Here a process to import some data from FreeSurfer into a brainvisa database and then run the Morphologist pipeline.
By using this process, you can import some data processed with FreeSurfer and reuse the computed segmentations and manual corrections when some have been performed. In fact, this segmentation can be computed with Morphologist pipeline but if you have already processed this kind of step with FreeSurfer, and wish to share the same segmentation with the rest of Morphologist computing, this process imports a Freesurfer segmentation and prevents Morphologist to reprocess it. In that way, the Morphologist pipeline will be launched with some unselected steps, starting at the "GreyWhite Surface" step. After that the pipeline will compute some meshes, and especially extract cortical fold graphs to drive an idenfication of sulci.
Note that if you run the Morphologist pipeline with the "Import From FreeSurfer to T1 pipeline", the version of cortical fold graphs is set to 3.1. By default, this value is set to 3.0 in the Morphologist pipeline. So it's a questionable choice ... if you prefer the 3.0 version, you can change it before the Morphologist pipeline is run (if the use_t1pipeline parameter is set to "graphically").
Note that outputs, which are computed by this process, will be locked before using the Morphologist pipeline (parameters with a padlock icon). These parameters correspond to the first steps of the Morphologist pipeline. So that, you can't rewrite the files. After running the Morphologist pipeline, you can unlock files by clicking on the contextual menu of locked parameters, if you like to allow overwriting files afterwards.
In order to use this process, you need to set 2 databases:
For more explanations, please refer to documentation of the freesurfer toolbox .
- one with freesurfer ontology (to import from the freesurfer organisation)
- one with brainvisa ontology (to manage new outputs in the brainvisa organisation)
T1_orig: T1 FreesurferAnat ( input )Input comes from freesurfer ontology, which corresponds to {directory_data_fressurfer}/{subject}/mri/ori.mgz
ribbon_image: Ribbon Freesurfer ( input )Input comes from freesurfer ontology, which corresponds to {directory_data_fressurfer}/{subject}/mri/ribbon.mgz
scanner_based_referential: Scanner Based Referential ( optional, input )
Talairach_Auto: Talairach Auto Freesurfer ( input )Input comes from freesurfer ontology, which corresponds to {directory_data_fressurfer}/{subject}/mri/transforms/talairach.auto
T1_output: Raw T1 MRI ( output )Output for brainvisa ontology
T1_referential: Referential of Raw T1 MRI ( output )
transform_to_scanner_based: Transformation to Scanner Based Referential ( optional, output )
bias_corrected_output: T1 MRI Bias Corrected ( output )
normalization_transformation: Transform Raw T1 MRI to Talairach-MNI template-SPM ( output )Output for brainvisa ontology
talairach_transform: Transform Raw T1 MRI to Talairach-AC/PC-Anatomist ( output )
commissure_coordinates: Commissure coordinates ( output )
histo_analysis: Histo Analysis ( output )Output for brainvisa ontologie.
brain_mask_output: T1 Brain Mask ( output )
split_brain_output: Split Brain Mask ( output )
right_grey_white_output: Right Grey White Mask ( output )
left_grey_white_output: Left Grey White Mask ( output )
use_morphologist: Choice ( input )
mni_referential: Referential ( input )
transform_chain_ACPC_to_Normalized: ListOf( Transformation ) ( input )
acpc_referential: Referential ( input )
Toolbox : Freesurfer
User level : 0
Identifier :
Import_FROM_FreeSurfer_TO_Morpho
File name :
brainvisa/toolboxes/freesurfer/processes/Import/Import_FROM_FreeSurfer_TO_Morpho.py
Supported file formats :
T1_orig :FreesurferMGZ, FreesurferMGZribbon_image :FreesurferMGZ, FreesurferMGZscanner_based_referential :Referential, ReferentialTalairach_Auto :MINC transformation matrix, MINC transformation matrixT1_output :gz compressed NIFTI-1 image, GIS image, NIFTI-1 image, gz compressed NIFTI-1 imageT1_referential :Referential, Referentialtransform_to_scanner_based :Transformation matrix, Transformation matrixbias_corrected_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 imagenormalization_transformation :Transformation matrix, Transformation matrixtalairach_transform :Transformation matrix, Transformation matrixcommissure_coordinates :Commissure coordinates, Commissure coordinateshisto_analysis :Histo Analysis, Histo Analysisbrain_mask_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 imagesplit_brain_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 imageright_grey_white_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 imageleft_grey_white_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 imagemni_referential :Referential, Referentialtransform_chain_ACPC_to_Normalized :Transformation matrix, Transformation matrixacpc_referential :Referential, Referential