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.
Another useful feature (best in MRIcroN) is the inclusion of Brodmann and aal structural templates. You can load up an SPM activation map (perhaps overlaying it on a default structural such as the ch2 brain in MRIcroN, or an average structural from your volunteers) and in another MRIcroN window, load a template. 'Yoke' the two, and you can click on your hotspots in one window, and see (approximate) Brodmann or structural labels of your hotspots in the other window.
Using MRIcro/MRIcron at the CBU
Download to a windows machine to run locally.
To start on the linux systems, use:
or, for 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!