View source for 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 ==

* [http://www.na-mic.org/Slicer/Download/Release/ Slicer 2.5] - done
* [http://www.na-mic.org/Slicer/Download/Release/ Slicer 2.6] - done
* [http://www.na-mic.org/Slicer/Download/Snapshots/ 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 ==

[http://surfer.nmr.mgh.harvard.edu/fswiki/Download 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 ==

* [http://www.cis.jhu.edu/software/lddmm-volume/ lddmm-volume] within Slicer 2.x - done
* [http://www.cis.jhu.edu/software/lddmm-surface lddmm-surface]
* [http://www.cis.jhu.edu/software/lddmm-similitude lddmm-similitude]
* [http://www.cis.jhu.edu/software/lddmm-landmark lddmm-landmark]
* [http://www.cis.jhu.edu/software/lddmm-dti 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
** [http://splweb.bwh.harvard.edu:8000/cgi-bin/develop/viewcvs.cgi/birndup/dcanon/a2mrml/a2mrml.c.diff?r1=1.1&r2=1.2 a2mrml] - done
* fBIRN upload script upload2.pl

== Workflows ==

* Gradient Unwarping

= Third Party Tools =

# FSL
# MATLAB
# R
# [http://www.fftw.org/ FFTW] - lddmm dependency
# [http://gts.sourceforge.net GTS] - lddmm dependency
# [http://www.oonumerics.org/blitz/ BLITZ++] - lddmm dependency