Difference between revisions of "Mbirn: Data Provenance:Documentation:ToolList"

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* BIRNDUP
 
* BIRNDUP
** Tcl scripts within Slicer 2.x - done
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** Tcl scripts within Slicer 2.x (ie dcanon.tcl) - done
 
** BIRN ID Generator - 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
 
** [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 ==
 
== Workflows ==

Latest revision as of 22:03, 25 April 2007

Home < 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

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

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