Dcmdb

From Bangor Imaging Unit

Dcmdb is a simple system for retrieving data from the scanner in NIfTI format. At 11PM every evening, dcmdb retrieves the previous day's studies to the dcmb shares on odin and saga. Studies are sorted into folders by Referring Physician Name. Studies without a referring physician name are put in the unknown folder.
Dcmdb is not an archive service. There is no off-site backup.
This page describes dcmdb as of October 2022.

Connecting to dcmdb

Dcmdb is a file share.
To connect from a Mac, use the Finder Go menu and choose connect to server. Enter smb://odin.ad.bangor.ac.uk or smb://saga.ad.bangor.ac.uk in the server address. Click connect. The user name and password are both mruser. Mount the volume dcmdb.

map network drive

To connect from Windows 10, open Windows Explorer and choose Map Network Drive... from the Tools menu. Enter \\saga.ad.bangor.ac.uk\dcmdb or \\odin.ad.bangor.ac.uk\dcmdb as the folder to map. Be sure to tick Connect using different credentials. Otherwise the PC will attempt to connect using your Bangor login and password. The username and password is mruser.

Finding Your Data

dcmdb network drive
At the top level, files are sorted by Referring Physician. Set Referring Physician when you create a new exam on the scanner. Typically you will set Referring Physician to the PI's name but it can be any useful text string up to a maximum of 30 characters. For example, the weekly QA tests are in the QA folder.

Do not use the characters ?,*, or / in the Referring Physician field. Automated preprocessing changes spaces to underscore '_'.

Inside the Referring Physician folders, studies are sorted by Patient Name and then by study date and series. For example, the path to a single study is dcmdb/Adams/SR0029/20110825.

Multiple studies from the same day using the same patient ID will break the sorting system. The work around is to change the patient name. For example SR0099_run01 and SR0099_run02. Dcmdb allows for special folders or patient comments with additional pre-processing. Currently neuropatient and bedpost are the special folders. All other folders use the standard pre-processing described in the next section.

Automated Preprocessing

Standard Preprocessing

Both servers convert DICOM to gziped 4D .nii.gz NIfTI with rescale and slope applied. Methods are slightly different.

Odin

For historical continuity dcmdb on Odin uses dcm2dcm to decompress the JPEG-2000 DICOM data. Odin then uses dcm2niix version v1.0.20210317 to convert the decompressed DICOM to NIfTI.
dcm2niix -o "$PWD" -f %n%d%e_%s -z y "$outdir"

Saga

Saga uses the JPEG-2000 decompressor built into dcm2niiX version v1.0.20220720. dcm2dcm is not used.
dcm2niix -o "$PWD" -f %n%d%e_%s -z y "$dir"

Automated Bedpostx

Automated Bedposting is presently disabled. Please contact Andrew if you would like it turned back on.


To use Automated FSL bedpostx pre-proccessing, set Referring Physician to bedpost or set the patient comment to Bepost. This instructs dcmb to place your data in the bedpost folder. Dcmb converts all dicom data in the bedpost folder to NifTi format.

For DTI scans, dcmb will also

  • Run eddy_correct
  • Copy the first volume to nodiff.nii.gz
  • Remove the last volume.
  • Remove the last column from the bval and bvec files.
  • Run bet.
  • Run dtifit.
  • Run bedpostx.

For details look at the shell script or ask Andrew.

Neuropatient folder

Neuropatient is not in use. Data in the neuropatient folder receives standard preprocessing.