surface-tutorial

Cortical Surface Morphometry Tutorial1 - Prepare data Convert images from DICOM to Nifti :• open the dicom image with Anatomist (one file per slice in DICOM, you just need to open the first one (name ends with .1). In the file selction box you need to chose the "dicom" filter otherwise you will not see it (default in Anatomist is another format). • Right click on the dataset in Anatomist main window and chose "file"->"save".• Save the file with a '.nii' extension. It is the Nifti format, this is the best one to use. If orientation is 'bottom to top' (upside down in sagittal view, see image), you need to flip it :AimsFlip -i image.nii -o image_flipped.nii -m ZZ'bottom to top' image and the 'top to bottom' flipped versionNote : before running Aims commands, such as AimsFlip, you might need to run another command : brainvisa_setup. Open a command window, type 'brainvisa_setup' and then all Aims commands will be available in this command window.2 - Import the Nifti file in the Brainvisa databaseThe flipped image needs to be imported in a Brainvisa database. Start Brainvisa and run the 'Data Management -> import -> T1 MRI -> Import T1 MRI' process. Choose the proper protocol and subject name. 3 - Run the T1 segmentation pipelineThis pipeline segment all tissues, compute all meshes and extract the sulci graph. Open it in 'T1 MRI'->'Segmentation Pipeline'->'T1 Pipeline 2007'Select the subject T1 image with the green database browser button and all other ...