Data Access

The CNI is developing an integrated neurobiological image management system (NIMS) to facilitate the stewardship of all data collected at the CNI. NIMS is currently under active development and we plan to roll out a beta-test version by the end of Summer of 2011. In the mean time, MR Steward, a key component of NIMS, is already installed at the CNI and is useful for organizing and archiving the data that you collect here. However, until the full NIMS system is in place, CNI users are responsible for managing their data and will want to copy their data to their own file server.

For more information on the NIMS and MR Steward software development efforts, see the CNI Software Development page.

Dirmonitor: Automatic data transfer to cnirt

A key part of NIMS is collating all data acquired in a scan session. A major aspect of that goal is already implemented and functional at the CNI. Dirmonitor and the related program pfilemonitor are two ever-running processes that manage images acquired on the MR scanner (cnimr). These processes automatically copy all imaging data acquired on cnimr to the linux box that sits to the right of the scanner (cnirt). On cnirt, the data are organized by PatientID and exam date. All data acquired during an exam are put into a folder with a name of the form YYYYMMDD_EXAMNUM. Dicoms are archived in zip files (one per series) and are also converted to a NIFTI file (also one per series), if possible. P-files are copied into this same folder. (Automatic recon of spiral data will be implemented soon!)

Should data stop showing up at any time, a variety of things could be to blame: Perhaps the mount of the pfile or dicom directories reset or is absent, or someone may have reset the scanner (or maybe even cnirt). Debugging should generally happen on cnirt:

To check if dirmon is running, try:

ps aux | grep dirmon

You should see something like:

cni      31446  6.8 29.3 3769888 3616544 ?     Sl   May09 200:00 /usr/bin/python ./dirmonitor.py

To check if pfilemon is running, try:

ps aux | grep pfilemon

You should see something like:

cni      15878 97.2  0.0  41548  8648 ?        Rl   12:45 350:59 /usr/bin/python ./pfilemonitor.py

Pfiles are located on the mount:

/net/cnimr/export/home/signa/research/mrraw/

Dicoms are located on the mount:

/net/cnimr/export/home1/sdc_image_pool/images

If you can ls both of those, you're in good shape.

Assuming you want to reset whichever process is not working (be it dirmonitor or pfilemonitor), use a killall and re-initialize it.

If you aren't getting dicoms/niftis try:

killall -9 dirmonitor.py
/home/cni/dirmonitor/dirmonitor.py &

If you aren't getting pfiles try:

killall -9 pfilemonitor.py
/home/cni/dirmonitor/pfilemonitor.py &