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| == Tract Statistics == This section of the tutorial will teach you to extract Statistical measures along the major White Matter tracts reconstructed by Tracula. There are two types of statistics files that are output for each White Matter Tract * path.overall.txt - This file gives Diffusion measures along the whole WM tract * path.byvoxel.txt - This files gives Diffusion measures for each voxel along the WM tract. To view the statistics files from Tracula for for the subject Diff001 (Left Cortico-Spinal Tract), type the following in the terminal ---- {{{ cd $TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/5cpts/priorcvs/seg14/initmni/regbbr/lh.cst_AS_avg23_cvs_bbr/ less path.overall.txt less path.byvoxel.txt }}} ---- == path.overall.txt == This text file gives various diffusion measures about the specific white matter tract along its complete path. Some of the measures include: * Count of the # of Fibers in the WM tract * Tract Volume * Maximum, Minimum and Average length of fibers * Length of the center fiber * Axial Diffusivity (both average and along the center) * Radial Diffusivity (both average and along the center) * Mean Diffusivity (both average and along the center) * Fractional Anisotropy (both average and along the center) ---- |
## page was renamed from FsTutorial/TractStatistics [[FsTutorial|Top]] | [[FsTutorial/TraculaOutputs|Previous]] = Tract statistics = === Remember... === For '''each new''' terminal that you open, you must do: {{{ setenv SUBJECTS_DIR $TUTORIAL_DATA/diffusion_recons cd $TUTORIAL_DATA/diffusion_tutorial }}} ------- This section of the tutorial will teach you how to extract statistics on anisotropy and diffusivity measures for the white-matter pathways reconstructed by TRACULA. There are two types of statistics files that are created for each white-matter tract: * pathstats.overall.txt - This file contains measures averaged over the whole tract * pathstats.byvoxel.txt - This files contains measures as a function of location along the trajectory of the tract. To view the statistics files from TRACULA for the left corticospinal tract of subject elmo.2012, {{{cd}}} into one subject's directory where the stats are located for this specific tract: {{{ cd $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.cst_AS_avg33_mni_bbr }}} == pathstats.overall.txt == You can view the overall path stats by doing: {{{ gedit $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt & }}} This file will look like this: |
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| # generating_program $FREESURFER_HOME/bin/dmri_pathstats | # generating_program /usr/local/freesurfer/dev/bin/dmri_pathstats |
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| # cmdline $FREESURFER_HOME/bin/dmri_pathstats --intrc $TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/5cpts/priorcvs/seg14/initmni/regbbr/lh.cst_AS_avg23_cvs_bbr --dtbase $TUTORIAL_DATA/diffusion_tutorial/Diff001/dmri/dtifit --path lh.cst --subj Diff001 --out $TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/5cpts/priorcvs/seg14/initmni/regbbr/lh.cst_AS_avg23_cvs_bbr/pathstats.overall.txt --outvox $TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/5cpts/priorcvs/seg14/initmni/regbbr/lh.cst_AS_avg23_cvs_bbr/pathstats.byvoxel.txt | # cmdline /usr/local/freesurfer/dev/bin/dmri_pathstats --intrc /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr --dtbase /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dmri/dtifit --path lh.ilf --subj elmo.2012 --out /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.overall.txt --outvox /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.byvoxel.txt |
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| # hostname compute-0-1.local | # hostname compute-0-29 |
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| # user rspriti | # user ayendiki |
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| # subjectname Diff001 # pathwayname lh.cst # Count 100 Volume 235 Len_Min 45 Len_Max 69 Len_Avg 55.3 Len_Center 53 AD_Avg 0.00108402 AD_Avg_Weight 0.00107521 AD_Avg_Center 0.00107062 RD_Avg 0.00046958 RD_Avg_Weight 0.000476065 RD_Avg_Center 0.000507009 MD_Avg 0.000674393 MD_Avg_Weight 0.000675781 MD_Avg_Center 0.000694881 FA_Avg 0.50122 FA_Avg_Weight 0.48976 FA_Avg_Center 0.456292 }}} ---- == path.byvoxel.txt == This text file gives us various diffusion measures in each voxel along the WM tract ---- {{{ |
