Mbirn: Data Provenance:Documentation:ToolList

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

Third Party Tools

1. FSL
2. MATLAB
3. R
4. FFTW - lddmm dependency
5. GTS - lddmm dependency
6. BLITZ++ - lddmm dependency