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= Tract Statistics = = Tract statistics =
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This section of the tutorial will teach you how to extract statistical measures for the major white-matter tracts 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 WM tract
 * pathstats.byvoxel.txt - This files contains measures as a function of location along the length of the WM tract.

To view the statistics files from TRACULA for the left cortico-spinal tract of subject Diff001, {{{cd}}} into one subject's directory where the stats are located for this specific tract:

{{{
cd $TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/lh.cst_AS_avg32_mni_flt		 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 inferior longitudinal fasciculus 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.ilf_AS_avg33_mni_bbr
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gedit $TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/lh.cst_AS_avg32_mni_flt/pathstats.overall.txt &
}}}
Note that lines preceded by the # sign are "commented out". When looking at this file you will see something like this:		 gedit $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.overall.txt &
}}}

This file will look like this:
Line 35: Line 36:
# cvs_version
# cmdline /usr/local/freesurfer/dev/bin/dmri_pathstats --intrc /autofs/cluster/f
reesurfer/subjects/diffusion_tutorial/Diff001/dpath/5cpts/priormni/seg14/initmni
/regflt/lh.cst_AS_avg32_mni_flt --dtbase /autofs/cluster/freesurfer/subjects/dif
fusion_tutorial/Diff001/dmri/dtifit --path lh.cst --subj Diff001 --out /autofs/c
luster/freesurfer/subjects/diffusion_tutorial/Diff001/dpath/5cpts/priormni/seg14
/initmni/regflt/lh.cst_AS_avg32_mni_flt/pathstats.overall.txt --outvox /autofs/c
luster/freesurfer/subjects/diffusion_tutorial/Diff001/dpath/5cpts/priormni/seg14
/initmni/regflt/lh.cst_AS_avg32_mni_flt/pathstats.byvoxel.txt		 # 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 
Line 45: Line 39:
# hostname compute-0-10.local # hostname compute-0-29
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# subjectname Diff001
# pathwayname lh.cst
#
Count 400
Volume 416
Len_Min 44
Len_Max 83
Len_Avg 59.0325
Len_Center 55
AD_Avg 0.00103
AD_Avg_Weight 0.00105892
AD_Avg_Center 0.00104386
RD_Avg 0.00047195
RD_Avg_Weight 0.000461937
RD_Avg_Center 0.000487178
MD_Avg 0.000657965
MD_Avg_Weight 0.000660932
MD_Avg_Center 0.000672737
FA_Avg 0.472827
FA_Avg_Weight 0.495202
FA_Avg_Center 0.457536
}}}
This text file contains various diffusion measures, averaged over the entire white-matter tract (for CST). The measures include:		 # 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:
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Now take a look at the by voxel stats:

