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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