Import T1 MRI

Places a T1 MRI image in BrainVISA database

Description

This process enables to copy a T1 MRI image initially out of BrainVISA database to its location in the database.
To do this, the parameter input cannot be set via the "database" icon since the input image is not in the database. You must use the standard file browser .
The output parameter can be set via the "database" icon , and this is what is strongly encouraged to do.
As the location in the database does not exist yet, it will have to be created using the user interface for the choice of the location: for example for a database organized according to the ontology proposed with BrainVISA, a "protocol" field must and a "subject" field must be assigned before any anatomical image can be placed into it. All this is done with the user interface triggered by the red "database" icon :

First, a database must be chosen (if you have several ones):

Then a protocol should be created or chosen:

If the protocol you wish does not exist yet, you can type a new name in the protocol field.
Then a new subject should be selected or created the same way:

Now you only have to select the image proposed on the right panel (here, morphee.ima and to validate.
This protocol / subject fields may vary according to the database organization in your site, but this is the default needed attributes.
Note: If you are using the iteration mode to import several images, you can create several output database entries at the same time: typically, you can type several "subject" values, separated by space characters. Then you can select several items in the right selection panel:

Parameters

input: T1 MRI ( input )

image to import in the database

output: Raw T1 MRI ( output )

where in the database the image should be placed

referential: Referential of Raw T1 MRI ( optional, output )

output_database: OpenChoice ( optional, input )

attributes_merging: Choice ( optional, input )

selected_attributes_from_header: ListOf( String ) ( optional, input )

Technical information

Toolbox : Data Management

User level : 0

Identifier : ImportT1MRI

File name : brainvisa/toolboxes/data management/processes/import/t1mri/ImportT1MRI.py

Supported file formats :

input :

gz compressed NIFTI-1 image, Aperio svs, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, FreesurferMGH, FreesurferMGZ, GIF image, GIS image, Hamamatsu ndpi, Hamamatsu vms, Hamamatsu vmu, JPEG image, Leica scn, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, Sakura svslide, TIFF image, TIFF image, TIFF(.tif) image, TIFF(.tif) image, VIDA image, Ventana bif, XBM image, XPM image, Zeiss czi, gz compressed MINC image, gz compressed NIFTI-1 image

output :

gz compressed NIFTI-1 image, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIF image, GIS image, JPEG image, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, TIFF image, TIFF(.tif) image, VIDA image, XBM image, XPM image, gz compressed MINC image, gz compressed NIFTI-1 image

referential :

Referential, Referential