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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: |
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| 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: |
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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!