# subjectname elmo.2012 # pathwayname lh.ilf # Count 1500 Volume 167 Len_Min 29 Len_Max 64 Len_Avg 45.008 Len_Center 37 AD_Avg 0.00131194 AD_Avg_Weight 0.00139891 AD_Avg_Center 0.001268 RD_Avg 0.000686486 RD_Avg_Weight 0.000770628 RD_Avg_Center 0.000635293 MD_Avg 0.00089497 MD_Avg_Weight 0.000980054 MD_Avg_Center 0.000846196 FA_Avg 0.414059 FA_Avg_Weight 0.392266 FA_Avg_Center 0.408256 }}} This text file contains various diffusion measures, averaged over the entire white-matter tract. The measures include: * Number of sample paths in the WM tract * Tract volume (in voxels) * Maximum, minimum and average length of sample paths * Length of the highest-probability (a.k.a. maximum a posteriori) path * Axial diffusivity (average over the entire support of the path distribution, weighted average over the entire support of the path distribution, and average over highest-probability path only) * Radial diffusivity (as above) * Mean diffusivity (as above) * Fractional anisotropy (as above) == pathstats.byvoxel.txt == Now take a look at the stats as a function of position along the trajectory of the tract: {{{ gedit $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.byvoxel.txt & }}} It will look like this: {{{ |
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| # generating_program $FREESURFER_HOME/dmri_pathstats | # generating_program /usr/local/freesurfer/dev/bin/dmri_pathstats |
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| # cmdline $FREESURFER_HOME/dmri_pathstats --intrc $TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/5cpts/priorcvs/seg14/initmni/regbbr/lh.cst_AS_avg23_cvs_bbr --dtbase $TUTORIAL_DATA/diffusion_tutorial/Diff001/dmri/dtifit --path lh.cst --subj Diff001 --out $TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/5cpts/priorcvs/seg14/initmni/regbbr/lh.cst_AS_avg23_cvs_bbr/pathstats.overall.txt --outvox $TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/5cpts/priorcvs/seg14/initmni/regbbr/lh.cst_AS_avg23_cvs_bbr/pathstats.byvoxel.txt | # cmdline /usr/local/freesurfer/dev/bin/dmri_pathstats --intrc /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr --dtbase /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dmri/dtifit --path lh.ilf --subj elmo.2012 --out /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.overall.txt --outvox /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.byvoxel.txt |
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| # hostname compute-0-1.local | # hostname compute-0-29 |
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| # user rspriti | # user ayendiki |
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| # subjectname Diff001 # pathwayname lh.cst |
# subjectname elmo.2012 # pathwayname lh.ilf |
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| x y z AD RD MD FA 62 63 10 0.000637887 0.000476948 0.000530594 0.178865 62 63 11 0.0006074 0.000433505 0.00049147 0.22773 63 63 12 0.000846852 0.000610935 0.000689574 0.251636 63 64 13 0.00123916 0.00105259 0.00111478 0.107897 63 64 14 0.000936783 0.000621757 0.000726766 0.264886 64 64 15 0.000869413 0.000500918 0.00062375 0.348479 64 64 16 0.000742746 0.000432898 0.000536181 0.357518 65 64 16 0.000729103 0.000361411 0.000483975 0.42985 66 65 17 0.000645165 0.000105291 0.000285249 0.86012 67 65 18 0.00115478 0.000351219 0.000619072 0.647404 68 66 19 0.00142292 0.000690686 0.000934763 0.432432 69 66 20 0.00166259 0.000912869 0.00116278 0.363279 69 66 21 0.00145087 0.000448438 0.000782583 0.639517 70 66 22 0.00124617 0.000204701 0.000551856 0.816332 70 66 23 0.00138642 0.000415134 0.000738896 0.650657 71 66 23 0.00136252 0.000330065 0.000674217 0.721118 71 66 24 0.00134187 0.000385197 0.000704089 0.678151 71 66 25 0.00108983 0.000289931 0.000556565 0.729769 72 66 26 0.00106165 0.000357968 0.000592529 0.650427 72 66 27 0.00117242 0.000398032 0.00065616 0.619191 73 65 28 0.00130606 0.000441963 0.000729994 0.61662 73 65 29 0.00132239 0.00034928 0.000673651 0.701421 74 65 30 0.00133145 0.000391918 0.000705096 0.652609 74 65 31 0.00130265 0.000371743 0.000682045 0.665608 74 65 32 0.00126357 0.000429947 0.000707822 