{{{
gedit $TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/lh.cst_AS_avg32_mni_flt/pathstats.byvoxel.txt &
}}}
It will look something like this:		 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.ilf_AS_avg33_mni_bbr/pathstats.byvoxel.txt &
}}}
It will look like this:
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# cvs_version
# cmdline /usr/local/freesurfer/dev/bin/dmri_pathstats --intrc /autofs/cluster/freesurfer/subjects/diffusion_tutorial/Diff001/dpath/5cpts/priormni/seg14/initmni/regflt/lh.cst_AS_avg32_mni_flt --dtbase /autofs/cluster/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dtifit --path lh.cst --subj Diff001 --out /autofs/cluster/freesurfer/subjects/diffusion_tutorial/Diff001/dpath/5cpts/priormni/seg14/initmni/regflt/lh.cst_AS_avg32_mni_flt/pathstats.overall.txt --outvox /autofs/cluster/freesurfer/subjects/diffusion_tutorial/Diff001/dpath/5cpts/priormni/seg14/initmni/regflt/lh.cst_AS_avg32_mni_flt/pathstats.byvoxel.txt		 # 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 
Line 98: Line 93:
# hostname compute-0-10.local # hostname compute-0-29
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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
64 63 9 0.000948384 0.00073031 0.000803001 0.208943
64 63 10 0.000925661 0.000457926 0.000613837 0.421615
65 63 11 0.000894246 0.000381521 0.000552429 0.498782
66 64 12 0.000968373 0.000502922 0.000658072 0.433094
66 64 13 0.000863534 0.000414835 0.000564402 0.461517
66 64 14 0.000770136 0.000358582 0.000495767 0.49394
67 64 15 0.000816154 0.000359865 0.000511961 0.547635
67 65 16 0.000948329 0.000367791 0.000561303 0.547419
68 65 17 0.00106946 0.000358134 0.000595243 0.606953
68 65 18 0.00151718 0.000592101 0.000900461 0.534194
68 65 19 0.00135883 0.000377419 0.000704556 0.675608
69 65 20 0.00126399 0.000470638 0.000735089 0.57121
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 24 0.00134187 0.000385197 0.000704089 0.678151
71 66 25 0.00108983 0.000289931 0.000556565 0.729769
71 66 26 0.00111074 0.000307493 0.000575241 0.693343
72 66 27 0.00117242 0.000398032 0.00065616 0.619191
72 66 28 0.00118738 0.000448541 0.000694819 0.568624
73 66 29 0.00116659 0.000379914 0.000642141 0.613363
73 66 30 0.00121899 0.000442094 0.000701061 0.578963
74 66 31 0.00122871 0.000405738 0.000680061 0.61046
74 66 32 0.00124634 0.000386429 0.000673065 0.632008
74 66 33 0.00114455 0.000346198 0.000612314 0.645275
75 66 34 0.00112261 0.000553555 0.000743239 0.42294
75 66 35 0.00110073 0.00039228 0.000628431 0.585723
75 66 36 0.00107757 0.000424713 0.000642332 0.547048
76 65 37 0.00118618 0.000364568 0.000638438 0.650797
76 65 38 0.00110045 0.000451365 0.000667728 0.549521
76 65 39 0.00106488 0.000434208 0.000644432 0.531777
77 65 40 0.000936571 0.000390726 0.000572674 0.504019
78 65 41 0.000790065 0.000547796 0.000628552 0.222685
79 64 41 0.000737992 0.000527606 0.000597735 0.200474
78 63 42 0.000864033 0.000533149 0.000643444 0.291817
78 63 43 0.000783214 0.000517068 0.000605783 0.256042
77 63 43 0.000805146 0.000489529 0.000594735 0.301222
77 62 44 0.000815787 0.000565983 0.000649251 0.224909
77 62 45 0.000750971 0.000602391 0.000651918 0.156881
76 62 45 0.000854533 0.000567732 0.000663332 0.252796
76 61 46 0.000677428 0.00050014 0.000559236 0.193441
75 61 47 0.000852325 0.000501722 0.00061859 0.339727
75 60 48 0.000760404 0.000537457 0.000611772 0.313612
74 60 49 0.000957188 0.000488566 0.000644774 0.472547
74 60 50 0.000904047 0.000427675 0.000586466 0.445552
73 59 51 0.00104383 0.000519813 0.000694486 0.428315
72 59 52 0.00104503 0.000475882 0.000665599 0.474443
72 59 53 0.00091483 0.00047261 0.000620017 0.409087
71 58 54 0.00108069 0.00052145 0.000707864 0.442797
71 58 55 0.00100269 0.00063635 0.000758462 0.300433
70 57 56 0.00104198 0.000577465 0.000732302 0.371814
70 57 57 0.000988028 0.000735057 0.000819381 0.208577
69 57 58 0.00118052 0.000811759 0.00093468 0.224508
69 56 59 0.00139945 0.00114833 0.00123204 0.117485
68 56 60 0.00123777 0.000847968 0.000977904 0.246951		 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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This text file contains various diffusion measures in each voxel along the highest-probability path. The first three entries in each row are the x, y, z coordinates of the voxel. The remaining entries are the axial diffusivity, radial diffusivity, mean diffusivity, and fractional anisotropy at that voxel.

