Workflow Detail Information

Name:FSL Registration and Segmentation
Type: Workflow
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Description:The simplest way to perform segmentation using FIRST is to use the run_first_all script which segments all the subcortical structures, producing mesh and volumetric outputs (applying boundary correction). It uses default settings for each structure which have been optimised empirically. run_first_all This script will run lower-level utilities (including first_flirt, run_first and first) on all the structures, with the settings (number of modes and boundary correction) tuned to be optimal for each structure. Both mesh (vtk) and volumetric (nifti) outputs are generated. Corrected and uncorrected volumetric representations of the native mesh are generated. The final stage of the script ensures that there is no overlap between structures in the 3D image, which can occur even when there is no overlap of the meshes, as can be seen in the individual, uncorrected segmentation images in the 4D image file. Example usage: run_first_all -i t1_image -o output_name The argument -i specifies the original T1-weighted structural image. The argument -o specifies the filename for the output image basename. run_first_all will include the type of boundary correction into the final file name. For example, the command above would produce output_name_all_fast_firstseg.nii.gz and output_name_all_fast_origsegs.nii.gz.

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