Run AssemblyNet

This process allows AssemblyNet (https://github.com/volBrain/AssemblyNet) to run. You nedd to already have it with apptainer/singularity image on your local host.

Parameters

assemblynet_image: String ( input )

Apptainer/singularity image of AssemblyNet

t1mri: Raw T1 MRI ( input )

T1mri to be segmented with AssemblyNet

output_folder: Acquisition ( output )

Output folder for AssemblyNet according to brainvisa database hierarchy.

age: Float ( optional, input )

Float representing subject age at scan time. If specified, the produced volumetry report report_filename.pdf will show the expected limits/normative bounds of normalized volumes in function of age.

sex: Choice ( optional, input )

Subject sex. If specified, the produced volumetry report report_filename.pdf will show the expected limits/normative bounds of normalized volumes in function of sex.

pdf_report: Boolean ( input )

Boolean to specify if PDF format volumetry report is produced.

transformation_to_mni: Transformation ( output )

mni_lobes: Brain Lobes ( output )

mni_macrostructures: Split Brain Mask ( output )

mni_mask: Intracranial mask ( output )

mni_structures: Brain Structures ( output )

mni_t1: T1 MRI Denoised and Bias Corrected ( output )

mni_tissues: Intracranial labels ( output )

native_lobes: Brain Lobes ( output )

native_macrostructures: Split Brain Mask ( output )

native_mask: Intracranial mask ( output )

native_structures: Brain Structures ( output )

native_t1: T1 MRI Denoised and Bias Corrected ( output )

native_tissues: Intracranial labels ( output )

report_csv: Analysis Report ( output )

report_pdf: Analysis Report ( output )

Technical information

Toolbox : Tools

User level : 1

Identifier : assemblynet

File name : brainvisa/toolboxes/tools/processes/assemblynet.py

Supported file formats :

t1mri :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

output_folder :

Directory, Directory

transformation_to_mni :

Text file, Text file

mni_lobes :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

mni_macrostructures :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

mni_mask :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

mni_structures :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

mni_t1 :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

mni_tissues :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

native_lobes :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

native_macrostructures :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

native_mask :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

native_structures :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

native_t1 :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

native_tissues :

gz compressed NIFTI-1 image, NIFTI-1 image, gz compressed NIFTI-1 image

report_csv :

CSV file, CSV file

report_pdf :

PDF File, PDF File