Hi Eugenio:

The command: kvlQuantifyHippocampalSubfieldSegmentations.sh I run this in the the directory that has the processed brains.

SUBJECTS_DIR /media/Alan_Francis/Freiburg

FREESURFER_HOME /usr/local/freesurfer/stable5_3/

thanks so much,

Alan

On Fri, Feb 7, 2014 at 2:52 PM, Juan Eugenio Iglesias < iglesias@nmr.mgh.harvard.edu> wrote:

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





    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.