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Protocols

MRIcron specifications

Information


Unique identifier OMICS_21610
Name MRIcron
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Input data A neuroimaging file.
Input format ANALYZE,DICOM,NIFTI-1
Output data A neuroimaging file.
Output format ANALYZE,DICOM,NPM,NIFTI
Operating system Unix/Linux, Mac OS, Windows
Programming languages Pascal
License BSD 2-clause “Simplified” License
Computer skills Medium
Stability Stable
Maintained Yes

Subtool


  • dcm2nii

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Versioning


No version available

Documentation


Additional information


https://www.nitrc.org/plugins/mwiki/index.php/mricron:MainPage http://people.cas.sc.edu/rorden/mricron/index.html

MRIcron citations

 (666)
library_books

Functional connectivity of hippocampal subregions in PTSD: relations with symptoms

2018
PMCID: 5952576
PMID: 29764396
DOI: 10.1186/s12888-018-1716-9

[…] nterior cingulate [], and to protect against Type 1 error involved in multiple ROI comparisons. As shown in Fig. , the hippocampal masks were manually sectioned into anterior and posterior ROIs using MRIcron [], based on guidelines for anatomical segmentation of the hippocampal head and tail, respectively [].Fig. 1 […]

library_books

Molecular, Pathological, Radiological, and Immune Profiling of Non brainstem Pediatric High Grade Glioma from the HERBY Phase II Randomized Trial

2018
Cancer Cell
PMCID: 5956280
PMID: 29763623
DOI: 10.1016/j.ccell.2018.04.004

[…] .ca/ServicesAtlases/NIHPD-obj1) (). A further manual correction step was performed to limit tumor mass effects. Once registered to a common space, overall tumor lesion overlap maps were created using MRIcron (). […]

call_split

Synchronization within, and interactions between, the default mode and dorsal attention networks in relapsing remitting multiple sclerosis

2018
PMCID: 5957478
DOI: 10.2147/NDT.S155478
call_split See protocol

[…] their T2WI by an experienced neuroradiologist (FZ or XZ, who have >10 years of experience in neuroradiology). The total WM lesion loads (TWMLLs) were calculated as the volumes within the masks using MRIcron software. After co-registration with the T1WI, the T2WI was normalized into Montreal Neurological Institute (MNI) space, and this information was used to warp the lesion mask into the standard […]

call_split

Prefrontoparietal dysfunction during emotion regulation in anxiety disorder: a meta analysis of functional magnetic resonance imaging studies

2018
PMCID: 5953307
PMID: 29785110
DOI: 10.2147/NDT.S165677
call_split See protocol

[…] ed adequate sensitivity and excellent control of false positive results (~2.5%) compared with other meta-analytical procedures. Significant clusters obtained from AES-SDM analysis were overlaid on an MRIcron high-resolution brain template for display purposes. Publication bias was assessed using Egger’s test, as implemented in the AES-SDM software (version 5.141). […]

call_split

Larger Gray Matter Volume in the Basal Ganglia of Heavy Cannabis Users Detected by Voxel Based Morphometry and Subcortical Volumetric Analysis

2018
PMCID: 5943550
PMID: 29773998
DOI: 10.3389/fpsyt.2018.00175
call_split See protocol

[…] tical structural atlases integrated into FSLView (part of FSL) and the AAL atlas (Anatomical Automatic Labeling), a macro-anatomical parcellation of the single subject MNI-space template brain within MRIcron software (http://people.cas.sc.edu/rorden/mricron/index.html). […]

library_books

Resting state fMRI study of brain activation using low intensity repetitive transcranial magnetic stimulation in rats

2018
Sci Rep
PMCID: 5928106
PMID: 29712947
DOI: 10.1038/s41598-018-24951-6

[…] (Digital Imaging and Communications in Medicine) format (http://dicom.nema.org/) and then converted into NifTI (Neuroimaging Informatics Technology Initiative, https://nifti.nimh.nih.gov/) using the dcm2nii converter (64-bit Linux version 5 May 2016). Pre-processing of fMRI data included: (i) upscaling the voxel sizes by a factor of 10; (ii) motion correction using FSL/MCFLIRT (Linear Image Regis […]

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