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.