Differences between revisions 50 and 57 (spanning 7 versions)
⇤ ← Revision 50 as of 2013-04-25 19:41:17 →
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Editor: AnastasiaYendiki
Comment:
← Revision 57 as of 2013-04-26 01:05:23 → ⇥
Size: 12080
Editor: AnastasiaYendiki
Comment:
Deletions are marked like this. Additions are marked like this.
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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		 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/elmo.2012/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt &
}}}

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:
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# generating_program /usr/local/freesurfer/stable5_1_0/bin/dmri_pathstats # generating_program /usr/local/freesurfer/dev/bin/dmri_pathstats
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# cmdline /usr/local/freesurfer/stable5_1_0/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 # 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 node0305 # hostname compute-0-29
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# user rspriti # user ayendiki
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# subjectname Diff001
# pathwayname lh.cst
#
Count 1000
Volume 327
Len_Min 35
Len_Max 70
Len_Avg 53.119
Len_Center 48
AD_Avg 0.00106102
AD_Avg_Weight 0.00108794
AD_Avg_Center 0.00105527
RD_Avg 0.000438781
RD_Avg_Weight 0.000430744
RD_Avg_Center 0.000441464
MD_Avg 0.000646195
MD_Avg_Weight 0.000649809
MD_Avg_Center 0.000646067
FA_Avg 0.519271
FA_Avg_Weight 0.539241
FA_Avg_Center 0.511358
}}}

This text file contains various diffusion measures, averaged over the entire white-matter tract (in case, left 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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gedit $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.byvoxel.txt &
}}}
It will look something like this:		 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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# generating_program /usr/local/freesurfer/stable5_1_0/bin/dmri_pathstats # generating_program /usr/local/freesurfer/dev/bin/dmri_pathstats
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# cmdline /usr/local/freesurfer/stable5_1_0/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 # 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 node0305 # 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
66 63 13 0.00103657 0.000574918 0.000728804 0.374774
66 63 14 0.00100453 0.000480365 0.000655088 0.478045
67 64 15 0.000816154 0.000359865 0.000511961 0.547635
67 64 16 0.000946625 0.000421327 0.000596426 0.521222
68 64 17 0.000967142 0.000305692 0.000526175 0.646745
68 64 18 0.00114626 0.000333594 0.000604484 0.658591
69 65 19 0.00152806 0.000740932 0.00100331 0.426333
69 65 20 0.00126399 0.000470638 0.000735089 0.57121
69 65 21 0.00140243 0.000482392 0.000789071 0.611696
70 65 21 0.00143949 0.000480912 0.000800438 0.618516
70 65 22 0.00116007 0.000156374 0.000490939 0.858895
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
73 66 31 0.00108715 0.000344163 0.000591825 0.649467
74 66 32 0.00124634 0.000386429 0.000673065 0.632008
74 65 33 0.00117648 0.000367445 0.000637124 0.632389
75 65 34 0.00121643 0.000516448 0.000749775 0.502467
75 65 35 0.00104831 0.000392371 0.000611016 0.558318
75 65 36 0.00104016 0.00040752 0.0006184 0.55437
76 64 37 0.00119495 0.000322181 0.000613105 0.688909
76 64 38 0.00105691 0.000334124 0.000575053 0.64994
76 64 39 0.00104479 0.000417371 0.000626511 0.542088
77 64 40 0.000869351 0.000385416 0.000546728 0.477069
77 63 40 0.00090553 0.000409442 0.000574804 0.47172
77 63 41 0.000867782 0.000433106 0.000577998 0.41296
77 63 42 0.000840253 0.000521921 0.000628032 0.287828
77 63 43 0.000805146 0.000489529 0.000594735 0.301222
77 62 44 0.000815787 0.000565983 0.000649251 0.224909
76 62 45 0.000854533 0.000567732 0.000663332 0.252796
76 61 46 0.000677428 0.00050014 0.000559236 0.193441
75 61 46 0.000882752 0.000537658 0.000652689 0.310019
75 60 47 0.000851777 0.000522 0.000631926 0.327071
74 60 48 0.000996004 0.000448845 0.000631231 0.488575
74 60 49 0.000957188 0.000488566 0.000644774 0.472547
73 59 50 0.000977348 0.000519754 0.000672285 0.429989
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 59 54 0.000982003 0.000566492 0.000704996 0.387962
71 58 55 0.00100269 0.00063635 0.000758462 0.300433
70 58 55 0.000978019 0.00032538 0.000542926 0.615096
70 58 56 0.000888766 0.000442273 0.000591104 0.424031		 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.
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.
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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
}}}
 1. The argument to the --inputs option specifies the input stats file.
 1. 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).
 1. The argument to the --tablefile option specifies the output file.		 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}}} and then used for doing GLM analyses with [[mri_glmfit]] or any other statistical software (SPSS, Excel, Statview etc.)

