.. _fp_postpre_IV: Post-preproc, IV: Tracking ====================================== .. contents:: :local: .. highlight:: Tcsh Overview -------- **under construction** Probabilistic tracking and **3dTrackID** ---------------------------------------------------------------- **under construction** **Proc:** This is an example of fully probabilistic tracking through the set of "inflated" GM regions from the previous ``3dROIMaker`` step. Of the two output FS aseg+aparc atlases, this uses the "2000" one:: # for I/O, same path variable as above set path_P_ss = data_proc/SUBJ_001 # for variable simplicity, just go to the dir with the ROI maps cd $path_P_ss/dwi_05 set gm_netw = sel_indt_aparc+aseg_REN_gm_GMI.nii.gz 3dTrackID \ -mode PROB \ -dti_in dt \ -netrois $gm_netw \ -uncert dt_UNC.nii.gz \ -prefix o.pr00 \ -nifti \ -no_indipair_out \ -dump_rois AFNI \ -alg_Thresh_FA 0.2 \ -alg_Thresh_Frac 0.1 \ -alg_Nseed_Vox 5 \ -alg_Nmonte 1000 \ -echo_edu \ -overwrite -> produces output in the same directory 'data_proc/SUBJ_001/dwi_05/', since all volume files occupy the same space/grid... **under construction** Visualizing WM connections and **fat_proc_connec_vis** ------------------------------------------------------ **Proc:** This is an example of viewing several WMCs together in one image that can be viewed in SUMA. Each WMC is surfaceized and colored individually. In this case all AND-logic WMCs that were found through the "Right-Thalamus-Proper" target are viewed:: fat_proc_connec_vis \ -in_rois o.pr00/NET_000_ROI_*Right-Thalamus-Proper*nii.gz \ -prefix o.pr00_Right-Thalamus-Proper \ -trackid_no_or -> produces output in the same directory 'data_proc/SUBJ_001/dwi_05/', since all volume files occupy the same space/grid... **under construction** .. list-table:: :header-rows: 1 :widths: 50 50 * - **under construction** - (just axi and cor views) * - .. image:: media/postpre_iv/autorecord.A.171219_191503.265.jpg :width: 100% :align: center - .. image:: media/postpre_iv/autorecord.A.171219_191508.798.jpg :width: 100% :align: center * - .. image:: media/postpre_iv/autorecord.A.171219_191622.585.jpg :width: 100% :align: center - .. image:: media/postpre_iv/autorecord.A.171219_191637.369.jpg :width: 100% :align: center Visualizing matrices of structural properties and **fat_proc_connec_vis** ------------------------------------------------------------------------------- **under construction** **Proc:** This is an example of viewing several WMCs together in one image that can be viewed in SUMA. Each WMC is surfaceized and colored individually. In this case all AND-logic WMCs that were found through the "Right-Thalamus-Proper" target are viewed:: fat_proc_connec_vis \ -in_rois o.pr00/NET_000_ROI_*Right-Thalamus-Proper*nii.gz \ -prefix o.pr00_Right-Thalamus-Proper \ -trackid_no_or -> produces output in the same directory 'data_proc/SUBJ_001/dwi_05/', since all volume files occupy the same space/grid... .. : .. list-table:: :header-rows: 1 :widths: 90 * - Directory structure for example data set * - .. image:: media/postpre_iii/fp_13_roi_sel_make.png :width: 100% :align: center * - *Output files made to select only clumpy GM ROIs and then to perform controlled inflation.* | .. list-table:: :header-rows: 1 :widths: 20 80 :stub-columns: 0 * - Outputs of - the above ``3dcalc``/\ ``3drefit``/\ ``3dROIMaker`` * - **sel_indt_aparc\*+aseg_REN_gm.nii.gz** - volumetric NIFTI file, 3D; the GM region map without the deselected ROIs. The same labeltable from the original input is contained within the file's header. * - **sel_indt_aparc\*+aseg_REN_gm_GMI.nii.gz** - volumetric NIFTI file, 3D; the output of ``3dROIMaker`` which contains the inflated map of ROIs. * - **sel_indt_aparc\*+aseg_REN_gm_GMI.niml.lt** - text file; the labeltable of the NIFTI file with the same root name. * - **sel_indt_aparc\*+aseg_REN_gm_GM.nii.gz** - volumetric NIFTI file, 3D; the output of ``3dROIMaker`` which contains the *non*\-inflated map of ROIs. (Having this output is useful if, for example, one uses ``3dROIMaker`` to subtract any regions from tissues, though that was not done here.) * - **sel_indt_aparc\*+aseg_REN_gm_GM.niml.lt** - text file; the labeltable of the NIFTI file with the same root name. | To view the dual points of 1) inflating the GM ROIs and 2) constraining that inflation, we show images of before-and-after inflation, for both the "2000" and "2009" parcellations. The b/w ulay is the binary mask where FA>0.2, representing the DTI-based proxy for WM (and within which tracking normally occurs for healthy adult humans). Note that in the pre-inflation cases, one can often see GM ROIs following the contours of the FA-WM, but there might be slight gaps due to either transformation, partial voluming, etc. Such regions might create artificial "misses" in the tracts, which don't leave the FA>0.2 boundaries to reach the GM they (possibly) should. Conversely, in cases where the GM follows the FA-WM boundary well, we wouldn't want inflation pouring out into the WM unnecessarily. .. note:: When viewing the following montages, it might make sense to open corresponding montages of the inflated and non-inflated maps in browser tabs and then toggling views between them-- that should highlight both of the main points. .. list-table:: :header-rows: 1 :widths: 50 50 * - Images comparing the "2000" inflated and non-inflated GM maps - (just axi and sag views) * - .. image:: media/postpre_iii/sel__qc2000_uFA02_gm.axi.png :width: 100% :align: center - .. image:: media/postpre_iii/sel__qc2000_uFA02_gm.sag.png :width: 100% :align: center .. list-table:: :header-rows: 0 :widths: 100 * - *Non-inflated "2000" parc/seg map (after the non-regional ROIs were removed) olayed on FA>0.2 binary map ulay.* .. list-table:: :header-rows: 0 :widths: 50 50 * - .. image:: media/postpre_iii/sel__qc2000_uFA02_GMI.axi.png :width: 100% :align: center - .. image:: media/postpre_iii/sel__qc2000_uFA02_GMI.sag.png :width: 100% :align: center .. list-table:: :header-rows: 0 :widths: 100 * - *Inflated "2000" parc/seg map (after the non-regional ROIs were removed) olayed on FA>0.2 binary map ulay.* | .. list-table:: :header-rows: 1 :widths: 50 50 * - Images comparing the "2009" inflated and non-inflated GM maps - (just axi and sag views) * - .. image:: media/postpre_iii/sel__qc2009_uFA02_gm.axi.png :width: 100% :align: center - .. image:: media/postpre_iii/sel__qc2009_uFA02_gm.sag.png :width: 100% :align: center .. list-table:: :header-rows: 0 :widths: 100 * - *Non-inflated "2009" parc/seg map (after the non-regional ROIs were removed) olayed on FA>0.2 binary map ulay.* .. list-table:: :header-rows: 0 :widths: 50 50 * - .. image:: media/postpre_iii/sel__qc2009_uFA02_GMI.axi.png :width: 100% :align: center - .. image:: media/postpre_iii/sel__qc2009_uFA02_GMI.sag.png :width: 100% :align: center .. list-table:: :header-rows: 0 :widths: 100 * - *Inflated "2009" parc/seg map (after the non-regional ROIs were removed) olayed on FA>0.2 binary map ulay.*