BrukerDataLocation - MRC CBU Imaging Wiki

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Getting Bruker data from the Wolfson Brain Imaging Centre

... will depend where you are sitting...

CBU

In the CBU, this is copied directly from the WBIC system to the CBU file space, and is stored in the directory /mridata/wbic_cbu. Don't forget this directory is automounted, see CbuComputingResources. An email is sent out to the ImagersCbuList as each dataset arrives. Sometimes, the data is copied before the reconstruction is finished. In this case, there may be no 2dseq file for some runs ( see the Bruker format page ). You can check for this by running pvshow.pl on your Bruker data directory. If your data has not been reconstructed, and you are sure that the data is not from an aborted run etc, then you will need to speak to the CBU computing staff to discuss how to arrange to copy the reconstructions.

Addenbrookes

Machines attached to the WBIC network can see the data directly. This will be in directories such as /pvData1/nmr/guest, or /pvData/nmr/guest.

Converting to analyze format

This is probably easiest to achieve using the perl utility "pvconv". See the pvconv web page for usage. pvconv.pl will write out SPM .mat files for the images which will reorient the images to neurological orientation, and to the orientation of the subject's head within the scanner.Another way of converting the data to analyze format is ImageJ. See Emma Williams' getting WBIC scan data page for the procedure. Note that ImageJ may not get the slice thickness correctly for some standard functional protocols, and the image header files may need more tweaking before you continue.

Matthew Brett 29/01/2002