp -r <path_to_dicoms>/95555-3-*.dcm 002/ cp -r <path_to_dicoms>/95555-7-*.dcm 003/ mri_convert -it dicom -ot mgz 001/ 001.mgz mri_convert -it dicom -ot mgz 002/ 002.mgz mri_convert -it dicom -ot mgz 003/ 003.mgz
Now you will have three .mgz files in mri/orig, and recon-all will automatically take these three structural scans and average/motion- correct them. Note that in your own case, the name of the dicom files will be different (in this example, 95555-2-*.dcm consisted of 128 files).
Tutorial
Download and install Tutorial data
# cd /tmp # wget ftp://surfer.nmr.mgh.harvard.edu/pub/dist/buckner_data-tutorial_subjs.tar.gz # wget ftp://surfer.nmr.mgh.harvard.edu/pub/dist/buckner_data-group_study.tar.gz # tar xzvf buckner_data-tutorial_subjs.tar.gz -C /usr/local/freesurfer/subjects # tar xzvf buckner_data-group_study.tar.gz -C /usr/local/freesurfer/subjects # rm /tmp/buckner_data-tutorial_subjs.tar.gz # rm /tmp/buckner_data-group_study.tar.gz
Setup Morphometry and Reconstruction Tutorial
# source $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs/scripts/setup_subjects.csh
Setup Group Study Analysis and Visualization
# source $FREESURFER_HOME/subjects/buckner_data/group_study/scripts/setup_subjects.csh
You can only source one setup_subjects.csh file at a time.
Help
Send email to: freesurfer AT nmr DOT mgh DOT harvard DOT edu Bug reports: analysis-bugs AT nmr DOT mgh DOT harvard DOT edu The Freesurfer website is: https://surfer.nmr.mgh.harvard.edu/
