Hello. I'm currently attempting to create structural connectivity matrix (adjacency matrix) using FSL.
I'm currently using Bash on Ubuntu on Windows as a platform (terminal) to launch FSL and FreeSurfer program.
I have successfully performed and obtained
1. BET->eddy-correct->dtifit->BEDPOSTX outputs (I'm currently using the latest version of FSL)
2. Desikan-Killiany atlas and Destrieux atlas parcellation (created by freesurfer's command: recon-all)
However, I'm stuck at the step of generating structural connectivity matrix.
I need to combine Desikan-Kiliany or Destrieux parcellated structural brain data of a subject and DTI-fitted data using the command probtrackx, but I still haven't grasped the practical implementation steps on using the command.
As I had so many things to know and consider using 'probtrackx2', I got mixed up about what command options I should use, what order of commands to execute (and any necessary prerequisite steps before executing probtrackx2 command) and of the tons of possible inputs, which ones I should use (and what kind of transformations needed).
With so many possibilities to consider, I couldn't even dare to attempt using probtrackx2 properly. Any impulsive attempts have failed.
I did tried to follow the steps mentioned in https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide.
However, the explanations were not concrete enough with real examples so that I could understand it clear-cut.
I also searched many kinds of relevant sites including the two below.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeview
http://sburns.org/2014/05/03/cortical-tractography-recipe.html
However, none of the sites I've searched had complete explanations with clear-cut examples.
So, the explanations were vague and abstract to me.
I could find a few people on the internet site with the same kind of errors that I've made, but it didn't critically helped either.
I'm not still clear about with what data and how I should feed into the seed space or seed mask (single or multiple),
whether I have to include waypoint mask, exclusion mask or termination mask, if so, which one I should use in my case.
I only vaguely know that the surface file? of the FreeSurfer should be converted to binary file using mri_convert or mri_label2vol, and before using the probtrackx command, registration to the DTI space? is needed. I'm also not sure whether I have to use surf_proj before using probtrackx2, and with what FreeSurfer file and how to implement it in the code.
Since I need adjacency matrix, I need to include omatrix1, 2 or 3 in the command but I'm not sure which one to use in my case.
This is all that I can explain to you that I don't clearly know.
Sorry that I couldn't explain it more concretely as my brain is mixed-up trying to do all sorts of things.
I've been stuck and struggling for over a month in this single tiny step. This step shouldn't be a groundbreaking thing for an ordinary neuroscientist analyzing MRI, fMRI or DTI data as thousands of neuroscientists have gone this step.
Here are all of the relevant files for the process (for concreteness).
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
Since I'm desperate, any help would be very appreciating :)
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