if recon-all works then you must have a license file. Are you sure that
FREESURFER_HOME is defined in your environment and points to the right
place? That's where we look for the license file (then in
/Applications/freesurfer on the mac if FREESURFER_HOME isn't defined in
the env0
cheers
Bruce
On Fri, 16 Dec 2016, Marco Ganzetti wrote:
At the current stage I can run recon-all and get the results without
problems.
If the license would not work I couldn't be able to run it.
Can someone send me the type of license file I should generate?
In the website it says that I should get a license.txt by email, but I
didn't get any file just instructions how to create a new file or modify the
existing LICENSE file.
Marco Ganzetti, PhD
Il 16 Dic 2016 19:47, Z K <zkauf...@nmr.mgh.harvard.edu> ha scritto:
Is the file you created located in /Applications/freesurfer?
Also, fir good measure, try creating the same file but naming it
.license in the /Applications/freesurfer
On 12/16/2016 11:20 AM, Marco Ganzetti wrote:
> Dear all,
> 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
> I created a new file and erased the existing LICENSE
>
> Thanks
> Marco Ganzetti
>
> 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 ($session) set to:
> surfer: /Users/Marco
> checking for nofix files in 'inflated'
> Reading image info (/Users/Marco/Desktop/surface_RORDEN/elab)
> Reading /Users/Marco/Desktop/surface_RORDEN/elab/mri/orig.mgz
> surfer: Reading header info from
> /Users/Marco/Desktop/surface_RORDEN/elab/mri/orig.mgz
>
--------------------------------------------------------------------------
> ERROR: FreeSurfer license file
/Applications/freesurfer/.license not found.
> If you are outside the NMR-Martinos Center,
> go to http://surfer.nmr.mgh.harvard.edu to
> get a valid license file (it's free).
> If you are inside the NMR-Martinos Center,
> make sure to source the standard environment.
>
--------------------------------------------------------------------------
> Binds-MacBook-Pro:~ Marco$
>
> - - -
>
> *Marco Ganzetti, PhD*
>
> Movement Control & Neuroplasticity Research Group
> Tervuursevest 101, 3001 Leuven
>
> email: marco.ganze...@kuleuven.be
<mailto:marco.ganze...@kuleuven.be>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
_______________________________________________
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The information in this e-mail is intended only for the person
to whom it is
addressed. If you believe this e-mail was sent to you in error
and the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
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but does not contain patient information, please contact the
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_______________________________________________
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
