Publicly released data sets

We release our brain atlas models on www.imaging.org.au

Data Conversion

Dicom to Minc:

dcm2mnc from the minc package can be used. Make sure you have minc sourced in your .bashrc: source /data/lfs2/software/ubuntu14/minc-itk4-1.9.11-20160202/minc-toolkit-config.sh

dcm2mnc [options] file1 file2 file3 ... destdir

Dicom to Nifti:

Chris Rorden’s dcm2nii works well for this job:

dcm2nii <options> <sourcenames>

SPM & MATLAB:

SPM has a converter from dicom to Nifti build in. After starting SPM, click SPM -> Util -> DICOM Import

Others:

Other conversions could be done using mri_convert included in FreeSurfer. Make sure to source FreeSurfer:

export FREESURFER_HOME=/data/lfs2/software/ubuntu14/freesurfer-v6beta-2016-05-14-centos6
source $FREESURFER_HOME/SetUpFreeSurfer.sh

then run mri_convert:

mri_convert [options] <in volume> <out volume>

Data Storage

Imagetrove:

At CAI we have a comprehensive data storage system available with help of Imagetrove. It is a web-based system used for storing data generated at CAI with help of different imaging modalities. It also provides easy access of this data to our collaborators in addition to a secured environment for data sharing.

Further information for Imagetrove can be found here