## page was renamed from MricroInformation
= MRIcro information =

MRIcro is an excellent free viewer for medical images written by [http://www.sph.sc.edu/comd/rorden/ Chris Rorden].  It has many facilities, most notably ROI drawing and analysis. The newer version of the software is [http://www.sph.sc.edu/comd/rorden/mricron/ MRIcron].

See the [http://www.sph.sc.edu/comd/rorden/mricro.html MRIcro manual], [http://www.sph.sc.edu/comd/rorden/mritut.html MRIcro tutorial] and [http://www.sph.sc.edu/comd/rorden/faq.html MRIcro FAQ] - as well as other links on [http://www.sph.sc.edu/comd/rorden/ 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 [http://www.sph.sc.edu/comd/rorden/faq.html#hotspot 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.

== Using DCM2NII ==

Type in a terminal:
{{{
dcm2nii &
}}}
to get the help info.

dcm2nii can do many useful things, but it's particularly useful if you are an FSL user, since you can use it to transform and import the DICOM files from the scanner into NIFTI (or ZIPPED NIFTI).

For example, say you ran a study and have a bunch of CBU EPI runs you want to import, the following command will import all CBU-EPI files found in a given CBUSession:
{{{
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!