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| 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. | 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. |
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| Download to a windows machine to run locally. To start on the linux systems, use: | |
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| Download to a windows machine to run locally. To start on the linux systems, use: | |
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| 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). | |
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| Type in a terminal: | you can either use it from the command-line (type dcm2nii to get the full help), or as a GUI: |
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| dcm2nii & | > dcm2nii > dcm2nii_gui & |
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| to get the help info. | 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! |
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
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!