=== pathstats.overall.txt to Table Conversion ===
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 Left Cortico-Spinal tract into a table do the following:

{{{
tractstats2table --inputs $TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/lh.cst_AS_avg32_mni_flt/pathstats.overall.txt --overall --tablefile $TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/lh.cst_AS_avg32_mni_flt/lh.cst_AS.All.table
}}}
 1. Notice we have specified the stats file with --inputs.
 1. The --overall flag tells tractstats2table to expect the overall path stats file (stats averaged over the entire WM tract) as opposed to the per voxel stats (specified with the --byvoxel flag instead).
 1. The output file will be called Diff001_LH.CST.All.table as specified by the --tablefile flag.
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 inferior longitudinal fasciculus into a table do the following:

{{{
tractstats2table --inputs $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.overall.txt --overall --tablefile $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr/lh.ilf_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 inferior longitudinal fasciculus), 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.
Line 182: Line 160:
gedit $TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/lh.cst_AS_avg32_mni_flt/lh.cst_AS.All.table &
}}}
Instead of extracting all the measures from pathstats.overall.txt for CST, we could grab just a few specific measures. For example, to extract only the Average Fractional Anisotropy along the Left Cortico-spinal tract, do the following:

{{{
tractstats2table --inputs $TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/lh.cst_AS_avg32_mni_flt/pathstats.overall.txt --overall --only-measures FA_Avg --tablefile $TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/lh.cst_AS_avg32_mni_flt/lh.cst_AS.FA_Avg.table
}}}
 1. Notice the --only-measures flag followed by FA_Avg to indicate we are only interested in having the average FA over the path in table format for this path (Left CST).		 gedit $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr/lh.ilf_AS.All.table &
}}}
Instead of extracting all the measures from pathstats.overall.txt, we could extract only a few specific measures. For example, to extract only the average FA along the left inferior longitudinal fasciculus, do the following:

{{{
tractstats2table --inputs $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.overall.txt --overall --only-measures FA_Avg --tablefile $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr/lh.ilf_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.
Line 194: Line 172:
gedit $TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/lh.cst_AS_avg32_mni_flt/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 CST path.overall.txt files into a single table that can be used for analysis with mri_glmfit or any other statistics software		 gedit $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr/lh.ilf_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.
Line 201: Line 179:
$TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/lh.cst_AS_avg32_mni_flt/pathstats.overall.txt
$TUTORIAL_DATA/diffusion_tutorial/Diff002/dpath/lh.cst_AS_avg32_mni_flt/pathstats.overall.txt
$TUTORIAL_DATA/diffusion_tutorial/Diff003/dpath/lh.cst_AS_avg32_mni_flt/pathstats.overall.txt
$TUTORIAL_DATA/diffusion_tutorial/Diff004/dpath/lh.cst_AS_avg32_mni_flt/pathstats.overall.txt
$TUTORIAL_DATA/diffusion_tutorial/Diff005/dpath/lh.cst_AS_avg32_mni_flt/pathstats.overall.txt
$TUTORIAL_DATA/diffusion_tutorial/Diff006/dpath/lh.cst_AS_avg32_mni_flt/pathstats.overall.txt
$TUTORIAL_DATA/diffusion_tutorial/Diff007/dpath/lh.cst_AS_avg32_mni_flt/pathstats.overall.txt
$TUTORIAL_DATA/diffusion_tutorial/Diff008/dpath/lh.cst_AS_avg32_mni_flt/pathstats.overall.txt
$TUTORIAL_DATA/diffusion_tutorial/Diff009/dpath/lh.cst_AS_avg32_mni_flt/pathstats.overall.txt
$TUTORIAL_DATA/diffusion_tutorial/Diff010/dpath/lh.cst_AS_avg32_mni_flt/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 it's 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 10 tutorial subjects for all the 18 tracts. They can be found here:

