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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 you will see something like this:
Line 32: Line 35:
# generating_program $FREESURFER_HOME/bin/dmri_pathstats # generating_program /usr/local/freesurfer/stable5_1_0/bin/dmri_pathstats
Line 34: Line 37:
# 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/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
Line 36: Line 39:
# hostname compute-0-1.local # hostname node0305
Line 44: Line 47:
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
----
{{{
 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:

 * 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 something like this:

{{{
Line 72: Line 89:
# generating_program $FREESURFER_HOME/dmri_pathstats # generating_program /usr/local/freesurfer/stable5_1_0/bin/dmri_pathstats
Line 74: Line 91:
# 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/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
Line 76: Line 93:
# hostname compute-0-1.local # hostname node0305
Line 86: Line 103:
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		 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
Line 101: Line 115:
71 66 23 0.00136252 0.000330065 0.000674217 0.721118
Line 104: Line 117:
72 66 26 0.00106165 0.000357968 0.000592529 0.650427 71 66 26 0.00111074 0.000307493 0.000575241 0.693343
Line 106: Line 119:
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		 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
Line 117: Line 130:
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		 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
Line 125: Line 140:
74 61 47 0.00100985 0.00048457 0.000659663 0.436199
74 61 48 0.00104135 0.000461786 0.000654973 0.482846		 75 60 47 0.000851777 0.000522 0.000631926 0.327071
74 60 48 0.000996004 0.000448845 0.000631231 0.488575
Line 128: Line 143:
73 60 50 0.00100422 0.00055232 0.000702954 0.378698
73 60 51 0.000938077 0.000492242 0.000640854 0.429111		 73 59 50 0.000977348 0.000519754 0.000672285 0.429989
73 59 51 0.00104383 0.000519813 0.000694486 0.428315
Line 132: Line 147:
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		 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
Line 141: Line 153:
----

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)

To convert the path.overall.txt for the above tract into a table that can be used by mri_glmfit, do the following

----
{{{
cd $TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/5cpts/priorcvs/seg14/initmni/regbbr/lh.cst_AS_avg23_cvs_bbr/
 
# To extract all diffusion measures into a table do the following

tractstats2table 		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.

=== 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
}}}
 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.

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 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.

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
}}}
 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]]

Top | 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 you will see something like this: 

# Title Pathway Statistics
#
# generating_program /usr/local/freesurfer/stable5_1_0/bin/dmri_pathstats
# cvs_version 
# 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 
# sysname Linux
# hostname node0305
# machine x86_64
# user rspriti
# anatomy_type pathway
#
# 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:

  • 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 something like this: 

# Title Pathway Statistics
#
# generating_program /usr/local/freesurfer/stable5_1_0/bin/dmri_pathstats
# cvs_version 
# 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 
# sysname Linux
# hostname node0305
# machine x86_64
# user rspriti
# anatomy_type pathway
#
# subjectname Diff001
# pathwayname lh.cst
#
# pathway start
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
# pathway end

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.

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
  1. The argument to the --inputs option specifies the input stats file.
  2. 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).
  3. 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 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.

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
  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.cst_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.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.

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