Differences between revisions 53 and 54
Deletions are marked like this. Additions are marked like this.
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This file you will see something like this: This file will look like this:
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# cmdline /usr/local/freesurfer/dev/bin/dmri_pathstats --intrc /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dpath/lh.cst_AS_avg33_mni_bbr --dtbase /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dmri/dtifit --path lh.cst --subj elmo.2012 --out /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt --outvox /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.byvoxel.txt # cmdline /usr/local/freesurfer/dev/bin/dmri_pathstats --intrc /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr --dtbase /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dmri/dtifit --path lh.ilf --subj elmo.2012 --out /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.overall.txt --outvox /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.byvoxel.txt
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# pathwayname lh.cst # pathwayname lh.ilf
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Volume 715
Len_Min 40
Len_Max 74
Len_Avg 55.5307
Len_Center 54
AD_Avg 0.00122351
AD_Avg_Weight 0.00122372
AD_Avg_Center 0.00130183
RD_Avg 0.000480397
RD_Avg_Weight 0.000459075
RD_Avg_Center 0.000466175
MD_Avg 0.000728101
MD_Avg_Weight 0.000713958
MD_Avg_Center 0.000744727
FA_Avg 0.546698
FA_Avg_Weight 0.567694
FA_Avg_Center 0.580328 		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
Line 84: Line 84:
It will look something like this: It will look like this:
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# cmdline /usr/local/freesurfer/dev/bin/dmri_pathstats --intrc /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dpath/lh.cst_AS_avg33_mni_bbr --dtbase /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dmri/dtifit --path lh.cst --subj elmo.2012 --out /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt --outvox /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.byvoxel.txt # cmdline /usr/local/freesurfer/dev/bin/dmri_pathstats --intrc /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr --dtbase /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dmri/dtifit --path lh.ilf --subj elmo.2012 --out /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.overall.txt --outvox /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.byvoxel.txt
Line 99: Line 99:
# pathwayname lh.cst # pathwayname lh.ilf
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65 57 7 0.00118293 0.000795514 0.000924652 0.29494 0.0012411 0.00065021 0.000847174 0.413312
65 58 8 0.00130461 0.000852312 0.00100308 0.303386 0.00126797 0.00067465 0.00087242 0.414197
66 58 9 0.000987039 0.000420614 0.000609422 0.564201 0.0011978 0.000575463 0.000782904 0.472474
66 58 10 0.000770995 0.000474497 0.00057333 0.511504 0.00116745 0.000572706 0.000770953 0.480807
66 59 10 0.00137465 0.000632992 0.000880213 0.482655 0.00117906 0.000579347 0.000779252 0.479925
67 59 11 0.0016693 0.000669555 0.0010028 0.546244 0.00130553 0.00062593 0.000852463 0.494413
67 60 12 0.00243464 0.00111706 0.00155625 0.455251 0.00174679 0.000866872 0.00116018 0.454145
67 60 13 0.00141842 0.000204362 0.000609048 0.839111 0.00151862 0.000585438 0.000896501 0.584521
68 61 14 0.00161836 0.000331843 0.000760683 0.763616 0.00134348 0.000325355 0.000664734 0.736045
68 61 15 0.00171234 0.000349839 0.000804007 0.774466 0.00136593 0.000278337 0.00064087 0.780897
68 62 16 0.00223797 0.000726919 0.0012306 0.617768 0.00137806 0.000254121 0.000628773 0.797351
69 62 17 0.00146993 -0.000136951 0.000398677 1.08495 0.00124989 0.000258965 0.000589274 0.758698
69 63 18 0.00159246 0.000313279 0.000739672 0.801038 0.00112357 0.000223923 0.000523805 0.763737
69 63 19 0.00133312 0.00056652 0.000822055 0.539529 0.00118196 0.000311433 0.000601611 0.715623
70 63 20 0.00135216 0.000249305 0.000616922 0.801477 0.00120898 0.000283001 0.000591658 0.760807
70 64 21 0.00139644 0.000311688 0.000673274 0.7436 0.00132602 0.000344539 0.0006717 0.713865
70 65 22 0.00134507 0.000401526 0.00071604 0.657404 0.00131613 0.00037062 0.000685787 0.670652
71 65 23 0.00145485 0.000366251 0.000729117 0.712095 0.00134477 0.000361736 0.000689413 0.688727
71 65 24 0.00123012 0.000327556 0.000628411 0.691863 0.00134998 0.000345911 0.000680602 0.700391
72 66 25 0.00143867 0.000401481 0.00074721 0.671129 0.00132081 0.000358823 0.000679491 0.679251
72 66 26 0.00147251 0.00033693 0.000715457 0.736761 0.00133327 0.000361708 0.000685562 0.680079
72 66 27 0.00150811 0.000357167 0.000740813 0.727197 0.00136524 0.00035091 0.00068902 0.697787
73 66 27 0.0015932 0.000392793 0.000792929 0.714821 0.0013719 0.000342011 0.000685308 0.707984
73 66 28 0.00143389 0.000347546 0.000709662 0.733078 0.00138414 0.000346106 0.00069212 0.71024
74 66 29 0.00139097 0.000313104 0.000672393 0.748987 0.00137769 0.000357109 0.000697305 0.699783
75 65 30 0.00138887 0.000296413 0.000660565 0.763204 0.00137445 0.000368675 0.000703935 0.685756
75 65 31 0.00123684 0.000369694 0.000658743 0.661917 0.00132519 0.000388873 0.000700977 0.655551
76 65 31 0.00135921 0.000378914 0.000705678 0.680003 0.00130156 0.000405338 0.000704078 0.633493
76 65 32 0.00127341 0.000386858 0.000682376 0.657603 0.00124293 0.000423528 0.000696662 0.605364
77 64 33 0.00113978 0.000411559 0.000654298 0.60531 0.00116676 0.000471894 0.000703512 0.542952
77 64 34 0.00128087 0.000422854 0.000708858 0.634704 0.00116979 0.000466386 0.000700857 0.546479
77 64 35 0.00119896 0.000503018 0.000734999 0.528921 0.00114853 0.000488113 0.000708253 0.509877
77 64 36 0.00113656 0.000497799 0.00071072 0.496202 0.00110451 0.000510057 0.00070821 0.461135
77 63 37 0.00119198 0.000515275 0.000740843 0.490595 0.00106561 0.000528038 0.000707233 0.419948
77 63 38 0.00104769 0.000504044 0.000685259 0.430811 0.00103929 0.00054131 0.000707305 0.394736
77 63 39 0.000976591 0.000553614 0.000694606 0.344894 0.00101994 0.000555465 0.000710295 0.373869
77 62 39 0.00105097 0.00053899 0.00070965 0.395267 0.00102415 0.00056409 0.000717448 0.370027
76 62 40 0.00108909 0.000598414 0.000761972 0.38261 0.0010056 0.000593542 0.000730896 0.335987
76 62 41 0.000953437 0.000555378 0.000688064 0.332705 0.000985674 0.000578395 0.000714153 0.334102
76 62 42 0.00103198 0.000585098 0.000734059 0.346136 0.0010228 0.000557608 0.00071267 0.37633
75 61 43 0.0013783 0.000493448 0.000788399 0.57846 0.00120485 0.000499852 0.000734854 0.520561
75 61 44 0.0013578 0.00041386 0.000728508 0.648035 0.00126744 0.000461535 0.000730173 0.584945
74 60 45 0.00146392 0.000421628 0.000769059 0.669326 0.00132196 0.000422634 0.00072241 0.640796
74 60 46 0.00139868 0.000468258 0.000778397 0.614758 0.0012875 0.000432798 0.000717696 0.624331
73 60 47 0.00123032 0.000420786 0.000690632 0.605954 0.00119442 0.000450472 0.000698453 0.582006
73 59 48 0.0011713 0.000516378 0.000734685 0.532527 0.00112359 0.000496344 0.000705423 0.516604
72 59 49 0.0010104 0.000479379 0.000656385 0.483854 0.0010846 0.000519347 0.000707763 0.474383
72 58 50 0.00120508 0.000578986 0.000787684 0.481221 0.00112665 0.000555061 0.000745586 0.450731
71 58 51 0.00124094 0.000534655 0.000770084 0.530706 0.00116266 0.000558386 0.000759811 0.45683
71 58 52 0.00120763 0.000423815 0.000685088 0.616712 0.00115987 0.000551248 0.000754122 0.460011
71 57 53 0.00090392 0.000602734 0.00070313 0.261814 0.0011224 0.000608472 0.000779781 0.391306
70 57 54 0.000903407 0.000462753 0.000609638 0.425374 0.00112904 0.000645592 0.000806739 0.375108
69 56 55 0.00080472 0.000352406 0.000503177 0.479572 0.00114323 0.000690293 0.000841274 0.344521
69 56 56 0.00094346 0.000762745 0.000822983 0.141438 0.00115186 0.0007132 0.000859425 0.331727 		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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Tract statistics

Remember...

For each new terminal that you open, you must do: 

setenv SUBJECTS_DIR $TUTORIAL_DATA/diffusion_recons
cd $TUTORIAL_DATA/diffusion_tutorial

This section of the tutorial will teach you how to extract statistics on anisotropy and diffusivity measures for the white-matter pathways reconstructed by TRACULA. There are two types of statistics files that are created for each white-matter tract:

  • pathstats.overall.txt - This file contains measures averaged over the whole tract
  • pathstats.byvoxel.txt - This files contains measures as a function of location along the trajectory of the tract.

To view the statistics files from TRACULA for the left corticospinal tract of subject elmo.2012, cd into one subject's directory where the stats are located for this specific tract: 

cd $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.cst_AS_avg33_mni_bbr

pathstats.overall.txt

You can view the overall path stats by doing: 

gedit $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt &

This file will look like this: 

# Title Pathway Statistics
#
# generating_program /usr/local/freesurfer/dev/bin/dmri_pathstats
# cvs_version 
# cmdline /usr/local/freesurfer/dev/bin/dmri_pathstats --intrc /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr --dtbase /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dmri/dtifit --path lh.ilf --subj elmo.2012 --out /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.overall.txt --outvox /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.byvoxel.txt 
# sysname Linux
# hostname compute-0-29
# machine x86_64
# user ayendiki
# anatomy_type pathway
#
# subjectname elmo.2012
# pathwayname lh.ilf
#
Count 1500
Volume 167
Len_Min 29
Len_Max 64
Len_Avg 45.008
Len_Center 37
AD_Avg 0.00131194
AD_Avg_Weight 0.00139891
AD_Avg_Center 0.001268
RD_Avg 0.000686486
RD_Avg_Weight 0.000770628
RD_Avg_Center 0.000635293
MD_Avg 0.00089497
MD_Avg_Weight 0.000980054
MD_Avg_Center 0.000846196
FA_Avg 0.414059
FA_Avg_Weight 0.392266
FA_Avg_Center 0.408256

This text file contains various diffusion measures, averaged over the entire white-matter tract. The measures include:

  • Number of sample paths in the WM tract
  • Tract volume (in voxels)
  • Maximum, minimum and average length of sample paths
  • Length of the highest-probability (a.k.a. maximum a posteriori) path
  • Axial diffusivity (average over the entire support of the path distribution, weighted average over the entire support of the path distribution, and average over highest-probability path only)
  • Radial diffusivity (as above)
  • Mean diffusivity (as above)
  • Fractional anisotropy (as above)

pathstats.byvoxel.txt

Now take a look at the stats as a function of position along the trajectory of the tract: 

gedit $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.byvoxel.txt &

It will look like this: 

# Title Pathway Statistics
#
# generating_program /usr/local/freesurfer/dev/bin/dmri_pathstats
# cvs_version 
# cmdline /usr/local/freesurfer/dev/bin/dmri_pathstats --intrc /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr --dtbase /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dmri/dtifit --path lh.ilf --subj elmo.2012 --out /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.overall.txt --outvox /space/freesurfer/subjects/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.byvoxel.txt 
# sysname Linux
# hostname compute-0-29
# machine x86_64
# user ayendiki
# anatomy_type pathway
#
# subjectname elmo.2012
# pathwayname lh.ilf
#
# pathway start
x y z AD RD MD FA AD_Avg RD_Avg MD_Avg FA_Avg
86 71 16 0.00124639 0.000810355 0.000955702 0.296343 0.00124166 0.000683586 0.000869599 0.375502
86 72 15 0.000758499 0.000690337 0.000713058 0.0665528 0.00120352 0.000674202 0.00085063 0.365702
85 72 14 0.000819579 0.000601256 0.00067403 0.196614 0.00111348 0.000618912 0.00078378 0.353662
84 72 13 0.000970979 0.00067094 0.000770953 0.227346 0.00115739 0.000679319 0.000838683 0.329086
84 71 13 0.0010519 0.000845654 0.000914402 0.174291 0.00117946 0.000675255 0.000843332 0.342993
84 70 13 0.00122524 0.00075747 0.000913395 0.295734 0.00127004 0.000700568 0.00089039 0.368428
84 69 13 0.0013762 0.000607907 0.000864005 0.475513 0.00130121 0.000666051 0.000877759 0.405086
83 68 14 0.00117165 0.000572571 0.000772264 0.433612 0.00127088 0.000631783 0.000844803 0.427719
83 67 14 0.00122987 0.000573616 0.000792367 0.452554 0.00123866 0.000625767 0.000830053 0.422219
83 66 14 0.00120132 0.000599483 0.000800095 0.411401 0.00118774 0.00062832 0.000814796 0.408966
83 65 14 0.00130532 0.000741545 0.000929471 0.341101 0.00117765 0.000649599 0.000825623 0.38951
83 64 15 0.00113069 0.000744614 0.000873306 0.303024 0.00124994 0.000716112 0.000894054 0.35574
83 63 15 0.00145392 0.000843014 0.00104665 0.338389 0.00160184 0.000956015 0.00117128 0.342898
83 62 15 0.00150758 0.000704525 0.000972208 0.454268 0.00184354 0.00110231 0.0013494 0.361096
82 61 15 0.00168556 0.000719335 0.00104141 0.500387 0.00187725 0.00105482 0.00132898 0.413339
82 60 16 0.00149165 0.000655993 0.000934546 0.482961 0.00174103 0.000915708 0.00119082 0.459582
82 59 16 0.00178469 0.000676534 0.00104592 0.547817 0.00181009 0.000942766 0.00123188 0.47797
82 58 16 0.00187731 0.000555021 0.000995783 0.650825 0.00176598 0.000879462 0.00117498 0.482668
82 57 17 0.00136583 0.000342585 0.000683666 0.706805 0.00183719 0.00101521 0.00128919 0.444575
82 56 17 0.00149454 0.000361014 0.000738857 0.718399 0.00172875 0.000879471 0.00116258 0.466697
82 55 17 0.00164246 0.000404404 0.000817091 0.714028 0.00143606 0.000654734 0.000915172 0.485324
81 54 17 0.00110069 0.000505138 0.000703656 0.462108 0.00123971 0.000546461 0.000777551 0.491684
81 53 18 0.00149581 0.000503958 0.000834577 0.601599 0.00138836 0.000547033 0.000827479 0.539068
81 52 18 0.00130913 0.000454745 0.00073954 0.597531 0.00133457 0.000539894 0.000804789 0.533393
81 51 18 0.00131507 0.000631822 0.000859572 0.448947 0.00131177 0.000606845 0.000841826 0.469117
81 50 18 0.00135444 0.000747886 0.000950069 0.362522 0.00129975 0.000659834 0.000873148 0.416883
81 49 18 0.00120955 0.000643043 0.000831879 0.404422 0.00126551 0.00064144 0.000849466 0.418424
80 48 19 0.00140649 0.000619495 0.000881827 0.476057 0.00134196 0.000607405 0.000852266 0.47251
80 47 19 0.00124703 0.00054436 0.000778584 0.493392 0.00129913 0.000595745 0.000830194 0.470203
80 46 19 0.00123713 0.000562425 0.000787325 0.473597 0.00131166 0.000608192 0.000842689 0.465411
80 45 19 0.00131702 0.000638351 0.000864576 0.436198 0.00131184 0.000638683 0.000863079 0.443722
79 44 20 0.000961184 0.000655564 0.000757438 0.251941 0.00120554 0.000691043 0.000862543 0.349984
79 43 20 0.00104516 0.000760429 0.000855339 0.211843 0.00118236 0.000713172 0.000869568 0.323664
79 42 20 0.0010671 0.000695726 0.000819518 0.290868 0.00118518 0.000688767 0.000854257 0.347132
79 41 20 0.000951325 0.000643122 0.000745857 0.290616 0.00115072 0.000662836 0.000825473 0.352023
80 40 20 0.00111846 0.000771887 0.00088741 0.232294 0.00118544 0.000701789 0.000863008 0.328079
81 40 20 0.000989299 0.000649715 0.00076291 0.283576 0.00114976 0.000669422 0.000829546 0.343642
# pathway end

This text file contains various diffusion measures, one row for each position along the trajectory of the path. The first three entries in each row are the x, y, z coordinates in native diffusion space. The next four entries are the axial diffusivity, radial diffusivity, mean diffusivity, and fractional anisotropy at that position on the maximum a posteriori path. The last four entries are the axial diffusivity, radial diffusivity, mean diffusivity, and fractional anisotropy at the same position, averaged over all sampled paths.

Converting pathstats.overall.txt to a table

Measures can be extracted from these files to be analyzed further, e.g., for tract-based group analysis. Specifically, the text files can be converted into a table using the command tractstats2table for doing GLM analyses using mri_glmfit or any other statistical software (SPSS, Excel, Statview etc.)

To extract all diffusion measures for the left corticospinal tract into a table do the following: 

tractstats2table --inputs $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt --overall --tablefile $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.cst_AS_avg33_mni_bbr/lh.cst_AS.All.table
  • The argument to the --inputs option specifies the input stats file.
  • The --overall option tells tractstats2table to expect the overall path stats file (stats averaged over the entire left CST), as opposed to the stats along the trajectory of the tract (which would be specified with the --byvoxel option instead).
  • The argument to the --tablefile option specifies the output file.

Take a look at the resulting table file: 

gedit $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.cst_AS_avg33_mni_bbr/lh.cst_AS.All.table &

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

tractstats2table --inputs $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt --overall --only-measures FA_Avg --tablefile $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.cst_AS_avg33_mni_bbr/lh.cst_AS.FA_Avg.table
  • Here the --only-measures option followed by FA_Avg was used to indicate we are only interested in having the average FA over the path in table format for this tract.

Take a look at the resulting table file: 

gedit $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.cst_AS_avg33_mni_bbr/lh.cst_AS.FA_Avg.table &

For a group analysis that has multiple subjects, tractstats2table can be used to combine all the subjects' diffusion measures from the path.overall.txt files into a single table that can be used for analysis with mri_glmfit or any other statistics software.

An easy way to do this is to create a text file that contains the names of the subjects and paths to their pathstats.overall.txt files. An example is given below: 

$TUTORIAL_DATA/diffusion_tutorial/elmo.2005/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt
$TUTORIAL_DATA/diffusion_tutorial/elmo.2008/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt
$TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt

Once this is created and saved as lh.cst_AS.overall.pathstats.list, it can be passed as a parameter to the tractstats2table command. This file has already been created for you. To open this file and view its contents, do the following: 

gedit $TUTORIAL_DATA/diffusion_tutorial/TraculaStatFiles/lh.cst_AS.overall.pathstats.list &

The following command will create a table with all the subjects specified in the lh.cst_AS.overall.pathstats file and all the diffusion measures from pathstats.overall.txt for each subject. 

tractstats2table --load-pathstats-from-file $TUTORIAL_DATA/diffusion_tutorial/TraculaStatFiles/lh.cst_AS.overall.pathstats.list --overall --tablefile $TUTORIAL_DATA/diffusion_tutorial/TraculaStatFiles/lh.cst_AS.All.table

We've generated tables of all Diffusion measures for the 3 tutorial subjects for all the 18 tracts. They can be found here: 

ls $TUTORIAL_DATA/diffusion_tutorial/TraculaStatFiles/*.All.table

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

tractstats2table --load-pathstats-from-file $TUTORIAL_DATA/diffusion_tutorial/TraculaStatFiles/lh.cst_AS.overall.pathstats.list --overall --only-measures FA_Avg --tablefile $TUTORIAL_DATA/diffusion_tutorial/TraculaStatFiles/lh.cst_AS.FA_Avg.table
  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)