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USERGUIDE

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Submit NIfTI T1 weighted MRI with the form in your userpage, standard or gzip format (*.nii.gz) are accepted. We don’t accept DICOM format but your can convert your dicom to NIfTI with multiple software. Our team use DICOM2NIFTI. You have to anonymize the data you would like to submit, no information has to be included in the file name or content. Please check the TERMS OF USE before sending datas.

Once you’ve send your data, we will process it as soon as possible. You will receive an email when the job is done or if the job failed. Note that results will be available for 7 days.You can get the results by downloading meshes or masks through the userpage table links.

Userpage table icons :

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Your data are currently being processed

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Preview your data on the web with ParaviewGlance

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Your data will be processed as soon as possible

Results informations

24 Regions Of Interest (ROI) from de Yeb-atlas below are available :

for the left and right hemisphere.

as VTK PolyData meshes in NII World convention (*.vtk)

as VTP PolyData meshes in ITK Convention (*.vtp)

as volume binary masks (*.nii.gz)

If you want more ROIs of the Yeb Atlas (about 80) , please contact us at yeb-cenir@icm-institute.org

Meshes or masks id Full name
EGP External globus pallidus
IGP Internal globus pallidus
RU Red nucleus
SN Substantia nigra
STN Subthalamic nucleus
STRAC Accubens nucleus
STRCD Caudate nucleus
STRPU Putamen
Meshes or masks id Full name
THAL Thalamus
THANT Anterior
THCM Centrum medianum
THMD Medial dorsal
THPF Parafascicular
THPU Pulvinar
THRPT Reticular formation
THSUP Superficialis
THVA Ventralis anterior
THVIM Ventralis intermedius
THVL Ventralis lateralis
THVPE Ventral posterior external
THVPI Ventral posterior internal
Meshes or masks id Full name
CP Cerebral peduncle
OT Optic track
H2 Forel’s field

Visualization

1. Meshes

On the web without any installation (Beta) :

We’ve embedded Paraview Glance (Kitware) viewer on our website. Paraview Glance use WebGL technologies. Just click on the eye link on your userpage table.

A new tab with Paraview Glance will be opened in your browser

By default , 6 meshes by hemisphere will be displayed on the viewer but you can add all the other YeB structures by dragging and dropping *.vtp structures on the paraview app

To center your NIfTI, click on the reset camera button :

With 3D Slicer

3D Slicer is an open source software platform for medical image informatics, image processing, and three-dimensional visualization. 3D Slicer is available for MacOS, Windows and Linux.

On 3D Slicer, meshes are in NII world convention, you have to load vtk meshes (*.vtk)

2. Masks

All kind of NIfTI volume viewer can read masks files. Paraview Glance and 3D Slicer are among those (left hemisphere thalamus masks on 3D Slicer below)