somerenserver data structure scripts

View the Project on GitHub germangh/somsds


A lightweight system for managing large neuroimaging datasets in a shared computing environment. There are two main components of somsds:

There is no public documentation yet on how to archive data. In any case, only superusers of the shared computing environment can archive data. Thus most users will only want to know how to retrieve data files from somsds.


somsds should work out of the box on most Linux distributions and on Mac OS X. In theory it should work also under Windows with some minor modifications.

clone git://
cd sosmds

Retrieving data

somsds_link2rec [recid] [--]

where [recid] is the ID of the recording from which data should be retrieved. A series of optional arguments will typically follow indicating the subset of data that we want to gain access to. For instance, one could retrieve all structural MRI datasets from recording ssmd using:

somsds_link2rec ssmd --condition rs-ec --modality smri

Apart from condition, modality, and subject there are several other tags that may be used to filter the set of files to be retrieved, e.g. subject, technique, device, sex, age, etc. See the command line documentation of script somsds_link2rec for more information.

Recording IDs, condition IDs, etc...

To produce a list of the available recordings together with a short description:


To list all valid condition IDs (together with a short description) for recording ssmd:

somsds_rec_get ssmd condition

In general, the accepted values of tag [tagname] for recording [recid] can be listed using:

somsds_rec_get [recid] [tagname]

Symbolic links

Script somsds_link2rec will not create copies of the relevant data files. Instead it will create symbolic links with to the actual data files. The main reasons for this being the desired behaviour are:


Released under the Creative Commons Attribution-NonCommercial-ShareAlike licence