|
Size: 2145
Comment:
|
Size: 2754
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 2: | Line 2: |
| = MRIcro information = |
= MRIcro and MRIcroN information = |
| Line 8: | Line 7: |
| 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. 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. |
| Line 11: | Line 12: |
| Download to a windows machine to run locally. | |
| Line 12: | Line 14: |
| Download to a windows machine to run locally. To start on the linux systems, use: | To start on the linux systems, use: |
| Line 16: | Line 19: |
| Line 22: | Line 24: |
| Line 29: | Line 29: |
| 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). | |
| Line 30: | Line 31: |
| Type in a terminal: | you can either use it from the command-line (type dcm2nii to get the full help), or as a GUI: |
| Line 32: | Line 34: |
| dcm2nii & | > dcm2nii > dcm2nii_gui & |
| Line 34: | Line 37: |
| 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: |
| Line 36: | Line 39: |
| 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: |
|
| Line 42: | Line 42: |
MRIcro and MRIcroN 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.
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:
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!