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Description:Usage: fsl_anat [options] -i or fsl_anat [options] -d Anatomical Processing Script (BETA version) - a flexible new tool that combines the existing features of brain extraction (BET+FNIRT-based masking), registration (FLIRT + FNIRT), tissue-type segmentation (FAST), subcortical segmentation (FIRST), with substantially enhanced bias-field correction and automatic reorientation and cropping. This tool provides a general pipeline for processing anatomical images (e.g. T1-weighted scans). Most of the pipeline involves standard use of FSL tools, but the bias-field correction has been substantially improved, especially for strong bias-fields typical of multi-coil arrays and high-field scanners. The stages in the pipeline (in order) are: reorient the images to the standard (MNI) orientation [fslreorient2std] automatically crop the image [robustfov] bias-field correction (RF/B1-inhomogeneity-correction) [FAST] registration to standard space (linear and non-linear) [FLIRT and FNIRT] brain-extraction [FNIRT-based or BET] tissue-type segmentation [FAST] subcortical structure segmentation [FIRST] The overall run-time is heavily dependent on the resolution of the image but anything between 30 and 90 minutes would be typical. By default: the bias-field correction assumes that the field is "strong", typical of that arising from a multi-coil array or a high-field scanner. For images acquired using birdcage coils or on 1.5T scanners, the --weakbias option will be faster and may produce equally good results. the brain extraction is based on transforming a standard-space mask to the input image using the FNIRT (non-linear) registration, and does not use the BET tool for this (and consequently the --betfparam setting does not change the brain extraction in this FNIRT-based mode of operation) Using the -d option the script can be run again (with a subset of stages) to update an existing result. Outputs This section describes the main output files - it is not a complete list, but highlights the most important outputs. Directory The output directory will end with .anat and by default will have the same basename as the input image (and be in the same directory). If the -o option is used the directory name will use the specified name, followed by .anat Original image The specified input image is copied into the output directory and named T1, T2 or PD, depending on the setting of the -t option (default is T1). Reorientation and Cropping If run, the original image (we shall call it T1 from here on in as an example), will be replaced by the reoriented and/or cropped version. The original versions are saved as files: T1_orig and T1_fullfov. In addition, transformation files are provided to allow images to be moved between spaces: i.e. T1_orig2std.mat and T1_nonroi2roi.mat and their inverses and combinations. Bias-correction The bias-corrected version of the image is called T1_biascorr. Registration and Brain-Extraction The registration (to standard space) produces the following images that are in MNI space with a 2mm resolution: T1_to_MNI_lin (linear registration output) T1_to_MNI (non-linear registration output) T1_to_MNI_nonlin_field (non-linear warp field) T1_to_MNI_nonlin_jac (Jacobian of the non-linear warp field) T1_vols.txt - a file containing a scaling factor and brain volumes, based on skull-contrained registration, suitable for head-size normalisation (as the scaling is based on the skull size, not the brain size) The brain-extraction produces: T1_biascorr_brain T1_biascorr_brain_mask Segmentation Tissue-type segmentation (done with FAST) produces: T1_biascorr - refined again in this stage T1_fast_pve_0, T1_fast_pve_1, T1_fast_pve_2 - partial volume segmentations (CSF, GM, WM respectively) T1_fast_pveseg - a summary image showing the tissue with the greatest partial volume fraction per voxel Subcortical segmentation (done with FIRST) produces: T1_subcort_seg - summary image of all subcortical segmentations all other outputs in the first_results subdirectory 'T1_first_all_fast_firstseg - same as T1_subcort_seg` a host of other images relating to individual segmentations T1_biascorr_to_std_sub.mat (in the main anat directory) - a transformation matrix of the subcortical optimised MNI registration
Input Parameters:
 - Structural image
 - Anatomy dir
 - clobber
 - weak bias
 - no reorient
 - no crop
 - no bias
 - no reg
 - no nonlinreg
 - no seg
 - smoothing
 - no subcortseg
 - image type
 - no search
 - BET f param
 - no cleanup
Output Parameters:
 - output directory
File size:25.92 KB
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