Hello. I have been attempting to generate structural adjacency (connectivity) matrices from the results of
1. BEDPOSTX
2. Desikan-Killiany atlas or Destrieux atlas (created by freesurfer's command: recon-all)
using the command probtrackx,
but I've been stuck and struggling for over a month in this single step.
 
What's worse is that I'm totally lost and distraught about
exactly what step I have to take (practically) to obtain the structural connectivity matrix.
I kind of know the step roughly, but it's at the tip of the tongue.
I've searched for the practical implementation in almost every webspace,
but none of the explanations were straightforward or complete (without any logical jump)
 
I'm not sure which seed? or mask? I should use from the freesurfer's result 'recon-all'
I think that in order to receive adjacency matrix, one should provide the output command 'omatrix1' or 2 or 3
Moreover, I think I need to project the data onto the surface and registrate the FreeSurfer surface.
Transformation between surface and DTI is also necessary but I'm not fully clear about the principles and implementations.
 
Here are all of the relevant files for the process.
 
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN/s3078815/seg3078815$ ls
label  mri  scripts  stats  surf  tmp  touch  trash
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN/s3078815/seg3078815$ ls label
BA_exvivo.ctab               lh.BA3b_exvivo.label         lh.BA6_exvivo.thresh.label  lh.aparc.annot                     rh.BA3a_exvivo.thresh.label  rh.BA6_exvivo.label         rh.aparc.a2009s.annot
BA_exvivo.thresh.ctab        lh.BA3b_exvivo.thresh.label  lh.BA_exvivo.annot          lh.cortex.label                    rh.BA3b_exvivo.label         rh.BA6_exvivo.thresh.label  rh.aparc.annot
aparc.annot.DKTatlas.ctab    lh.BA44_exvivo.label         lh.BA_exvivo.thresh.annot   lh.entorhinal_exvivo.label         rh.BA3b_exvivo.thresh.label  rh.BA_exvivo.annot          rh.cortex.label
aparc.annot.a2009s.ctab      lh.BA44_exvivo.thresh.label  lh.MT_exvivo.label          lh.entorhinal_exvivo.thresh.label  rh.BA44_exvivo.label         rh.BA_exvivo.thresh.annot   rh.entorhinal_exvivo.label
aparc.annot.ctab             lh.BA45_exvivo.label         lh.MT_exvivo.thresh.label   lh.perirhinal_exvivo.label         rh.BA44_exvivo.thresh.label  rh.MT_exvivo.label          rh.entorhinal_exvivo.thresh.label
lh.BA1_exvivo.label          lh.BA45_exvivo.thresh.label  lh.V1_exvivo.label          lh.perirhinal_exvivo.thresh.label  rh.BA45_exvivo.label         rh.MT_exvivo.thresh.label   rh.perirhinal_exvivo.label
lh.BA1_exvivo.thresh.label   lh.BA4a_exvivo.label         lh.V1_exvivo.thresh.label   rh.BA1_exvivo.label                rh.BA45_exvivo.thresh.label  rh.V1_exvivo.label          rh.perirhinal_exvivo.thresh.label
lh.BA2_exvivo.label          lh.BA4a_exvivo.thresh.label  lh.V2_exvivo.label          rh.BA1_exvivo.thresh.label         rh.BA4a_exvivo.label         rh.V1_exvivo.thresh.label
lh.BA2_exvivo.thresh.label   lh.BA4p_exvivo.label         lh.V2_exvivo.thresh.label   rh.BA2_exvivo.label                rh.BA4a_exvivo.thresh.label  rh.V2_exvivo.label
lh.BA3a_exvivo.label         lh.BA4p_exvivo.thresh.label  lh.aparc.DKTatlas.annot     rh.BA2_exvivo.thresh.label         rh.BA4p_exvivo.label         rh.V2_exvivo.thresh.label
lh.BA3a_exvivo.thresh.label  lh.BA6_exvivo.label          lh.aparc.a2009s.annot       rh.BA3a_exvivo.label               rh.BA4p_exvivo.thresh.label  rh.aparc.DKTatlas.annot
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN/s3078815/seg3078815$ ls mri
T1.mgz                      aparc.a2009s+aseg.mgz                    aseg.mgz                brainmask.auto.mgz     junk                        nu.mgz       rawavg.mgz             talairach.label_intensities.txt  wm.mgz
aparc+aseg.mgz              aparc.a2009s+aseg.nii.gz                 aseg.presurf.hypos.mgz  brainmask.mgz          lh.ribbon.mgz               orig         rh.ribbon.mgz          talairach.log                    wm.seg.mgz
aparc+aseg.nii.gz           aseg.auto.mgz                            aseg.presurf.mgz        ctrl_pts.mgz           mri_nu_correct.mni.log      orig.mgz     ribbon.mgz             talairach_with_skull.log         wmparc.mgz
aparc.DKTatlas+aseg.mgz     aseg.auto_noCCseg.label_intensities.txt  brain.finalsurfs.mgz    filled.mgz             mri_nu_correct.mni.log.bak  orig.nii.gz  segment.dat            transforms
aparc.DKTatlas+aseg.nii.gz  aseg.auto_noCCseg.mgz                    brain.mgz               freesurfer2struct.mat  norm.mgz                    orig_nu.mgz  struct2freesurfer.mat  wm.asegedit.mgz
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN/s3078815/seg3078815$ ls scripts
build-stamp.txt  lastcall.build-stamp.txt  patchdir.txt  pctsurfcon.log  pctsurfcon.log.old  ponscc.cut.log  recon-all-status.log  recon-all.cmd  recon-all.done  recon-all.env  recon-all.local-copy  recon-all.log
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN/s3078815/seg3078815$ ls stats
aseg.stats          lh.BA_exvivo.thresh.stats  lh.aparc.a2009s.stats  lh.aparc.stats  lh.w-g.pct.stats    rh.BA_exvivo.thresh.stats  rh.aparc.a2009s.stats  rh.aparc.stats  rh.w-g.pct.stats
lh.BA_exvivo.stats  lh.aparc.DKTatlas.stats    lh.aparc.pial.stats    lh.curv.stats   rh.BA_exvivo.stats  rh.aparc.DKTatlas.stats    rh.aparc.pial.stats    rh.curv.stats   wmparc.stats
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN/s3078815/seg3078815$ ls surf
error.log     lh.defect_borders  lh.jacobian_white   lh.smoothwm.C.crv   lh.smoothwm.nofix  lh.white             rh.area.mid        rh.defect_labels   rh.orig.nofix       rh.smoothwm.H.crv   rh.sphere.reg   rh.white.K
lh.area       lh.defect_chull    lh.orig             lh.smoothwm.FI.crv  lh.sphere          lh.white.H           rh.area.pial       rh.inflated        rh.pial             rh.smoothwm.K.crv   rh.sulc         rh.white.preaparc
lh.area.mid   lh.defect_labels   lh.orig.nofix       lh.smoothwm.H.crv   lh.sphere.reg      lh.white.K           rh.avg_curv        rh.inflated.H      rh.qsphere.nofix    rh.smoothwm.K1.crv  rh.thickness    rh.white.preaparc.H
lh.area.pial  lh.inflated        lh.pial             lh.smoothwm.K.crv   lh.sulc            lh.white.preaparc    rh.curv            rh.inflated.K      rh.smoothwm         rh.smoothwm.K2.crv  rh.volume       rh.white.preaparc.K
lh.avg_curv   lh.inflated.H      lh.qsphere.nofix    lh.smoothwm.K1.crv  lh.thickness       lh.white.preaparc.H  rh.curv.pial       rh.inflated.nofix  rh.smoothwm.BE.crv  rh.smoothwm.S.crv   rh.w-g.pct.mgh
lh.curv       lh.inflated.K      lh.smoothwm         lh.smoothwm.K2.crv  lh.volume          lh.white.preaparc.K  rh.defect_borders  rh.jacobian_white  rh.smoothwm.C.crv   rh.smoothwm.nofix   rh.white
lh.curv.pial  lh.inflated.nofix  lh.smoothwm.BE.crv  lh.smoothwm.S.crv   lh.w-g.pct.mgh     rh.area              rh.defect_chull    rh.orig            rh.smoothwm.FI.crv  rh.sphere           rh.white.H
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN/s3078815/seg3078815$ ls tmp
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN/s3078815/seg3078815$ ls touch
aparc.DKTatlas2aseg.touch  fill.touch            lh.final_surfaces.touch  lh.sphmorph.touch       rh.aparc2.touch          rh.jacobian_white.touch  rh.topofix.touch                  rusage.mris_inflate.rh.dat   wmaparc.touch
aparc.a2009s2aseg.touch    inorm1.touch          lh.inflate.H.K.touch     lh.sphreg.touch         rh.aparcstats.touch      rh.pctsurfcon.touch      rh.white.H.K.touch                rusage.mris_register.lh.dat  wmsegment.touch
apas2aseg.touch            inorm2.touch          lh.inflate1.touch        lh.surfvolume.touch     rh.aparcstats2.touch     rh.pial_surface.touch    rh.white_surface.touch            rusage.mris_register.rh.dat
asegmerge.touch            lh.aparc.touch        lh.inflate2.touch        lh.tessellate.touch     rh.aparcstats3.touch     rh.qsphere.touch         rusage.mri_ca_register.dat        rusage.mris_sphere.lh.dat
ca_label.touch             lh.aparc2.touch       lh.jacobian_white.touch  lh.topofix.touch        rh.avgcurv.touch         rh.smoothwm1.touch       rusage.mri_em_register.dat        rusage.mris_sphere.rh.dat
ca_normalize.touch         lh.aparcstats.touch   lh.pctsurfcon.touch      lh.white.H.K.touch      rh.curvstats.touch       rh.smoothwm2.touch       rusage.mri_em_register.skull.dat  segstats.touch
ca_register.touch          lh.aparcstats2.touch  lh.pial_surface.touch    lh.white_surface.touch  rh.final_surfaces.touch  rh.sphmorph.touch        rusage.mri_watershed.dat          skull.lta.touch
conform.touch              lh.aparcstats3.touch  lh.qsphere.touch         nu.touch                rh.inflate.H.K.touch     rh.sphreg.touch          rusage.mris_fix_topology.lh.dat   skull_strip.touch
cortical_ribbon.touch      lh.avgcurv.touch      lh.smoothwm1.touch       relabelhypos.touch      rh.inflate1.touch        rh.surfvolume.touch      rusage.mris_fix_topology.rh.dat   talairach.touch
em_register.touch          lh.curvstats.touch    lh.smoothwm2.touch       rh.aparc.touch          rh.inflate2.touch        rh.tessellate.touch      rusage.mris_inflate.lh.dat        wmaparc.stats.touch
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN/s3078815/seg3078815$ ls trash
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN/s3078815/seg3078815$ ls ../../s3097367/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s3097367/
20110217_211141ACEAXIAL723097s011a1001.bval    DTI_FA.nii.gz  DTI_L3.nii.gz  DTI_S0.nii.gz  DTI_V3.nii.gz  b0_brain.nii.gz       bvecs          data.nii.gz
20110217_211141ACEAXIAL723097s011a1001.bvec    DTI_L1.nii.gz  DTI_MD.nii.gz  DTI_V1.nii.gz  MRDC           b0_brain_mask.nii.gz  data           data_eddy.ecclog
20110217_211141ACEAXIAL723097s011a1001.nii.gz  DTI_L2.nii.gz  DTI_MO.nii.gz  DTI_V2.nii.gz  b0.nii.gz      bvals                 data.bedpostX  data_eddy.nii.gz
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN/s3078815/seg3078815$ ls ../../s3097367/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s3097367/data
bedpostcom_log.tcl  bvals  bvecs  data.nii.gz  nodif_brain_mask.nii.gz
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN/s3078815/seg3078815$ ls ../../s3097367/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s3097367/data.bedpostX/
bvals          dyads1_dispersion.nii.gz  dyads2_thr0.05_modf2.nii.gz  mean_dsamples.nii.gz     mean_ph1samples.nii.gz  merged_f1samples.nii.gz   merged_th1samples.nii.gz  xfms
bvecs          dyads2.nii.gz             logs                         mean_f1samples.nii.gz    mean_ph2samples.nii.gz  merged_f2samples.nii.gz   merged_th2samples.nii.gz
commands.txt   dyads2_dispersion.nii.gz  mean_S0samples.nii.gz        mean_f2samples.nii.gz    mean_th1samples.nii.gz  merged_ph1samples.nii.gz  monitor
dyads1.nii.gz  dyads2_thr0.05.nii.gz     mean_d_stdsamples.nii.gz     mean_fsumsamples.nii.gz  mean_th2samples.nii.gz  merged_ph2samples.nii.gz  nodif_brain_mask.nii.gz
 
Any help would be very appreciating :)
Once again, sorry that the questions were vague, but I'm desperate.