Hey Alex, Just from looking at the first two lines of your environment variables I think you might have forgot the 's' on Applications for FREESURFER_HOME.

...

...

String[] env = {"FREESURFER_HOME=/Application/freesurfer", "FSFAST_HOME=/Applications/freesurfer/fsfast",

mishkin

On Mon, Feb 25, 2008 at 6:13 PM, Alexander Zaitsev (CNI) azaitsev@bwh.harvard.edu wrote:

Hello:

I need to call mri_convert utility from Java code. The problem is when I am making a system call, I am getting the following error :

...

...

...

...

...

FreeSurfer license file /Application/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. <<<<<<

The mri_convert runs from the shell without problem and the .license file is in the right directory.

I am including the following env variables into the system call:

...

...

...

   String[] env = {"FREESURFER_HOME=/Application/freesurfer",
       "FSFAST_HOME=/Applications/freesurfer/fsfast",
       "SUBJECTS_DIR=/Applications/freesurfer/subjects",
       "MNI_DIR=/Applications/freesurfer/mni",
       "GSL_DIR=/Applications/freesurfer/lib/gsl",
       "FSL_DIR=/Applications/freesurfer/fsl",
       "FUNCTIONALS_DIR=$FREESURFER_HOME/sessions",
       "FSLOUTPUTTYPE=NIFTI_GZ", sPATH, "DISPLAY=:0.0", "HOME=/tmp",
       "DYLD_LIBRARY_PATH=/Applications/freesurfer/lib/gsl/lib",
       "MINC_BIN_DIR=/Applications/freesurfer/mni/bin",
       "MINC_LIB_DIR=/Applications/freesurfer/mni/lib",
       "MNI_DATAPATH=/Applications/freesurfer/mni/data",
       "LOCAL_DIR=/Applications/freesurfer/local",
       "FMRI_ANALYSIS_DIR=/Applications/freesurfer/fsfast",

"MNI_PERL5LIB=/Applications/freesurfer/mni/lib/../System/Library/Perl/5.8.6",

"PERL5LIB=/Applications/freesurfer/mni/lib/../System/Library/Perl/5.8.6", "LD_LIBRARY_PATH=/Applications/freesurfer/lib/gsl/lib", "FSLDIR=/Applications/freesurfer/fsl", "FSL_BIN=/Applications/freesurfer/fsl/bin", "FSLTCLSH=/Applications/freesurfer/fsl/bin/tclsh", "FSLWISH=/Applications/freesurfer/fsl/bin/wish", "FSLGNUPLOT=/Applications/freesurfer/fsl/bin/gnuplot", "FSLDISPLAY=/Applications/freesurfer/fsl/bin/display", "FSLCONVERT=/Applications/freesurfer/fsl/bin/convert", "FSLBROWSER=/Applications/freesurfer/fsl/tcl/fslwebbrowser", "FSLCONFDIR=/Applications/freesurfer/fsl/config" };

<<<

Am I missing something?

Yes, the mri_convert runs fine when called from the shell. And I don't see any other env variables related to the free surfer.

Thank you,

Alex

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer