open-discussion > probtrackx adjacency matrix practical problem
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Oct 26, 2017 01:10 AM | Mir Jeong
probtrackx adjacency matrix practical problem
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.
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.