Dec 31, 2017 Mac › Design & Photo ›. MRIcron and many other brain imaging tools. NIfTI is a modern incarnation of the Analyze format, but includes important information like the orientation of the imag. Share your experience: Write a review about this program Read more. The latest version of mricron is 1.0 on Mac Informer. It is a perfect match for Science in the Education category. The app is developed by NITRC.
The cerebellum is a functionally highly diverse structure: Different regions have their unique pattern of connectivity with the neocortex, and therefore likely a specialized functional role. To promote accurate anatomical reference for human functional and anatomical imaging studies, we present here a probabilistic atlas of the cerebellar lobules in the space defined by the MNI152 template. The anatomical definitions are based on the fMRI atlas of an individual cerebellum by Schmahmann et al. (2000). To obtain a representative anatomical atlas, we annotated the lobules on T1-weighted MRI scans (1mm isotropic resolution) of 20 individual healthy young participants (10 male, 10 female, average age 23.7 yrs). Using a different set of 23 participants, we also identified the location of the deep cerebellar nuclei. The individual cerebella were then aligned using different commonly used normalization algorithms.
The resultant probabilistic maps allow for the valid assignment of functional activations to specific cerebellar lobules and the nuclei, while providing a quantitative measure of the certainty of such assignments. Furthermore, maximum probability maps derived from these atlases can be used to define regions of interest (ROIs, more on this here). The atlas is included in the newer releases of FSL and the Anatomy toolbox. More versions of the atlases for use with MRIcron or AFNI are also available here.
The resultant probabilistic maps allow for the valid assignment of functional activations to specific cerebellar lobules and the nuclei, while providing a quantitative measure of the certainty of such assignments. Furthermore, maximum probability maps derived from these atlases can be used to define regions of interest (ROIs, more on this here). The atlas is included in the newer releases of FSL and the Anatomy toolbox. More versions of the atlases for use with MRIcron or AFNI are also available here.
Please cite the atlas as:
- Diedrichsen J., Balster J.H., Flavell J., Cussans E., Ramnani N. (2009). A probabilistic MR atlas of the human cerebellum. Neuroimage.
- Diedrichsen J., Maderwald S., K�per M., Th�rling M., Rabe K., Gizewski ER, Ladd M, Timmann D (2011). Imaging the deep cerebellar nuclei:A probabilistic atlas and normalization procedure. Neuroimage.
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The generation of the atlas was supported by a Grant by the National Science foundation (NSF) - BSC 0726685.
Why a probabilistic anatomical atlas?
Individual brains are often normalized to MNI-space, and activation foci from group analysis assigned to cerebellar lobules using the a standard atlas (Schmahmann et al., 2000). Our analysis shows that such assignments can be incorrect (often by as much as a full lobule) for up to 2/3 of cerebellar voxels for some normalisation methods. There are two reasons for this:
These problems stress the importance of a representative atlas and of good correspondence between the normalization method used for the atlas and for the group analysis. For this reason we provide the atlas generated with a number of different normalization methods. |
The probabilistic atlas also provides a measure of the certainty with with anatomical assignments can be made. The image shows the proportion of the 20 individuals that overlapped with the same lobule in atlas space. We generated the atlas for:
The overlap in SUIT (A) often reaches 100% whereas the overlap using affine methods (FLIRT, B) is somewhat poorer. |
The left figure shows the percent overlap between different lobules after normalization.Newer non-linear methods (Segmentation in SPM, FNIRT) lead to a good correspondence and to relatively high accuracies. Cerebellum-only normalization with SUIT leads to the best overlap. Thus, for new imaging studies of the cerebellum we would strong recommend one of the newer non-linear methods, or ideally the use of SUIT. For the interpretation of older results (for example for meta-analyses of cerebellar imaging results), we also make the atlas for the SPM nonlinear normalization also available. |
In collaboration with Prof. Timmann from the University of Duisburg-Essen we also imaged the deep cerebellar nuclei in a set of 23 separate subjects at 7T, using susceptibility-weighted imaging. The dentate, emboliform, globose and fastigial nuclei play an important part of the cerebellar circuit, as the relay all output of the cerebellum. In the latest versions of the probabilistic atlas we provide probabilistic ROIs for the dentate, the interposed (emboliform and globose) and fastigial nuclei. Note that given the small size of the cerebellar nuclei, the overlap is relatively poor even after SUIT normalization. For studies of these structures, we therefore recommend spatial normalization using a dentate ROI. |
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The Atlas for FSL View
The atlas can be used with the Atlas Widget in FSLView, part of the FSL package. The atlas for FSLView is available for
The FLIRT and FNIRT versions are already included in newer distributions of FSL. The lobular assignment is approximately spatially unbiased in these atlases, however the maximal probabilities after SUIT alignment is in general higher. To install the atlas(es)
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The Atlas for MRICroN
The atlas can be used MRIcron, which is an image viewer written by Chris Rorden and which is freely available for Linux, Windows, and Mac OS X.The atlas for MRICroN is available for:
The necessary files (Maximum-probabiliy-map, size of maximum probability, full probability maps, color map (lut) and text files are all included. To use MRICroN to look up probabilities
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The Atlas for Anatomy Toolbox in SPM
The atlas is now included in the Anatomy toolbox, which was developed S. Eickhoff and colleagues. For the generation of the maps, we used the Segementation and Normalisation algorithm in SPM5/8. To make the maps fit with the rest of the toolbox, they were then warped into the space defined by the Colin-brain. |
![Micron macro Micron macro](/uploads/1/1/8/3/118375263/384014620.jpg)
The Atlas for AFNI
Thanks to Daniel Glen, the atlas is now also available for the AFNI whereAmI atlas GUI. Note that any atlas that has a reachable space is queried, so atlases that are in Talairach or MNI_ANAT space are shown there also. The whereAmI output is continuously updated as the user moves the cross-hair in the viewer, so the information is quite interactive. The command line version of whereAmI shows similar information. The command 'whereami -show_atlases' gives this relevant output. To use, please download SUIT for AFNI to a new directory and untar with tar -xzvf AFNI_SUITCerebellum.tgz and then add this directory to be searched in AFNI's atlas functions with this: @AfniEnv -set AFNI_SUPP_ATLAS_DIR directoryname If you find the atlases and templates useful, please cite using the references includedin whereami -show_atlases |
Registration and Download
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Note that the SUIT-MRICro version of the probabilistic atlas comes with the new release (v. 2.4) of the SUIT toolbox.
The SUIT toolbox distributed under the Creative Commons Attribution-NonCommercial 3.0 Unported License, meaning that it can be freely used for non-commercial purposes, as long as proper attribution in form of acknowledgments and links (for online use) or citations (in publications) are given. The relevant references are:
Probabilistic atlas for cerebellar lobules
- Diedrichsen, J., Balsters, J. H., Flavell, J., Cussans, E., & Ramnani, N. (2009).A probabilistic atlas of the human cerebellum. Neuroimage.46(1), 39-46.
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Probabilistic atlas and normalisation for deep cerebellar nuclei
- Diedrichsen, J., Maderwald, S., Kuper, M., Thurling, M., Rabe, K., Gizewski, E. R., et al. (2011).Imaging the deep cerebellar nuclei: A probabilistic atlas and normalization procedure.Neuroimage. 54(3), 1786-1794.
This is the web page for information about downloadable MRI neuroanatomy teaching materials. The instructions below describe how to download MRI datasets and a freely available viewing program to look at them.
REQUIRED Step 1: Download MRIcroN (free software for viewing MRI datasets)Download the correct installer package for your computer. Windows, Mac and Linux are supported; detailed installation instructions are provided for Windows and Mac but not Linux. For Windows:The following instructions were tested with Windows 7 running Internet Explorer 9. For different version of Windows or other web browsers, the steps may be slightly different.
After successfully starting the program, you should see the following window. To make the images easier to see, you can enlarge the window. Go to Step 2, below. Windows MRIcroN window For Macintosh:The following instructions were tested with Mac OSX 10.8.2 running Safari. For different versions of OSX or other web browsers, the steps may be slightly different.
