https://www.na-mic.org/w/index.php?action=history&feed=atom&title=Mbirn%3A_Data_Provenance%3ADocumentation%3AToolList 2026-04-13T16:56:31Z Revision history for this page on the wiki MediaWiki 1.33.0 https://www.na-mic.org/w/index.php?title=Mbirn:_Data_Provenance:Documentation:ToolList&diff=9726&oldid=prev 2007-04-25T22:03:37Z

<p><span dir="auto"><span class="autocomment">Processing scripts</span></span></p> <table class="diff diff-contentalign-left" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 22:03, 25 April 2007</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l138" >Line 138:</td> <td colspan="2" class="diff-lineno">Line 138:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* BIRNDUP</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* BIRNDUP</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>** Tcl scripts within Slicer 2.x - done</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>** Tcl scripts within Slicer 2.x <ins class="diffchange diffchange-inline">(ie dcanon.tcl) </ins>- done</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>** BIRN ID Generator - done</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>** BIRN ID Generator - done</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>** [http://splweb.bwh.harvard.edu:8000/cgi-bin/develop/viewcvs.cgi/birndup/dcanon/a2mrml/a2mrml.c.diff?r1=1.1&amp;r2=1.2 a2mrml] - done</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>** [http://splweb.bwh.harvard.edu:8000/cgi-bin/develop/viewcvs.cgi/birndup/dcanon/a2mrml/a2mrml.c.diff?r1=1.1&amp;r2=1.2 a2mrml] - done</div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">* fBIRN upload script upload2.pl</ins></div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Workflows ==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Workflows ==</div></td></tr> </table>

Naucoin https://www.na-mic.org/w/index.php?title=Mbirn:_Data_Provenance:Documentation:ToolList&diff=3895&oldid=prev 2006-12-18T13:31:39Z