{{{
ls $TUTORIAL_DATA/diffusion_tutorial/TraculaStatFiles/*.All.table		 $TUTORIAL_DATA/diffusion_tutorial/elmo.2005/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.overall.txt
$TUTORIAL_DATA/diffusion_tutorial/elmo.2008/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.overall.txt
$TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.overall.txt

}}}
Once this is created and saved as lh.ilf_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/lh.ilf_AS.overall.pathstats.list &
}}}
The following command will create a table with all the subjects specified in the lh.ilf_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/lh.ilf_AS.overall.pathstats.list --overall --tablefile $TUTORIAL_DATA/diffusion_tutorial/lh.ilf_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/*.All.table
Line 231: Line 203:
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 tractstats2table --load-pathstats-from-file $TUTORIAL_DATA/diffusion_tutorial/lh.ilf_AS.overall.pathstats.list --overall --only-measures FA_Avg --tablefile $TUTORIAL_DATA/diffusion_tutorial/lh.ilf_AS.FA_Avg.table
Line 234: Line 206:
 1. --load-pathstats-from-file will load the statistics from all the subjects specific in lh.cst_AS.overall.pathstats.list file  1. --load-pathstats-from-file will load the statistics from all the subjects specific in lh.ilf_AS.overall.pathstats.list file
Line 237: Line 209:
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		 You can look at these tables in !OpenOffice (or any other spreadsheet program). For example, to open the table '''lh.ilf_AS.All.table''' in !OpenOffice, do the following:

{{{
oocalc $TUTORIAL_DATA/diffusion_tutorial/lh.ilf_AS.All.table

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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 inferior longitudinal fasciculus 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.ilf_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.ilf_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.ilf_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 inferior longitudinal fasciculus into a table do the following: 

tractstats2table --inputs $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.overall.txt --overall --tablefile $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr/lh.ilf_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 inferior longitudinal fasciculus), 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.ilf_AS_avg33_mni_bbr/lh.ilf_AS.All.table &

Instead of extracting all the measures from pathstats.overall.txt, we could extract only a few specific measures. For example, to extract only the average FA along the left inferior longitudinal fasciculus, do the following: 

tractstats2table --inputs $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.overall.txt --overall --only-measures FA_Avg --tablefile $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr/lh.ilf_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.ilf_AS_avg33_mni_bbr/lh.ilf_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.ilf_AS_avg33_mni_bbr/pathstats.overall.txt
$TUTORIAL_DATA/diffusion_tutorial/elmo.2008/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.overall.txt
$TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.overall.txt

Once this is created and saved as lh.ilf_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/lh.ilf_AS.overall.pathstats.list &

The following command will create a table with all the subjects specified in the lh.ilf_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/lh.ilf_AS.overall.pathstats.list --overall --tablefile $TUTORIAL_DATA/diffusion_tutorial/lh.ilf_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/*.All.table

To extract only specific measures like FA_Avg, do the following: 

tractstats2table --load-pathstats-from-file $TUTORIAL_DATA/diffusion_tutorial/lh.ilf_AS.overall.pathstats.list --overall --only-measures FA_Avg --tablefile $TUTORIAL_DATA/diffusion_tutorial/lh.ilf_AS.FA_Avg.table
  1. Note the use of the --only-measures flag again.
  2. --load-pathstats-from-file will load the statistics from all the subjects specific in lh.ilf_AS.overall.pathstats.list file
  3. 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.ilf_AS.All.table in OpenOffice, do the following: 

oocalc $TUTORIAL_DATA/diffusion_tutorial/lh.ilf_AS.All.table

From here, you could use these stats files to run a group analysis on the tracts.

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FsTutorial/TraculaStatistics (last edited 2023-07-17 02:37:25 by AnastasiaYendiki)