Mbirn: Data Provenance:Documentation:ToolList
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Tool List
This is a collection of the processing tools that are developed within the BIRN consortium, as well as third party tools that are used in our work flows.
First draft - Jan/05, Second draft - Nov 14/06
BIRN Tools
Internal BIRN tools are characterised by our access to the source code so that we can instrument them to respond to the --all-info command line argument with the appropriate data provenance information. A notation of "done" after a tool means that it will respond to the --all-info flag.
Slicer
- Slicer 2.5 - done
- Slicer 2.6 - done
- Slicer 2.7 (aka current CVS head) - done
- Slicer 3.0Alpha (xml CLI interface won't allow --all-info, must be --all_info) - done
FreeSurfer
Freesurfer provided tools
- mri_probedicom - done
- mri_ca_tissue_parms - done
- mri_extract_conditions - done
- mri_concat - done
- mri_train - done
- mri_tessellate - done
- mri_convert_mdh - done
- mri_compute_overlap - done
- mri_mcsim - done
- mri_label2vol - done
- mri_cnr - done
- mri_ca_train - done
- mri_strip_nonwhite - done
- mri_surf2surf - done
- mri_deface - done
- mri_extract - done
- mri_ms_EM - done
- mri_copy_values - done
- mri_make_register - done
- mri_make_bem_surfaces - done
- mri_ca_normalize - done
- mri_extract_largest_CC - done
- mri_average - done
- mri_apply_inu_correction - done
- mri_glmfit - done
- mri_extract_label - done
- mri_strip_skull - done
- mri_histo_eq - done
- mri_ms_LDA - done
- mri_label2label - done
- mri_add_xform_to_header - done
- mri_convert - done
- mri_modify - done
- mri_compute_seg_overlap - done
- mri_linear_register - done
- mri_joint_density - done
- mri_annotation2label - done
- mri_make_template - done
- mri_partial_ribbon - done
- mri_pretess - done
- mri_paint - done
- mri_concatenate_lta - done
- mri_cor2label - done
- mri_ms_EM_with_atlas - done
- mri_aparc2wmseg - done
- mri_label_vals - done
- mri_gca_ambiguous - done
- mri_synthesize - done
- mri_label_volume - done
- mri_twoclass - done
- mri_morphology - done
- mri_mask - done
- mri_ca_label - done
- mri_volcluster - done
- mri_register - done
- mri_watershed - done
- mri_wmfilter - done
- mri_normalize_tp2 - done
- mri_fslmat_to_lta - done
- mri_diff - done
- mri_probe_ima - done
- mri_ca_register - done
- mri_surfacemask - done
- mri_edit_wm_with_aseg - done
- mri_aparc2aseg - done
- mri_auto_fill - done
- mri_parselabel - done
- mri_normalize - done
- mri_surf2vol - done
- mri_vol2surf - done
- mri_vol2vol - done
- mri_bc_sc_bias_correct - done
- mri_build_priors - done
- mri_vol2roi - done
- mri_xvolavg - done
- mri_threshold - done
- mri_mark_temporal_lobe - done
- mri_matrix_multiply - done
- mri_nlfilter - done
- mri_edit_segmentation - done
- mri_rigid_register - done
- mri_fill - done
- mri_head - done
- mri_copy_params - done
- mri_surfcluster - done
- mri_fwhm - done
- mri_segstats - done
- mri_transform_to_COR - done
- mri_estimate_tissue_parms - done
- mri_em_register - done
- mri_ribbon - done
- mri_make_density_map - done
- mri_strip_subject_info - done
- mri_remove_neck - done
- mri_segment - done
- mri_gdfglm - done
- mri_voldiff - done
- mri_polv - done
- mri_reduce - done
- mri_ms_fitparms - done
- mri_info - done
- mri_label_histo - done
- mri_stats2seg - done
- mri_evaluate_morph - done
LDDMM Suite
- lddmm-volume within Slicer 2.x - done
- lddmm-surface
- lddmm-similitude
- lddmm-landmark
- lddmm-dti
Processing scripts
These scripts reference other executables and are usually rife with special cases
- BIRNDUP
- Tcl scripts within Slicer 2.x (ie dcanon.tcl) - done
- BIRN ID Generator - done
- a2mrml - done
- fBIRN upload script upload2.pl
Workflows
- Gradient Unwarping
