7T Bruker - Data Convert

• How-to Convert To Analyze Format?
• How To Save Bruker Images In The DICOM Format?
• What is the Bruker Data Format?

• How-to Convert To Analyze Format?

pvconv.pl script, is a perl script that will convert bruker format to analyze format, fsl viewer can be used to view the data, The script has been installed on all main servers.

Usage: pvconv.pl <bstudyname>

Note:
<bstudyname> is the name you used as a study name + a random extentsion.
(Please see Data Transfer for details on finding <bstudyname> on the scanner)
This script generates two files a .hdr and .img
To read into Amira, load the .hdr file and select the Analyze 7.5 format.

• How To Save Bruker Images In The DICOM Format?

1. Click on the Data Manager Icon
2. Select the study to be transferred
3. Click on the Rader like icon.
4. Confirm the dicom transfer is one selected under Transfer Target Options
5. Click on File -> Start Transfer
6. Dicom files for your study will be saved under the following dir (~fmriuser/dicom)
7. *Do this once* create a directory for dicom files on your data directory on the server
   1. cd data
   2. mkdir dicomfiles
8. scp (transfer) the converted study directory in ~fmriuser/dicom to the server
   1. Command: scp -r <studyname>* <username>@<server name>:<directory name>
   2. ex: scp -r sample* emang@cfmri.ucsd.edu:/mnt/raid3/emang/data/dicomfiles
9. Once transferred, please remove the dicomfiles off the scanner
   1. cd dicom
   2. rm -rf sample*

• What is the Bruker Data Format?

Bruker data format notes:
Data format is basically a 3D or 4D (for functional) binary file stored for each run, accompanied by several text files that describes the different imaging/acq parameters, URL below for a good reference.
URL: http://imaging.mrc-cbu.cam.ac.uk/imaging/FormatBruker

• How to determine my raid number?

• Login to your server
• cd data
• pwd (this will list the raid number and the full path to your data directory)