0.596254 75 65 33 0.00126146 0.000533254 0.000775991 0.499365 75 64 34 0.00117235 0.000465188 0.00070091 0.536046 75 64 35 0.00111144 0.000424831 0.000653701 0.560041 76 64 36 0.00128036 0.000299521 0.000626469 0.731721 76 64 37 0.00119495 0.000322181 0.000613105 0.688909 76 64 38 0.00105691 0.000334124 0.000575053 0.64994 76 63 39 0.00106784 0.000449252 0.000655449 0.514129 76 63 40 0.00113234 0.000537139 0.000735539 0.463226 76 63 41 0.000990485 0.000493054 0.000658864 0.446701 76 63 42 0.000798778 0.000477672 0.000584708 0.336071 76 62 43 0.000870652 0.000483175 0.000612334 0.362795 75 62 44 0.000878542 0.000493417 0.000621792 0.376378 75 62 45 0.000897465 0.000514559 0.000642194 0.348244 75 61 46 0.000882752 0.000537658 0.000652689 0.310019 74 61 47 0.00100985 0.00048457 0.000659663 0.436199 74 61 48 0.00104135 0.000461786 0.000654973 0.482846 74 60 49 0.000957188 0.000488566 0.000644774 0.472547 73 60 50 0.00100422 0.00055232 0.000702954 0.378698 73 60 51 0.000938077 0.000492242 0.000640854 0.429111 72 59 52 0.00104503 0.000475882 0.000665599 0.474443 72 59 53 0.00091483 0.00047261 0.000620017 0.409087 72 59 54 0.000792557 0.000632776 0.000686036 0.174565 71 59 55 0.000961412 0.000680667 0.000774249 0.243739 71 58 56 0.001061 0.000895478 0.000950651 0.133396 70 58 57 0.000862592 0.000663684 0.000729986 0.162365 70 58 58 0.00119199 0.00103056 0.00108437 0.086213 69 57 59 0.00120589 0.000980809 0.00105584 0.127098 69 57 60 0.00102806 0.000829161 0.000895461 0.141788 |
x y z AD RD MD FA AD_Avg RD_Avg MD_Avg FA_Avg 86 71 16 0.00124639 0.000810355 0.000955702 0.296343 0.00124166 0.000683586 0.000869599 0.375502 86 72 15 0.000758499 0.000690337 0.000713058 0.0665528 0.00120352 0.000674202 0.00085063 0.365702 85 72 14 0.000819579 0.000601256 0.00067403 0.196614 0.00111348 0.000618912 0.00078378 0.353662 84 72 13 0.000970979 0.00067094 0.000770953 0.227346 0.00115739 0.000679319 0.000838683 0.329086 84 71 13 0.0010519 0.000845654 0.000914402 0.174291 0.00117946 0.000675255 0.000843332 0.342993 84 70 13 0.00122524 0.00075747 0.000913395 0.295734 0.00127004 0.000700568 0.00089039 0.368428 84 69 13 0.0013762 0.000607907 0.000864005 0.475513 0.00130121 0.000666051 0.000877759 0.405086 83 68 14 0.00117165 0.000572571 0.000772264 0.433612 0.00127088 0.000631783 0.000844803 0.427719 83 67 14 0.00122987 0.000573616 0.000792367 0.452554 0.00123866 0.000625767 0.000830053 0.422219 83 66 14 0.00120132 0.000599483 0.000800095 0.411401 0.00118774 0.00062832 0.000814796 0.408966 83 65 14 0.00130532 0.000741545 0.000929471 0.341101 0.00117765 0.000649599 0.000825623 0.38951 83 64 15 0.00113069 0.000744614 0.000873306 0.303024 0.00124994 0.000716112 0.000894054 0.35574 83 63 15 0.00145392 0.000843014 0.00104665 0.338389 0.00160184 0.000956015 0.00117128 0.342898 83 62 15 0.00150758 0.000704525 0.000972208 0.454268 0.00184354 0.00110231 0.0013494 0.361096 82 61 15 0.00168556 0.000719335 0.00104141 0.500387 0.00187725 0.00105482 0.00132898 0.413339 82 60 16 0.00149165 0.000655993 0.000934546 0.482961 0.00174103 0.000915708 0.00119082 0.459582 82 59 16 0.00178469 0.000676534 0.00104592 0.547817 0.00181009 0.000942766 0.00123188 0.47797 82 58 16 0.00187731 0.000555021 0.000995783 0.650825 0.00176598 0.000879462 0.00117498 0.482668 82 57 17 0.00136583 0.000342585 0.000683666 0.706805 0.00183719 0.00101521 0.00128919 0.444575 82 56 17 0.00149454 0.000361014 0.000738857 0.718399 0.00172875 0.000879471 0.00116258 0.466697 82 55 17 0.00164246 0.000404404 0.000817091 0.714028 0.00143606 0.000654734 0.000915172 0.485324 81 54 17 0.00110069 0.000505138 0.000703656 0.462108 0.00123971 0.000546461 0.000777551 0.491684 81 53 18 0.00149581 0.000503958 0.000834577 0.601599 0.00138836 0.000547033 0.000827479 0.539068 81 52 18 0.00130913 0.000454745 0.00073954 0.597531 0.00133457 0.000539894 0.000804789 0.533393 81 51 18 0.00131507 0.000631822 0.000859572 0.448947 0.00131177 0.000606845 0.000841826 0.469117 81 50 18 0.00135444 0.000747886 0.000950069 0.362522 0.00129975 0.000659834 0.000873148 0.416883 81 49 18 0.00120955 0.000643043 0.000831879 0.404422 0.00126551 0.00064144 0.000849466 0.418424 80 48 19 0.00140649 0.000619495 0.000881827 0.476057 0.00134196 0.000607405 0.000852266 0.47251 80 47 19 0.00124703 0.00054436 0.000778584 0.493392 0.00129913 