Loading Freesurfer 5.1 data into XNAT

[Mohana Ramaratnam]

Hello,

We are sharing some scripts that we use to:

a) Generate the Freesurfer assessor using the information in the
aseg.stats and aparc.stats file. This is done by the perl script
stats2xml_fs5.1.pl. All dependencies have been included. You may have
to edit the paths to the appropriate location of the fs2xml folder.

b) If you have data already processed and want this data to be
imported, I have included a script - import_fs5.sh which can be used
as a template for your needs.

The scripts are available here:
http://hg.xnat.org/scripts/src/18bf75b9d777/washu_freesurfer_v5.1

Happy Segmenting!!
Mohana

[Alexis]

Hi Mohana,

This is great news, although we now have indexed our freesurfer data
with the schema you provided. This will definitely be useful for many
groups and possibly in the future we should think of a system to share
not only a schema but a triple ( schema + sample display file + upload
script ).

Alexis

[Satrajit Ghosh]

hi mohana/alexis,

where can i download the xnatrestclient? is it a single binary and can it be installed independent of xnat?

cheers,

satra

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[Mohana Ramaratnam]

Hi Satra,

You could replace XnatRestClient with curl.

XnatRestClient can be installed independent of XNAT. The required jar
is attached (its also available in
XNAT_HOME/plugin-resources/repository/xdat/jars). The way to execute
it would be:

java -jar JAR_DIR_PATH_HERE/xdat-restClient-1.jar OS_ARG_SYM_HERE

Mohana

[Mohana Ramaratnam]

We are thinking of XNAT plugins and this is where we see such things available.

Mohana