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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 bert norm.mgz -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt

Note: you may need to include 'mri/' in the aseg.mgz path shown above on older versions of tkmedit.

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 | less

will print text on the overall functionality of Freesurfer.

recon-all -all

To re-create all volume and surface files, on the command-line type:

recon-all -s bert -all

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). The -autorecon1 stage completes in less than a half an hour, and is worth running to test your installation, as it exercises most of the libraries. To run, type:

recon-all -s bert -autorecon1

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 two 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