0.000595745 0.000830194 0.470203 80 46 19 0.00123713 0.000562425 0.000787325 0.473597 0.00131166 0.000608192 0.000842689 0.465411 80 45 19 0.00131702 0.000638351 0.000864576 0.436198 0.00131184 0.000638683 0.000863079 0.443722 79 44 20 0.000961184 0.000655564 0.000757438 0.251941 0.00120554 0.000691043 0.000862543 0.349984 79 43 20 0.00104516 0.000760429 0.000855339 0.211843 0.00118236 0.000713172 0.000869568 0.323664 79 42 20 0.0010671 0.000695726 0.000819518 0.290868 0.00118518 0.000688767 0.000854257 0.347132 79 41 20 0.000951325 0.000643122 0.000745857 0.290616 0.00115072 0.000662836 0.000825473 0.352023 80 40 20 0.00111846 0.000771887 0.00088741 0.232294 0.00118544 0.000701789 0.000863008 0.328079 81 40 20 0.000989299 0.000649715 0.00076291 0.283576 0.00114976 0.000669422 0.000829546 0.343642 |
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| ---- These two files can be used to extract measures that can be further used group analysis. This can also be converted into a table using tractstats2table for doing GLM analyses using mri_glmfit or any other statistical software (SPSS, Excel, Statview etc) === path.overall.txt to Table Conversion === To extract all diffusion measures into a table do the following: ---- {{{ tractstats2table --inputs $TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/5cpts/priorcvs/seg14/initmni/regbbr/lh.cst_AS_avg23_cvs_bbr/pathstats.overall.txt --overall --tablefile Diff001_LH.CST.All.Priorcvs.table }}} ---- Instead of extracting all the measures from path.overall.txt, we can get specific measures that can be used for group analysis.For example, to extract only the Average Fractional Anisotropy along Left Cortico-spinal tract, do the following: ---- {{{ tractstats2table --inputs $TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/5cpts/priorcvs/seg14/initmni/regbbr/lh.cst_AS_avg23_cvs_bbr/pathstats.overall.txt --overall --only-measures FA_Avg --tablefile Diff001_LH.CST.FA.Priorcvs.table }}} ---- For a group analysis that has multiple subjects, '''tractstats2table''' can be used to combine all the subjects' diffusion measures from path.overall.txt into a single table that can be used for analysis with mri_glmfit or any other statistics software An easy way to do this is to create a text file that contains the names of the subjects and paths to their path.overall.txt files. An example is given below: ---- {{{ $TUTORIAL_DATA/Diff001/dpath/priorcvs/regbbr/lh.cst_AS_avg23_cvs_bbr/pathstats.overall.txt $TUTORIAL_DATA/Diff002/dpath/priorcvs/regbbr/lh.cst_AS_avg23_cvs_bbr/pathstats.overall.txt $TUTORIAL_DATA/Diff003/dpath/priorcvs/regbbr/lh.cst_AS_avg23_cvs_bbr/pathstats.overall.txt $TUTORIAL_DATA/Diff004/dpath/priorcvs/regbbr/lh.cst_AS_avg23_cvs_bbr/pathstats.overall.txt $TUTORIAL_DATA/Diff005/dpath/priorcvs/regbbr/lh.cst_AS_avg23_cvs_bbr/pathstats.overall.txt $TUTORIAL_DATA/Diff006/dpath/priorcvs/regbbr/lh.cst_AS_avg23_cvs_bbr/pathstats.overall.txt $TUTORIAL_DATA/Diff007/dpath/priorcvs/regbbr/lh.cst_AS_avg23_cvs_bbr/pathstats.overall.txt $TUTORIAL_DATA/Diff008/dpath/priorcvs/regbbr/lh.cst_AS_avg23_cvs_bbr/pathstats.overall.txt $TUTORIAL_DATA/Diff009/dpath/priorcvs/regbbr/lh.cst_AS_avg23_cvs_bbr/pathstats.overall.txt $TUTORIAL_DATA/Diff010/dpath/priorcvs/regbbr/lh.cst_AS_avg23_cvs_bbr/pathstats.overall.txt }}} ---- Once this is created and saved as lh_cst_priorcvs_overall_pathstats, it can be passed as a parameter in tractstats2table command. The following command will create a table with all the subjects specified in the lh_cst_priorcvs_overall_pathstats file and all the diffusion measures from '''path.overall.txt''' for each subject. ---- {{{ tractstats2table --load-pathstats-from-file $TUTORIAL_DATA/diffusion_tutorial/TraculaGLM/LesionStudy/lh_cst_priorcvs_overall_pathstats --overall --tablefile LH.CST.All.Priorcvs.table }}} ---- |