To extract all diffusion measures for the left inferior longitudinal fasciculus from subject elmo.2012 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/lh.ilf.elmo.2012.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.
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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 grab just 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
}}}
 1. 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.		 gedit $TUTORIAL_DATA/diffusion_tutorial/lh.ilf.elmo.2012.All.table &
}}}

For a group analysis, {{{tractstats2table}}} can be used to combine the diffusion measures in path.overall.txt from multiple subjects into a single table, which can then be used for analysis with [[mri_glmfit]] or any other statistical software.

To do this, you will have to create a text file that lists the full path to every subject's pathstats.overall.txt file. An example of such a list for all 3 tutorial subjects is shown 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
}}}

Create a text file that contains the list above and name it as follows:

{{{
gedit $TUTORIAL_DATA/diffusion_tutorial/lh.ilf.list &
}}}

The following command will use this list to create a table with the diffusion measures from all the files listed above:

{{{
tractstats2table --load-pathstats-from-file $TUTORIAL_DATA/diffusion_tutorial/lh.ilf.list --overall --tablefile $TUTORIAL_DATA/diffusion_tutorial/lh.ilf.All.table
}}}
 * The argument to the --load-pathstats-from-file option specifies the text file that contains the list of all the statistics files that will be loaded.
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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
}}}
 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.		 gedit $TUTORIAL_DATA/diffusion_tutorial/lh.ilf.All.table &
}}}

Instead of extracting all measures included in the tract statistics files, we may be interested only in a few specific measures. For example, to extract only the average FA for each subject, do the following:

{{{
tractstats2table --load-pathstats-from-file $TUTORIAL_DATA/diffusion_tutorial/lh.ilf.list --overall --only-measures FA_Avg --tablefile $TUTORIAL_DATA/diffusion_tutorial/lh.ilf.FA_Avg.table
}}}
 * The argument to the --only-measures option specifies which measure we want to extract from the statistics files. Instead of FA_Avg, this could be the name of any of the measures included in pathstats.overall.txt.

You can look at these tables in !OpenOffice (or any other spreadsheet program). For example, to open the table '''lh.ilf.All.table''' in !OpenOffice, do the following:

{{{
oocalc $TUTORIAL_DATA/diffusion_tutorial/lh.ilf.All.table
}}}
From here, you could use these stats tables to run a group analysis on the tracts.

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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 and then used for doing GLM analyses with mri_glmfit or any other statistical software (SPSS, Excel, Statview etc.)

To extract all diffusion measures for the left inferior longitudinal fasciculus from subject elmo.2012 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/lh.ilf.elmo.2012.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/lh.ilf.elmo.2012.All.table &

For a group analysis, tractstats2table can be used to combine the diffusion measures in path.overall.txt from multiple subjects into a single table, which can then be used for analysis with mri_glmfit or any other statistical software.

To do this, you will have to create a text file that lists the full path to every subject's pathstats.overall.txt file. An example of such a list for all 3 tutorial subjects is shown 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

Create a text file that contains the list above and name it as follows: 

gedit $TUTORIAL_DATA/diffusion_tutorial/lh.ilf.list &

The following command will use this list to create a table with the diffusion measures from all the files listed above: 

tractstats2table --load-pathstats-from-file $TUTORIAL_DATA/diffusion_tutorial/lh.ilf.list --overall --tablefile $TUTORIAL_DATA/diffusion_tutorial/lh.ilf.All.table
  • The argument to the --load-pathstats-from-file option specifies the text file that contains the list of all the statistics files that will be loaded.

Take a look at the resulting table file: 

gedit $TUTORIAL_DATA/diffusion_tutorial/lh.ilf.All.table &

Instead of extracting all measures included in the tract statistics files, we may be interested only in a few specific measures. For example, to extract only the average FA for each subject, do the following: 

tractstats2table --load-pathstats-from-file $TUTORIAL_DATA/diffusion_tutorial/lh.ilf.list --overall --only-measures FA_Avg --tablefile $TUTORIAL_DATA/diffusion_tutorial/lh.ilf.FA_Avg.table
  • The argument to the --only-measures option specifies which measure we want to extract from the statistics files. Instead of FA_Avg, this could be the name of any of the measures included in pathstats.overall.txt.

You can look at these tables in OpenOffice (or any other spreadsheet program). For example, to open the table lh.ilf.All.table in OpenOffice, do the following: 

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

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

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