You should see the following window. To make the images easier to see, you can enlarge the window. To see only one plane enlarged, click View/Axial Only. Macintosh MRIcroN window For Linux (or if the above instructions don't work): please go tohttp://www.mccauslandcenter.sc.edu/mricro/mricron/install.htmlYou are on your own for installation! REQUIRED Step 2: Explore the brain and learn structures found in labs 8 and 9Regardless of the platform (PC or Mac), the top left of the window shows a coronal view of the brain. The top right of the window shows a sagittal view of the brain. The bottom left of the window shows an axial (horizontal) view of the brain. Click the mouse at any brain location to move the blue viewing crosshairs.The dataset name is listed at the top of the MRIcroN window in Windows, at the bottom of the window for Mac. The correct brain to view is the 'ch2' file (ch2.nii.gz). Load this file by selecting 'File/Open/Templates/ch2.nii.gz'.At the top of the program window are three boxes labelled 'x', 'y' and 'z' that show the brain location. Enter each of the co-ordinates (x,y,z) listed below into MRIcron. This will take you to the structure whose name is on the first column.This material will make up part of the testing materials for these laboratories (lab exams). Name of structure / Coordinates of structure (enter into x,y,z boxes in MriCron)
Structures in lab 11Limbic System
Teaching Aid: Colored Overlay to show different anatomical regionsWhile the above co-ordinates show examples of single locations and their label, it can also be nice to see the complete extent of an area. This can be done as follows:
MRIcroN with anatomical labels Surf around the brain. When clicking on a colored region, you will see the anatomical label for that colored area of the brain. The label (e.g. Putamen_L for left putamen) will appear in the bottom of the viewing window on PC, in the top of the viewing window on Mac. OPTIONAL Step 3: Different kinds of brain MRIMRI is clinically very useful because it is non-invasive and safe. Because no exposure to radiation is involved, patients can receive many different kinds of MRI imaging procedures without risk. The MRI scanner can be programmed to create different kinds of images that reveal different tissue properties. The three main kinds of images are T1, T2 and Proton Density (FLAIR). The names of the image types refer to the physical priniciples used to create the images. The three links below link to three datasets, all collected from the same normal subject, that show the three different image types. Click on each link and save the file to your computer. After you have downloaded the datasets, you can load and view them in MriCroN by clicking File/Open. Navigate to the directory where you saved them and select the dataset name. OPTIONAL Step 4: Different kinds of spine MRIBecause the spine is so long, it is typically imaged in three separate scans covering the cervical, thoracic, and lumbar+sacral portions of the cord. The following archive file contains T1, T2 and IR datasets for each spine portion. Download the file and unzip the 12 datasets that it contains. It is easiest if they are unzipped to the same directory as the datasets in Step 3. The datasets can then be opened in MRIcroN. OPTIONAL Step 5: Cerebral VasculatureHere are two movies that show the results of a Magnetic Resonance Angiogram (MRA). Click to download the movies to your desktop. Then double-click on the movies to view them. They have been tested with Apple Quicktime, free software downloadable from www.apple.com. After the movie is loaded, press the left and right arrow to scroll through the frames of the movie. License Information for MRIcron software.Chris Rorden's MRIcron, copyright 2012, all rights reserved. Redistribution and use in binary forms, with or without modification, are permitted provided inclusion of the copyright notice, this list of conditions and the following disclaimer is provided with the distribution: Neither the name of the copyright owner nor the name of this project (MRIcron) may be used to endorse or promote products derived from this software without specific prior written permission.This software is provided by the copyright holder 'as is' and any express or implied warranties, including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose are disclaimed. In no event shall the copyright owner be liable for any direct, indirect, incidental, special, exemplary, or consequential damages (including, but not limited to, procurement of substitute goods or services; loss of use, data, or profits; or business interruption) however caused and on any theory of liability, whether in contract, strict liability, or tort (including negligence or otherwise) arising in any way out of the use of this software, even if advised of the possibility of such damage. |
Mricon
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