Data Access: Difference between revisions

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The CNI is developing an integrated neurobiological image management system ([https://cni.stanford.edu/nims/ 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.  
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. A preliminary version of NIMS ([https://cni.stanford.edu/nims/ NIMS lite]) is currently deployed and used by all CNI users to securely access their scan data. This system is useful for organizing and archiving the data that users collect here.  


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


= Dirmonitor: Automatic data transfer to cnirt =
= mrReaper: Automatic data transfer to nims =


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!)
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. ''mrReaper'' is an ever-running processes that manage images acquired on the MR scanner ('''cnimr'''). This process automatically copies all imaging data acquired on '''cnimr''' to the secure file server ('''nims'''). From there, the data are available to all authorized users via the [http://webauth.stanford.edu/ WebAuth]-protected site at [https://cni.stanford.edu/nims/]. On '''nims''', the data are organized by the PI's Name, an optional experiment name (both set at scan-time in the '''PatientID''' field), 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, and P-files from our custom spiral PSD are reconned and a NIFTI of the resulting images is also offered to the user. Physio data, if recorded, are saved on nims as well.
 
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 &

Revision as of 17:12, 29 August 2011

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. A preliminary version of NIMS (NIMS lite) is currently deployed and used by all CNI users to securely access their scan data. This system is useful for organizing and archiving the data that users collect here.

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

mrReaper: Automatic data transfer to nims

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. mrReaper is an ever-running processes that manage images acquired on the MR scanner (cnimr). This process automatically copies all imaging data acquired on cnimr to the secure file server (nims). From there, the data are available to all authorized users via the WebAuth-protected site at [1]. On nims, the data are organized by the PI's Name, an optional experiment name (both set at scan-time in the PatientID field), 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, and P-files from our custom spiral PSD are reconned and a NIFTI of the resulting images is also offered to the user. Physio data, if recorded, are saved on nims as well.

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