To follow this exercise exactly be sure you've downloaded the tutorial data set before you begin. If you choose not to download the data set you can follow these instructions on your own data, but you will have to substitute your own specific paths and subject names.
1. Resampling the parametric map onto a surface
To resample the brain activation volume onto the individual's surface, use the following commands:
cd $TUTORIAL_DATA/buckner_data/tutorial_subjs mri_vol2surf --src spm001.img --srcreg register.dat --hemi lh \ --projfrac 0.5 --out ./spm001-lh.w --out_type paint
In this example, the --src option represents the brain activation volume, the --srcreg option represents the registration matrix (used to register the functional volumes to the anatomical reference), --hemi specifies hemisphere (lh or rh), --projfrac specifies normalized radial distance between the grey matter boundaries with white matter (0.0) and pial surface(1.0) at which to sample the activation volume, --out specifies output path and file name, and --out_type specifies the output format.
When an output type of 'paint' is specified as in the above example, the output data (a binary '.w file') can be easily read by tksurfer. The output file should be specified with a relative path (e.g., ./data-lh.w), otherwise output will be placed by default into the subject's anatomical directory.
Upon completion, check to see that mri_vol2surf wrote the file spm001-lh.w in the directory from which it was run by typing:
ls -l spm001-lh.h
in that directory.