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Testing your FreeSurfer installation

tkmedit

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.

tksurfer

To view a surface, type:

tksurfer bert rh pial

To increase brightness on that surface, in tksurfer:

To view cortical parcellation labels, in tksurfer:

recon-all -help

The Freesurfer command:

recon-all --help

will print text on the overall functionality of Freesurfer.

recon-all -autorecon-all

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).

Getting started with your own data

Given a subject having two sets of DICOMS (two 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 002
mkdir 003
cp -r <path_to_dicoms>/95555-2-*.dcm 002/
cp -r <path_to_dicoms>/95555-3-*.dcm 003/
mri_convert -it dicom -ot mgz 002/ 002.mgz
mri_convert -it dicom -ot mgz 003/ 003.mgz

Now you will have two .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).

Questions?

Send email to: freesurfer AT nmr DOT mgh DOT harvard DOT edu

Bug reports: analysis-bugs AT nmr DOT mgh DOT harvard DOT edu