<p>Update from Wiki</p> <p><b>New page</b></p><div>= Tool List =<br /> <br /> 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.<br /> <br /> ''First draft - Jan/05'', ''Second draft - Nov 14/06''<br /> <br /> = BIRN Tools =<br /> <br /> 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 &quot;done&quot; after a tool means that it will respond to the --all-info flag.<br /> <br /> == Slicer ==<br /> <br /> * [http://www.na-mic.org/Slicer/Download/Release/ Slicer 2.5] - done<br /> * [http://www.na-mic.org/Slicer/Download/Release/ Slicer 2.6] - done<br /> * [http://www.na-mic.org/Slicer/Download/Snapshots/ Slicer 2.7 (aka current CVS head)] - done<br /> * Slicer 3.0Alpha (xml CLI interface won't allow --all-info, must be --all_info) - done<br /> <br /> == FreeSurfer ==<br /> <br /> [http://surfer.nmr.mgh.harvard.edu/fswiki/Download Freesurfer] provided tools<br /> <br /> * mri_probedicom - done<br /> * mri_ca_tissue_parms - done<br /> * mri_extract_conditions - done<br /> * mri_concat - done<br /> * mri_train - done<br /> * mri_tessellate - done<br /> * mri_convert_mdh - done<br /> * mri_compute_overlap - done<br /> * mri_mcsim - done<br /> * mri_label2vol - done<br /> * mri_cnr - done<br /> * mri_ca_train - done<br /> * mri_strip_nonwhite - done<br /> * mri_surf2surf - done<br /> * mri_deface - done<br /> * mri_extract - done<br /> * mri_ms_EM - done<br /> * mri_copy_values - done<br /> * mri_make_register - done<br /> * mri_make_bem_surfaces - done<br /> * mri_ca_normalize - done<br /> * mri_extract_largest_CC - done<br /> * mri_average - done<br /> * mri_apply_inu_correction - done<br /> * mri_glmfit - done<br /> * mri_extract_label - done<br /> * mri_strip_skull - done<br /> * mri_histo_eq - done<br /> * mri_ms_LDA - done<br /> * mri_label2label - done<br /> * mri_add_xform_to_header - done<br /> * mri_convert - done<br /> * mri_modify - done<br /> * mri_compute_seg_overlap - done<br /> * mri_linear_register - done<br /> * mri_joint_density - done<br /> * mri_annotation2label - done<br /> * mri_make_template - done<br /> * mri_partial_ribbon - done<br /> * mri_pretess - done<br /> * mri_paint - done<br /> * mri_concatenate_lta - done<br /> * mri_cor2label - done<br /> * mri_ms_EM_with_atlas - done<br /> * mri_aparc2wmseg - done<br /> * mri_label_vals - done<br /> * mri_gca_ambiguous - done<br /> * mri_synthesize - done<br /> * mri_label_volume - done<br /> * mri_twoclass - done<br /> * mri_morphology - done<br /> * mri_mask - done<br /> * mri_ca_label - done<br /> * mri_volcluster - done<br /> * mri_register - done<br /> * mri_watershed - done<br /> * mri_wmfilter - done<br /> * mri_normalize_tp2 - done<br /> * mri_fslmat_to_lta - done<br /> * mri_diff - done<br /> * mri_probe_ima - done<br /> * mri_ca_register - done<br /> * mri_surfacemask - done<br /> * mri_edit_wm_with_aseg - done<br /> * mri_aparc2aseg - done<br /> * mri_auto_fill - done<br /> * mri_parselabel - done<br /> * mri_normalize - done<br /> * mri_surf2vol - done<br /> * mri_vol2surf - done<br /> * mri_vol2vol - done<br /> * mri_bc_sc_bias_correct - done<br /> * mri_build_priors - done<br /> * mri_vol2roi - done<br /> * mri_xvolavg - done<br /> * mri_threshold - done<br /> * mri_mark_temporal_lobe - done<br /> * mri_matrix_multiply - done<br /> * mri_nlfilter - done<br /> * mri_edit_segmentation - done<br /> * mri_rigid_register - done<br /> * mri_fill - done<br /> * mri_head - done<br /> * mri_copy_params - done<br /> * mri_surfcluster - done<br /> * mri_fwhm - done<br /> * mri_segstats - done<br /> * mri_transform_to_COR - done<br /> * mri_estimate_tissue_parms - done<br /> * mri_em_register - done<br /> * mri_ribbon - done<br /> * mri_make_density_map - done<br /> * mri_strip_subject_info - done<br /> * mri_remove_neck - done<br /> * mri_segment - done<br /> * mri_gdfglm - done<br /> * mri_voldiff - done<br /> * mri_polv - done<br /> * mri_reduce - done<br /> * mri_ms_fitparms - done<br /> * mri_info - done<br /> * mri_label_histo - done<br /> * mri_stats2seg - done<br /> * mri_evaluate_morph - done<br /> <br /> == LDDMM Suite ==<br /> <br /> * [http://www.cis.jhu.edu/software/lddmm-volume/ lddmm-volume] within Slicer 2.x - done<br /> * [http://www.cis.jhu.edu/software/lddmm-surface lddmm-surface]<br /> * [http://www.cis.jhu.edu/software/lddmm-similitude lddmm-similitude]<br /> * [http://www.cis.jhu.edu/software/lddmm-landmark lddmm-landmark]<br /> * [http://www.cis.jhu.edu/software/lddmm-dti lddmm-dti]<br /> <br /> == Processing scripts ==<br /> <br /> These scripts reference other executables and are usually rife with special cases<br /> <br /> * BIRNDUP<br /> ** Tcl scripts within Slicer 2.x - done<br /> ** BIRN ID Generator - done<br /> ** [http://splweb.bwh.harvard.edu:8000/cgi-bin/develop/viewcvs.cgi/birndup/dcanon/a2mrml/a2mrml.c.diff?r1=1.1&amp;r2=1.2 a2mrml] - done<br /> <br /> == Workflows ==<br /> <br /> * Gradient Unwarping<br /> <br /> = Third Party Tools =<br /> <br /> # FSL<br /> # MATLAB<br /> # R<br /> # [http://www.fftw.org/ FFTW] - lddmm dependency<br /> # [http://gts.sourceforge.net GTS] - lddmm dependency<br /> # [http://www.oonumerics.org/blitz/ BLITZ++] - lddmm dependency</div>

Andy