This text file contains various diffusion measures, one row for each position along the trajectory of the path. The first three entries in each row are the x, y, z coordinates in native diffusion space. The next four entries are the axial diffusivity, radial diffusivity, mean diffusivity, and fractional anisotropy at that position on the maximum a posteriori path. The last four entries are the axial diffusivity, radial diffusivity, mean diffusivity, and fractional anisotropy at the same position, averaged over all sampled paths. === Converting pathstats.overall.txt to a table === Measures can be extracted from these files to be analyzed further, e.g., for tract-based group analysis. Specifically, the text files can be converted into a table using the command tractstats2table for doing GLM analyses using [[mri_glmfit]] or any other statistical software (SPSS, Excel, Statview etc.) To extract all diffusion measures for the left corticospinal tract into a table do the following: {{{ tractstats2table --inputs $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt --overall --tablefile $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.cst_AS_avg33_mni_bbr/lh.cst_AS.All.table }}} * The argument to the --inputs option specifies the input stats file. * The --overall option tells tractstats2table to expect the overall path stats file (stats averaged over the entire left CST), as opposed to the stats along the trajectory of the tract (which would be specified with the --byvoxel option instead). * The argument to the --tablefile option specifies the output file. Take a look at the resulting table file: {{{ gedit $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.cst_AS_avg33_mni_bbr/lh.cst_AS.All.table & }}} Instead of extracting all the measures from pathstats.overall.txt for CST, we could extract only a few specific measures. For example, to extract only the average FA along the left corticospinal tract, do the following: {{{ tractstats2table --inputs $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt --overall --only-measures FA_Avg --tablefile $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.cst_AS_avg33_mni_bbr/lh.cst_AS.FA_Avg.table }}} * Here the --only-measures option followed by FA_Avg was used to indicate we are only interested in having the average FA over the path in table format for this tract. Take a look at the resulting table file: {{{ gedit $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.cst_AS_avg33_mni_bbr/lh.cst_AS.FA_Avg.table & }}} For a group analysis that has multiple subjects, '''tractstats2table''' can be used to combine all the subjects' diffusion measures from the path.overall.txt files into a single table that can be used for analysis with [[mri_glmfit]] or any other statistics software. An easy way to do this is to create a text file that contains the names of the subjects and paths to their pathstats.overall.txt files. An example is given below: {{{ $TUTORIAL_DATA/diffusion_tutorial/elmo.2005/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt $TUTORIAL_DATA/diffusion_tutorial/elmo.2008/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt }}} Once this is created and saved as lh.cst_AS.overall.pathstats.list, it can be passed as a parameter to the tractstats2table command. This file has already been created for you. To open this file and view its contents, do the following: {{{ gedit $TUTORIAL_DATA/diffusion_tutorial/TraculaStatFiles/lh.cst_AS.overall.pathstats.list & }}} The following command will create a table with all the subjects specified in the lh.cst_AS.overall.pathstats file and all the diffusion measures from '''pathstats.overall.txt''' for each subject. {{{ tractstats2table --load-pathstats-from-file $TUTORIAL_DATA/diffusion_tutorial/TraculaStatFiles/lh.cst_AS.overall.pathstats.list --overall --tablefile $TUTORIAL_DATA/diffusion_tutorial/TraculaStatFiles/lh.cst_AS.All.table }}} We've generated tables of all Diffusion measures for the 3 tutorial subjects for all the 18 tracts. They can be found here: {{{ ls $TUTORIAL_DATA/diffusion_tutorial/TraculaStatFiles/*.All.table }}} |
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| ---- {{{ tractstats2table --load-pathstats-from-file $TUTORIAL_DATA/diffusion_tutorial/TraculaGLM/LesionStudy/lh_cst_priorcvs_overall_pathstats --overall --only-measures FA_Avg --tablefile LH.CST.FA.Priorcvs.table }}} ---- You can look at these tables in OpenOffice's spreadsheet program. For example, to open the table '''LH.CST.All.Priorcvs.table''' in a spreadsheet, do the following: ---- {{{ oocalc $TUTORIAL_DATA/diffusion_tutorial/TraculaGLM/LesionStudy/LH.CST.All.Priorcvs.table (Not sure if this will be the final directory...things may have moved around by weekend) }}} ---- |
