Hi again, Alan,
can you please send me the exact command you are running, as well as the
value of SUBJECTS_DIR, FREESURFER_HOME, and so on?
Cheers,
/E

On Fri, 2014-02-07 at 14:46 -0500, Alan Francis wrote:
> Hi Eugenio:
>
>
> Thanks for responding. I am running the script in the directory that
> the brains are saved not the /user/local etc. Here is the error
> message that it gives me:
>
>
> /usr/local/freesurfer/stable5_3_0//bin/kvlQuantifyHippocampalSubfieldSegmentations.sh: line 22: volumeStats_left.txt: Permission denied
> failed to do
> kvlQuantifyPosteriorProbabilityImages /usr/local/freesurfer/stable5_3_0//data/GEMS/compressionLookupTable_left.txt             posterior_Left-Hippocampus.mgz             posterior_left_presubiculum.mgz             posterior_left_CA1.mgz             posterior_left_CA2_3.mgz             posterior_left_fimbria.mgz             posterior_left_subiculum.mgz             posterior_left_CA4_DG.mgz             posterior_left_hippocampal_fissure.mgz             > volumeStats_left.txt
>
>
>
>
> thanks so much,
>
>
> Alan
>
>
>
>
>
>
> On Fri, Feb 7, 2014 at 1:45 PM, Juan Eugenio Iglesias
> <iglesias@nmr.mgh.harvard.edu> wrote:
>         Hi Alan
>         by default, the script saves the file in the directory you're
>         on. So,
>         you just need to run it from your own space, e.g.,
>         cd ~
>         kvlQuantify......
>         Cheers,
>         /E
>         PD: I assumed the problem was that you ran the script
>         from /usr/local/freesurfer/stable_5_3/data
>
>
>
>         On Fri, 2014-02-07 at 12:33 -0500, Alan Francis wrote:
>         > Hi Eugenio;
>         >
>         >
>         > I ran the kvl quantify script for 70 processed Asperger
>         brains.
>         > However, it was not able to save the output since the the
>         nmr center
>         > disallows folks from saving data in the pathway
>         >
>         >
>         > /usr/local/freesurfer/stable_5_3/data
>         >
>         >
>         > is there anyway I can modify the script to save the data
>         elsewhere?
>         >
>         >
>         > thanks so much,
>         >
>         >
>         > Alan Francis
>         > Martinos Center
>
>
>
>
>
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