.. _FATCAT_Demo: ======================== **FATCAT Visualization** ======================== This visualiztion ties in with the current FATCAT Demo, which has a number of data sets and commented scripts. If you don't have it already (?!?!), then please check out the :ref:`Demo installation instructions?`. .. Paul: Do you want to add a few words here? .. _Do_00_PRESTO_ALL_RUNS.tcsh: .. _Do_01_RUNdti_convert_grads.tcsh: .. _Do_01_RUNhardi_convert_grads.tcsh: .. _Do_02_RUNdti_DW_to_DTI.tcsh: .. _Do_03_RUNdti_make_network_ROIs.tcsh: .. _Do_04_RUNdti_match_network_ROIs.tcsh: .. _Do_05_RUNdti_DET_tracking.tcsh: .. _Do_05_RUNhardi_DET_tracking.tcsh: .. _Do_07_RUNdti_uncertainty_est.tcsh: .. _Do_07_RUNhardi_uncertainty_est.tcsh: .. _Do_08_RUNdti_miniprob_track.tcsh: .. _Do_08_RUNhardi_miniprob_track.tcsh: .. _Do_10_RUNdti_fullprob_track.tcsh: .. _Do_10_RUNhardi_fullprob_track.tcsh: .. _Do_11_RUNdti_Connectome_Examp.tcsh: .. _Do_12_RUNrsfc_netw_corr.tcsh: .. _Do_13_RUNrsfc_RSFCfilt_param.tcsh: .. _Do_14_RUNrsfc_ReHo_param.tcsh: .. _Do_PostTORTOISE_2014.tcsh: At some point you should read the README file under FATCAT_Demo, and go over the comments in each of the scripts that provide context to the different commands used. Scripts Do_*_VIS* are meant to illustrate interactive visualization of the results. The scripts will open results in AFNI and SUMA and a prompt window will guide throuh basic viewing steps. See also the :ref:`quick tour for tract viewing`. You should be able to create images such as the ones shown above. Fun times! .. _Do_06_VISdti_SUMA_visual_ex1.tcsh: Do_06_VISdti_SUMA_visual_ex1.tcsh --------------------------------- Results visualized by script Do_06_VISdti_SUMA_visual_ex1.tcsh .. figure:: media/Do_06_vis1.jpg :align: left :figwidth: 40% :target: ../../_images/Do_06_vis1.jpg :name: media/Do_06_vis1.jpg Tracts going though an interactively positioned :ref:`maskColoring_Controls->Masks>` in the midbrain area. :ref:`Slice transparencySlice_Controls->Trn>` set to 8. :ref:`(link)` .. figure:: media/Do_06_vis2.jpg :align: right :figwidth: 40% :target: ../../_images/Do_06_vis2.jpg :name: media/Do_06_vis2.jpg Tracts going though one ROI, with :ref:`volume renderingVR->Ns->v>` turned on. :ref:`(link)` .. container:: clearer .. image:: media/blank.jpg .. _Do_09_VISdti_SUMA_visual_ex2.tcsh: Do_09_VISdti_SUMA_visual_ex2.tcsh --------------------------------- Results visualized by script Do_09_VISdti_SUMA_visual_ex2.tcsh .. figure:: media/Do_09_vis2.1.jpg :align: left :figwidth: 40% :target: ../../_images/Do_09_vis2.1.jpg :name: media/Do_09_vis2.1.jpg Surfaces with surface contour (see :ref:`IsoSurface`) of ROI in color, slices, and tracts barely visible. ref:`(link)` .. figure:: media/Do_09_vis2.2.jpg :align: right :figwidth: 40% :target: ../../_images/Do_09_vis2.2.jpg :name: media/Do_09_vis2.2.jpg Surfaces hidden to reveal deterministic tracts through ROIs of the DMN. ref:`(link)` .. figure:: media/Do_09_vis2.3.jpg :align: center :figwidth: 50% :target: ../../_images/Do_09_vis2.3.jpg :name: media/Do_09_vis2.3.jpg Connection is maintained with AFNI which is displaying intersection of surfaces with the volume. Clicking anywhere in SUMA will cause AFNI to jump to the corresponding location. :ref:`(link)` .. container:: clearer .. image:: media/blank.jpg Comparison of deterministic to mini-probabilistic results. .. figure:: media/Do_09_vis2.4.jpg :align: left :figwidth: 44% :target: ../../_images/Do_09_vis2.4.jpg :name: media/Do_09_vis2.4.jpg :ref:`Deterministic.` .. figure:: media/Do_09_vis2.5.jpg :align: right :figwidth: 44% :target: ../../_images/Do_09_vis2.4.jpg :name: media/Do_09_vis2.5.jpg :ref:`Probabilistic.` .. container:: clearer .. image:: media/blank.jpg Composite display of :ref:`connectivity matrices` .. figure:: media/Do_09_vis3.1.jpg :align: center :name: media/Do_09_vis3.1.jpg :ref:`(link)` .. Do_09_VISdti_SUMA_visual_ex3.tcsh --------------------------------- .. _Do_09_VISdti_SUMA_visual_ex3.tcsh: .. _F+A_Conn: Script Do_09_VISdti_SUMA_visual_ex3.tcsh can be used to demonstrate simultaneous, interactive, functional and anatomical connectivity. Just follow the directions that come up on the screen when you launch the script. .. figure:: ../../SUMA/media/f+a_conn.jpg :align: center :name: SUMA/media/f+a_conn.jpg :ref:`(link)` Connectoming ------------ Results of script Do_11_RUNdti_Connectome_Examp.tcsh which finds connections between a large number of ROIs. .. figure:: media/Connectoming.jpg :align: center :target: ../../_images/Connectoming.jpg :name: media/Connectoming.jpg The tracts here are :ref:`coloredColoring_Controls->Switch_Dset>` depending on which pair of ROIs they join. :ref:`(link)`. To launch suma with the results displayed here, use:: suma -tract CONNECTOMING/o.OME8_000.niml.tract