{{{ tractstats2table --load-pathstats-from-file $TUTORIAL_DATA/diffusion_tutorial/TraculaStatFiles/lh.cst_AS.overall.pathstats.list --overall --only-measures FA_Avg --tablefile $TUTORIAL_DATA/diffusion_tutorial/TraculaStatFiles/lh.cst_AS.FA_Avg.table }}} 1. Note the use of the --only-measures flag again. 1. --load-pathstats-from-file will load the statistics from all the subjects specific in lh.cst_AS.overall.pathstats.list file 1. The FA_Avg parameter for the --only-measures flag can be replaced with other measures specified in pathstats.overall.txt file You can look at these tables in !OpenOffice (or any other spreadsheet program). For example, to open the table '''lh.cst_AS.All.table''' in !OpenOffice, do the following: {{{ oocalc $TUTORIAL_DATA/diffusion_tutorial/TraculaStatFiles/lh.cst_AS.All.table }}} From here, you could use these stats files to run a group analysis on the tracts. [[FsTutorial/Diffusion|Top]] | [[FsTutorial/TraculaOutputs|Previous]] |
Tract statistics
Remember...
For each new terminal that you open, you must do:
setenv SUBJECTS_DIR $TUTORIAL_DATA/diffusion_recons cd $TUTORIAL_DATA/diffusion_tutorial
This section of the tutorial will teach you how to extract statistics on anisotropy and diffusivity measures for the white-matter pathways reconstructed by TRACULA. There are two types of statistics files that are created for each white-matter tract:
- pathstats.overall.txt - This file contains measures averaged over the whole tract
- pathstats.byvoxel.txt - This files contains measures as a function of location along the trajectory of the tract.
To view the statistics files from TRACULA for the left corticospinal tract of subject elmo.2012, cd into one subject's directory where the stats are located for this specific tract:
cd $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.cst_AS_avg33_mni_bbr
pathstats.overall.txt
You can view the overall path stats by doing:
gedit $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt &
This file will look like this:
# Title Pathway Statistics # # generating_program /usr/local/freesurfer/dev/bin/dmri_pathstats # cvs_version # cmdline /usr/local/freesurfer/dev/bin/dmri_pathstats --intrc /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr --dtbase /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dmri/dtifit --path lh.ilf --subj elmo.2012 --out /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.overall.txt --outvox /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.byvoxel.txt # sysname Linux # hostname compute-0-29 # machine x86_64 # user ayendiki # anatomy_type pathway # # subjectname elmo.2012 # pathwayname lh.ilf # Count 1500 Volume 167 Len_Min 29 Len_Max 64 Len_Avg 45.008 Len_Center 37 AD_Avg 0.00131194 AD_Avg_Weight 0.00139891 AD_Avg_Center 0.001268 RD_Avg 0.000686486 RD_Avg_Weight 0.000770628 RD_Avg_Center 0.000635293 MD_Avg 0.00089497 MD_Avg_Weight 0.000980054 MD_Avg_Center 0.000846196 FA_Avg 0.414059 FA_Avg_Weight 0.392266 FA_Avg_Center 0.408256
This text file contains various diffusion measures, averaged over the entire white-matter tract. The measures include:
- Number of sample paths in the WM tract
- Tract volume (in voxels)
- Maximum, minimum and average length of sample paths
- Length of the highest-probability (a.k.a. maximum a posteriori) path
- Axial diffusivity (average over the entire support of the path distribution, weighted average over the entire support of the path distribution, and average over highest-probability path only)
- Radial diffusivity (as above)
- Mean diffusivity (as above)
- Fractional anisotropy (as above)
pathstats.byvoxel.txt
Now take a look at the stats as a function of position along the trajectory of the tract:
gedit $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.byvoxel.txt &
It will look like this:
# Title Pathway Statistics # # generating_program /usr/local/freesurfer/dev/bin/dmri_pathstats # cvs_version # cmdline /usr/local/freesurfer/dev/bin/dmri_pathstats --intrc /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr --dtbase /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dmri/dtifit --path lh.ilf --subj elmo.2012 --out /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.overall.txt --outvox /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.byvoxel.txt # sysname Linux # hostname compute-0-29 # machine x86_64 # user ayendiki # anatomy_type pathway # # subjectname elmo.2012 # pathwayname lh.ilf # # pathway start x y z AD RD MD FA AD_Avg RD_Avg MD_Avg FA_Avg 86 71 16 0.00124639 0.000810355 0.000955702 0.296343 0.00124166 0.000683586 0.000869599 0.375502 86 72 15 0.000758499 0.000690337 0.000713058 0.0665528 0.00120352 0.000674202 0.00085063 0.365702 85 72 14 0.000819579 0.000601256 0.00067403 0.196614 0.00111348 0.000618912 0.00078378 0.353662 84 72 13 0.000970979 0.00067094 0.000770953 0.227346 0.00115739 0.000679319 0.000838683 0.329086 84 71 13 0.0010519 0.000845654 0.000914402 0.174291 0.00117946 0.000675255 0.000843332 0.342993 84 70 13 0.00122524 0.00075747 0.000913395 0.295734 0.00127004 0.000700568 0.00089039 0.368428 84 69 13 0.0013762 0.000607907 0.000864005 0.475513 0.00130121 0.000666051 0.000877759 0.405086 83 68 14 0.00117165 0.000572571 0.000772264 0.433612 0.00127088 0.000631783 0.000844803 0.427719 83 67 14 0.00122987 0.000573616 0.000792367 0.452554 0.00123866 0.000625767 0.000830053 0.422219 83 66 14 0.00120132 0.000599483 0.000800095 0.411401 0.00118774 0.00062832 0.000814796 0.408966 83 65 14 0.00130532 0.000741545 0.000929471 0.341101 0.00117765 0.000649599 0.000825623 0.38951 83 64 15 0.00113069 0.000744614 0.000873306 0.303024 0.00124994 0.000716112 0.000894054 0.35574 83 63 15 0.00145392 0.000843014 0.00104665 0.338389 0.00160184 0.000956015 0.00117128 0.342898 83 62 15 0.00150758 0.000704525 0.000972208 0.454268 0.00184354 0.00110231 0.0013494 0.361096 82 61 15 0.00168556 0.000719335 0.00104141 0.500387 0.00187725 0.00105482 0.00132898 0.413339 82 60 16 0.00149165 0.000655993 0.000934546 0.482961 0.00174103 0.000915708 0.00119082 0.459582 82 59 16 0.00178469 0.000676534 0.00104592 0.547817 0.00181009 0.000942766 0.00123188 0.47797 82 58 16 0.00187731 0.000555021 0.000995783 0.650825 0.00176598 0.000879462 0.00117498 0.482668 82 57 17 0.00136583 0.000342585 0.000683666 0.706805 0.00183719 0.00101521 0.00128919 0.444575 82 56 17 0.00149454 0.000361014 0.000738857 0.718399 0.00172875 0.000879471 0.00116258 0.466697 82 55 17 0.00164246 0.000404404 0.000817091 0.714028 0.00143606 0.000654734 0.000915172 0.485324 81 54 17 0.00110069 0.000505138 0.000703656 0.462108 0.00123971 0.000546461 0.000777551 0.491684 81 53 18 0.00149581 0.000503958 0.000834577 0.601599 0.00138836 0.000547033 0.000827479 0.539068 81 52 18 0.00130913 0.000454745 0.00073954 0.597531 0.00133457 0.000539894 0.000804789 0.533393 81 51 18 0.00131507 0.000631822 0.000859572 0.448947 0.00131177 0.000606845 0.000841826 0.469117 81 50 18 0.00135444 0.000747886 0.000950069 0.362522 0.00129975 0.000659834 0.000873148 0.416883 81 49 18 0.00120955 0.000643043 0.000831879 0.404422 0.00126551 0.00064144 0.000849466 0.418424 80 48 19 0.00140649 0.000619495 0.000881827 0.476057 0.00134196 0.000607405 0.000852266 0.47251 80 47 19 0.00124703 0.00054436 0.000778584 0.493392 0.00129913 0.000595745 0.000830194 0.470203 80 46 19 0.00123713 0.000562425 0.000787325 0.473597 0.00131166 0.000608192 0.000842689 0.465411 80 45 19 0.00131702 0.000638351 0.000864576 0.436198 0.00131184 0.000638683 0.000863079 0.443722 79 44 20 0.000961184 0.000655564 0.000757438 0.251941 0.00120554 0.000691043 0.000862543 0.349984 79 43 20 0.00104516 0.000760429 0.000855339 0.211843 0.00118236 0.000713172 0.000869568 0.323664 79 42 20 0.0010671 0.000695726 0.000819518 0.290868 0.00118518 0.000688767 0.000854257 0.347132 79 41 20 0.000951325 0.000643122 0.000745857 0.290616 0.00115072 0.000662836 0.000825473 0.352023 80 40 20 0.00111846 0.000771887 0.00088741 0.232294 0.00118544 0.000701789 0.000863008 0.328079 81 40 20 0.000989299 0.000649715 0.00076291 0.283576 0.00114976 0.000669422 0.000829546 0.343642 # pathway end
This text file contains various diffusion measures, one row for each position along the trajectory of the path. The first three entries in each row are the x, y, z coordinates in native diffusion space. The next four entries are the axial diffusivity, radial diffusivity, mean diffusivity, and fractional anisotropy at that position on the maximum a posteriori path. The last four entries are the axial diffusivity, radial diffusivity, mean diffusivity, and fractional anisotropy at the same position, averaged over all sampled paths.
