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_3dImage: ListOf( 3D Volume ) ( input )

ListOf_Input_3dImage_ROI: ListOf( ROI ) ( input )

ListOf_Input_Motion_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_3dImage :

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

ListOf_Input_3dImage_ROI :

Graph and data, BMP image, Directory, ECAT i image, ECAT v image, FDF image, FreesurferMGH, FreesurferMGZ, GIF image, GIS image, Graph and data, 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, Z compressed ECAT i image, Z compressed ECAT v image, Z compressed GIS image, Z compressed SPM image, Z compressed VIDA 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, gz compressed VIDA image

ListOf_Input_Motion_3dImage_TO_ROI :

Transformation matrix, Transformation matrix

Hierarchy :

Hierarchy, Hierarchy

ListOf_Output_Text_Results :

Text file, Text file

Synthesis_Result :

Text file, Text file