MriCro - MRC CBU Imaging Wiki

Revision 12 as of 2009-11-10 16:39:28

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MRIcro information

MRIcro is an excellent free viewer for medical images written by [ Chris Rorden]. It has many facilities, most notably ROI drawing and analysis. The newer version of the software is [ MRIcron].

See the [ MRIcro manual], [ MRIcro tutorial] and [ MRIcro FAQ] - as well as other links on [ Chris Rorden's home page]. The MRIcro tutorial has instructions on creating a region of interest, and on how to prepare scans of damaged brains for spatial normalisation.

One of the features in MRIcro is the ability to display points on selected slices - such as maxima from various imaging studies. This is covered in the [ hotspot section] of the MRIcro FAQ, and also (for an older version) by our MricroPoints page.

Using MRIcro/MRIcron at the CBU

Download to a windows machine to run locally. To start on the linux systems, use:

startmricro &

or, for MRIcron,

mricron &

(the '&' at the end has the effect of returning you to the terminal where you typed the command rather than leaving it hanging until MriCro closes)

MRIcron is located in /imaging/local/linux/bin/mricron.


This is a nice little tool, part of MRICroN, that allows you to do several things, in particular it allows you to transform a bunch of DICOM files into a series of 3D NIFTI images (if you are an SPM user) or one 4D NIFTI file (if you are an FSL user).

you can either use it from the command-line (type dcm2nii to get the full help), or as a GUI:

> dcm2nii
> dcm2nii_gui &

For example, say you ran a study and have a bunch of CBU EPI runs. The following command will turn each DICOM run into one 4D nii.gz file you can feed into the FSL analysis:

dcm2nii -g y -o /imaging/destinationpath /mridata/cbu/CBUSession_*/*/*_CBU_EPI_*

NOTE: the g option makes the output a nii.gz (as opposed to a nii) file, which is absolutely recommended!