VolumeROIAnalysis

This process enables you to perform a conventional ROI-based analysis of 3D reconstructed autoradiographic volumes. The information is extracted from specified ROI(s) and then used to compute ordinary statistics (volume in mm³, mean, standard deviation, min, max).

NOTE:
¹ In the demonstration data set, the region of interest was the superior colliculus. It has been manually segmented on each section of the 3D rigidly aligned histological volume (Test_volume_rat_cresyl_aligned.ima) yielding a volume of interest (VOI) and allowing assessment of its 3D shape (see next process). As the histological (reference) and autoradiographic volumes have been co-registered, this VOI can be directly mapped on the autoradiographic volume.

² After running the process, you will be able to retrieve results by opening the output text file with a common text editor such as gedit, kate, kwrite under Linux or with a spreadsheet.

Parameters

ListOf_Input_Volume: ListOf( 3D Volume ) ( input )

ListOf_Input_Volume_ROI: ListOf( ROI ) ( input )

ListOf_Input_Transformation_3dImage_TO_ROI: ListOf( Transformation matrix ) ( optional, input )

Hierarchy: Hierarchy ( optional, input )

Hierarchy_Use_Path: Boolean ( optional, input )

ListOf_Output_Text_Results: ListOf( Text file ) ( optional, output )

Synthesis_Result: Text file ( optional, output )

Technical information

Toolbox : BrainRAT

User level : 0

Identifier : VolumeROIAnalysis

File name : brainvisa/toolboxes/brainrat/processes/pmianalysis/VolumeROIAnalysis.py

Supported file formats :

ListOf_Input_Volume :

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

ListOf_Input_Volume_ROI :

Graph and data, Directory, ECAT i image, ECAT v image, FDF image, FreesurferMGH, FreesurferMGZ, GIS image, Graph and data, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, Z compressed ECAT i image, Z compressed ECAT v image, Z compressed GIS image, Z compressed SPM image, gz compressed ECAT i image, gz compressed ECAT v image, gz compressed GIS image, gz compressed MINC image, gz compressed NIFTI-1 image, gz compressed SPM image

ListOf_Input_Transformation_3dImage_TO_ROI :

Transformation matrix, Transformation matrix

Hierarchy :

Hierarchy, Hierarchy

ListOf_Output_Text_Results :

Text file, Text file

Synthesis_Result :

Text file, Text file