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 zkaufman@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.ganzetti@kuleuven.be mailto:marco.ganzetti@kuleuven.be
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
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 zkaufman@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.ganzetti@kuleuven.be <mailto:marco.ganzetti@kuleuven.be> > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Marco Ganzetti