Converting pathstats.overall.txt to a table
Measures can be extracted from these files to be analyzed further, e.g., for tract-based group analysis. Specifically, the text files can be converted into a table using the command tractstats2table for doing GLM analyses using mri_glmfit or any other statistical software (SPSS, Excel, Statview etc.)
To extract all diffusion measures for the left corticospinal tract into a table do the following:
tractstats2table --inputs $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt --overall --tablefile $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.cst_AS_avg33_mni_bbr/lh.cst_AS.All.table
- The argument to the --inputs option specifies the input stats file.
- The --overall option tells tractstats2table to expect the overall path stats file (stats averaged over the entire left CST), as opposed to the stats along the trajectory of the tract (which would be specified with the --byvoxel option instead).
- The argument to the --tablefile option specifies the output file.
Take a look at the resulting table file:
gedit $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.cst_AS_avg33_mni_bbr/lh.cst_AS.All.table &
Instead of extracting all the measures from pathstats.overall.txt for CST, we could extract only a few specific measures. For example, to extract only the average FA along the left corticospinal tract, do the following:
tractstats2table --inputs $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt --overall --only-measures FA_Avg --tablefile $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.cst_AS_avg33_mni_bbr/lh.cst_AS.FA_Avg.table
- Here the --only-measures option followed by FA_Avg was used to indicate we are only interested in having the average FA over the path in table format for this tract.
Take a look at the resulting table file:
gedit $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.cst_AS_avg33_mni_bbr/lh.cst_AS.FA_Avg.table &
For a group analysis that has multiple subjects, tractstats2table can be used to combine all the subjects' diffusion measures from the path.overall.txt files into a single table that can be used for analysis with mri_glmfit or any other statistics software.
An easy way to do this is to create a text file that contains the names of the subjects and paths to their pathstats.overall.txt files. An example is given below:
$TUTORIAL_DATA/diffusion_tutorial/elmo.2005/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt $TUTORIAL_DATA/diffusion_tutorial/elmo.2008/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt
Once this is created and saved as lh.cst_AS.overall.pathstats.list, it can be passed as a parameter to the tractstats2table command. This file has already been created for you. To open this file and view its contents, do the following:
gedit $TUTORIAL_DATA/diffusion_tutorial/TraculaStatFiles/lh.cst_AS.overall.pathstats.list &
The following command will create a table with all the subjects specified in the lh.cst_AS.overall.pathstats file and all the diffusion measures from pathstats.overall.txt for each subject.
tractstats2table --load-pathstats-from-file $TUTORIAL_DATA/diffusion_tutorial/TraculaStatFiles/lh.cst_AS.overall.pathstats.list --overall --tablefile $TUTORIAL_DATA/diffusion_tutorial/TraculaStatFiles/lh.cst_AS.All.table
We've generated tables of all Diffusion measures for the 3 tutorial subjects for all the 18 tracts. They can be found here:
ls $TUTORIAL_DATA/diffusion_tutorial/TraculaStatFiles/*.All.table
To extract only specific measures like FA_Avg, do the following:
tractstats2table --load-pathstats-from-file $TUTORIAL_DATA/diffusion_tutorial/TraculaStatFiles/lh.cst_AS.overall.pathstats.list --overall --only-measures FA_Avg --tablefile $TUTORIAL_DATA/diffusion_tutorial/TraculaStatFiles/lh.cst_AS.FA_Avg.table
- Note the use of the --only-measures flag again.
- --load-pathstats-from-file will load the statistics from all the subjects specific in lh.cst_AS.overall.pathstats.list file
- The FA_Avg parameter for the --only-measures flag can be replaced with other measures specified in pathstats.overall.txt file
You can look at these tables in OpenOffice (or any other spreadsheet program). For example, to open the table lh.cst_AS.All.table in OpenOffice, do the following:
oocalc $TUTORIAL_DATA/diffusion_tutorial/TraculaStatFiles/lh.cst_AS.All.table
From here, you could use these stats files to run a group analysis on the tracts.