I am trying to display a volumetric file to a surface using mri_vol2surf and then tksurfer.
Here is the error message I get.
I have obtained the email with the few license lines to copy in a file (that i created) name license.txt
Last login: Fri Dec 16 16:56:54 on ttys002
-------- freesurfer-Darwin-lion-stable-pub-v5.3.0 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Applications/freesurfer/subjects
MNI_DIR /Applications/freesurfer/mni
FSL_DIR /usr/local/fsl
Binds-MacBook-Pro:~ Marco$ source ~/.bash_profile
-------- freesurfer-Darwin-lion-stable-pub-v5.3.0 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Applications/freesurfer/subjects
MNI_DIR /Applications/freesurfer/mni
FSL_DIR /usr/local/fsl
Binds-MacBook-Pro:~ Marco$ export SUBJECTS_DIR=/Users/Marco/Desktop/surface_RORDEN
Binds-MacBook-Pro:~ Marco$ mri_vol2surf --src /Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1.nii --regheader elab --hemi lh --o /Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1_SURF_LH.mgh
srcvol = /Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1.nii
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Computing registration from header.
Using /Users/Marco/Desktop/surface_RORDEN/elab/mri/orig.mgz as target reference.
Reading surface /Users/Marco/Desktop/surface_RORDEN/elab/surf/lh.white
Done reading source surface
Mapping Source Volume onto Source Subject Surface
1 0 0 0
using old
Done mapping volume to surface
Number of source voxels hit = 41923
Writing to /Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1_SURF_LH.mgh
Dim: 116772 1 1
Binds-MacBook-Pro:~ Marco$ tksurfer elab lh inflated -overlay /Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1_SURF_LH.mgh
subject is elab
hemi is lh
surface is inflated
surfer: current subjects dir: /Users/Marco/Desktop/surface_RORDEN
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer: /Users/Marco
checking for nofix files in 'inflated'
Reading image info (/Users/Marco/Desktop/surface_RORDEN/elab)
Reading /Users/Marco/Desktop/surface_RORDEN/elab/mri/orig.mgz
surfer: Reading header info from /Users/Marco/Desktop/surface_RORDEN/elab/mri/orig.mgz
--------------------------------------------------------------------------
ERROR: FreeSurfer license file /Applications/freesurfer/.license not found.
If you are outside the NMR-Martinos Center,
get a valid license file (it's free).
If you are inside the NMR-Martinos Center,
make sure to source the standard environment.
--------------------------------------------------------------------------
Binds-MacBook-Pro:~ Marco$
- - -
Marco Ganzetti, PhD
Movement Control & Neuroplasticity Research Group
Tervuursevest 101, 3001 Leuven