This is an post to demonstrate how to run the old/legacy anonymization procedure. The process would likly break because the executable was build with MATLAB in centos6 while we now only have centos7 on cbica-cluster. Even if the executable still works, it is a piece of inefficient program that would take a lot of time for large amount of studies or large amount of DICOM files.
When you have a batch of data in $input_dir you want to anonymize, and make available only to an $allowed_user in a designated directory $output_dir. You could do the following:
In anonymizationExe_R44.sh, anonymization of the DICOM studies is performed serially for all sub-directories. After the anonymization, another script /cbica/comp_space/CBIG/Scripts/setPermission.sh would be called to assign the read permission of the $output_dir to a specific user/project user. setPermission.sh has to be executed on a compute node through SGE submission and will not take effect if executed on an interactive node, i.e. crete, agora, etc... See Mark's notes on how to use the Anonymized_to_Distribute directory and
on where to execute setPermission.sh for more information.
This is an post to demonstrate how to run the old/legacy anonymization procedure. The process would likly break because the executable was build with MATLAB in centos6 while we now only have centos7 on cbica-cluster. Even if the executable still works, it is a piece of inefficient program that would take a lot of time for large amount of studies or large amount of DICOM files.
When you have a batch of data in
$input_dir
you want to anonymize, and make available only to an$allowed_user
in a designated directory$output_dir
. You could do the following:In
anonymizationExe_R44.sh
, anonymization of the DICOM studies is performed serially for all sub-directories. After the anonymization, another script/cbica/comp_space/CBIG/Scripts/setPermission.sh
would be called to assign the read permission of the$output_dir
to a specific user/project user.setPermission.sh
has to be executed on a compute node through SGE submission and will not take effect if executed on an interactive node, i.e. crete, agora, etc... See Mark's notes on how to use the Anonymized_to_Distribute directory and on where to execute setPermission.sh for more information.