Pipeline de conversion des sorties de FreeSurfer vers BrainVisa

Description

STEP DESCRIPTION

03b Convert FreeSurfer anatomical image to Nifti format Data managed by FreeSurfer are in MGZ format, which is not used in BrainVISA. This step just performs a conversion from MGZ to Nifti format.

04 Conversion of FreeSurfer meshes to Gifti format Data managed by FreeSurfer are in MGZ format, which is not used in BrainVISA. This step just performs a conversion from MGZ to Gifti format.

06 Computation of resampling parameters Create the isin file:

Extraction of projection information about the inflated (right/left) hemisphere to sphere and the registration to (right/left) spherical surfaces with surface-based atlas (?h.sphere.reg.gii file).

Projection onto an icosphere (the ico100_7.mesh file) in order to normalize the number of nodes and their indexation. This way allows to compare meshes nodes by nodes across subjects.

07 Mesh resampling Resample ?h.pial.gii and ?h.white.gii with the ?h.isin file.

08 Conversion of meshes to aims referential Resample ?h.r.pial.gii and ?h.r.white.gii to use the aims coordinate system. Otherwise data are displayed upside down.

09/10 Converting freesurfer unreadable labels to aims textures Conversion ?h.aparc.annot and ?h.aparc.a2009s.annot.More information about ?h.aparc.annot and ?h.aparc.a2009s.annot .

11 Resample label textures Resample label textures ?h.aparc.annot.gii and ?h.aparc.a2009s.annot.gii with the ?h.isin file.

12 Converting freesurfer textures to Gifti format Conversion ?h.curv, ?h.avg_curv, ?h.curv.pial and ?h.thickness to Gifti format.
?h.avg.curv corresponds to the resample of the average curvature from the atlas to the subject.

14 Resampling freesurfer data textures Resample ?h.curv.gii, ?h.avg_curv.gii, ?h.curv.pial.gii and ?h.thickness.gii with the ?h.isin file.

15 Meshes inflate Inflate ?h.r.aims.white.gii.

16 Concatenate meshes Concatenate white, pial and inflated meshes.

17 Concatenate textures Concatenate right and left textures to bh.r.aparc.annot.gii and bh.r.aparc.a2009s.annot.gii.

Paramètres

anat: RawFreesurferAnat ( entrée )

leftPial: FreesurferType ( entrée )

leftWhite: FreesurferType ( entrée )

leftSphereReg: FreesurferType ( entrée )

leftThickness: FreesurferType ( entrée )

leftCurv: FreesurferType ( entrée )

leftAvgCurv: FreesurferType ( entrée )

leftCurvPial: FreesurferType ( entrée )

leftGyri: FreesurferGyriTexture ( entrée )

leftSulciGyri: FreesurferSulciGyriTexture ( entrée )

rightPial: FreesurferType ( entrée )

rightWhite: FreesurferType ( entrée )

rightSphereReg: FreesurferType ( entrée )

rightThickness: FreesurferType ( entrée )

rightCurv: FreesurferType ( entrée )

rightAvgCurv: FreesurferType ( entrée )

rightCurvPial: FreesurferType ( entrée )

rightGyri: FreesurferGyriTexture ( entrée )

rightSulciGyri: FreesurferSulciGyriTexture ( entrée )

Informations techniques

Toolbox : FreeSurfer

Niveau d'utilisateur : 1

Identifiant : freesurferToBrainvisaConversionPipeline

Nom de fichier : brainvisa/toolboxes/freesurfer/processes/Tools/freesurferToBrainvisaConversionPipeline.py

Supported file formats :
anat :
FreesurferMGZ

leftPial :
FreesurferPial

leftWhite :
FreesurferWhite

leftSphereReg :
FreesurferSphereReg

leftThickness :
FreesurferThickness

leftCurv :
FreesurferCurv

leftAvgCurv :
FreesurferAvgCurv

leftCurvPial :
FreesurferCurvPial

leftGyri :
FreesurferParcellation

leftSulciGyri :
FreesurferParcellation

rightPial :
FreesurferPial

rightWhite :
FreesurferWhite

rightSphereReg :
FreesurferSphereReg

rightThickness :
FreesurferThickness

rightCurv :
FreesurferCurv

rightAvgCurv :
FreesurferAvgCurv

rightCurvPial :
FreesurferCurvPial

rightGyri :
FreesurferParcellation

rightSulciGyri :
FreesurferParcellation

STEP	DESCRIPTION
03b Convert FreeSurfer anatomical image to Nifti format	Data managed by FreeSurfer are in MGZ format, which is not used in BrainVISA. This step just performs a conversion from MGZ to Nifti format.
04 Conversion of FreeSurfer meshes to Gifti format	Data managed by FreeSurfer are in MGZ format, which is not used in BrainVISA. This step just performs a conversion from MGZ to Gifti format.
06 Computation of resampling parameters	Create the isin file: Extraction of projection information about the inflated (right/left) hemisphere to sphere and the registration to (right/left) spherical surfaces with surface-based atlas (?h.sphere.reg.gii file). Projection onto an icosphere (the ico100_7.mesh file) in order to normalize the number of nodes and their indexation. This way allows to compare meshes nodes by nodes across subjects.
07 Mesh resampling	Resample ?h.pial.gii and ?h.white.gii with the ?h.isin file.
08 Conversion of meshes to aims referential	Resample ?h.r.pial.gii and ?h.r.white.gii to use the aims coordinate system. Otherwise data are displayed upside down.
09/10 Converting freesurfer unreadable labels to aims textures	Conversion ?h.aparc.annot and ?h.aparc.a2009s.annot.More information about ?h.aparc.annot and ?h.aparc.a2009s.annot .
11 Resample label textures	Resample label textures ?h.aparc.annot.gii and ?h.aparc.a2009s.annot.gii with the ?h.isin file.
12 Converting freesurfer textures to Gifti format	Conversion ?h.curv, ?h.avg_curv, ?h.curv.pial and ?h.thickness to Gifti format. ?h.avg.curv corresponds to the resample of the average curvature from the atlas to the subject.
14 Resampling freesurfer data textures	Resample ?h.curv.gii, ?h.avg_curv.gii, ?h.curv.pial.gii and ?h.thickness.gii with the ?h.isin file.
15 Meshes inflate	Inflate ?h.r.aims.white.gii.
16 Concatenate meshes	Concatenate white, pial and inflated meshes.
17 Concatenate textures	Concatenate right and left textures to bh.r.aparc.annot.gii and bh.r.aparc.a2009s.annot.gii.