Hello, I've followed the guidelines from the site below.
http://sburns.org/2014/05/03/cortical-tractography-recipe.html
I used Destrieux atlas produced by FreeSurfer in 2009, having 74 regions for each hemisphere (total: 148).
I have successfully performed up to fsl's 'probtrackx2' without errors.
However, according to the guideline on the site above (using omatrix1),
it seems very tedious to repeat 'probtrackx2' 148 times for each region (it took about 400s for each run).
Are there any methods to directly obtain 148*148 connectivity matrix in just one execution of 'probtrackx2'?
I was unable to run 'probtrackx2' directly on the terminal by copying and pasting the commands listed on the site.
So, I used GUI(?) (by typing 'fsl', then clicking 'FDT Diffusion' then going to 'PROBTRACKX Probabilistic tracking')
in order to execute 'probtrackx2' (I attached 'data.png' and 'options.png' for illustration).
I was unable to add 'satastext' or 'network' (as I couldn't run 'probtrackx2' directly on the terminal).
As I didn't obtain 'matrix_seeds_to_all_targets.nii.gz', a 2D voxel-by target matrix,
I have troubles in generating 148*148 structural connectivity matrices.
I prefer using MATLAB over using python (the subrns.org site used python, which makes it hard for me to understand the code).
At least I have fdt_matrix1.dot, is it true that you can obtain 148*148 connectivity matrix directly using the MATLAB code below?
x=load('fdt_matrix1.dot');
M=full(spconvert(x));
I still don't have a clear concept of seeds and masks, what the 'probtrackx2' outputs represent,
what 'omatrix1'~'omatrix4', 'network' in 'probtrackx2' represents, so I still don't have a clear idea what to do.
It would be very appreciating if you could show me a concrete sequence of codes (and program executions)
for generating 148*148 matrix that I want.
Here are the codes to help you debug for me.
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN/s3078815/seg3078815$ ls
anat fa2fs.mat fa2str.mat fs2fa.mat fs2str.mat junk label label_order.txt mri results results2 scripts seeds.txt stats str2fa.mat str2fs.mat surf tmp touch trash waypoints.txt
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN/s3078815/seg3078815$ ls anat
fs.nii.gz str.nii.gz ventricles.nii.gz wm.lh.nii.gz wm.rh.nii.gz
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN/s3078815/seg3078815$ ls label
BA_exvivo.ctab lh.G_oc-temp_lat-fusifor.label lh.S_circular_insula_sup.label lh.entorhinal_exvivo.thresh.label rh.G_oc-temp_med-Lingual.nii.gz rh.S_collat_transv_ant.nii.gz
BA_exvivo.thresh.ctab lh.G_oc-temp_lat-fusifor.nii.gz lh.S_circular_insula_sup.nii.gz lh.perirhinal_exvivo.label rh.G_oc-temp_med-Parahip.label rh.S_collat_transv_post.label
aparc.annot.DKTatlas.ctab lh.G_oc-temp_med-Lingual.label lh.S_collat_transv_ant.label lh.perirhinal_exvivo.thresh.label rh.G_oc-temp_med-Parahip.nii.gz rh.S_collat_transv_post.nii.gz
aparc.annot.a2009s.ctab lh.G_oc-temp_med-Lingual.nii.gz lh.S_collat_transv_ant.nii.gz rh.BA1_exvivo.label rh.G_occipital_middle.label rh.S_front_inf.label
aparc.annot.ctab lh.G_oc-temp_med-Parahip.label lh.S_collat_transv_post.label rh.BA1_exvivo.thresh.label rh.G_occipital_middle.nii.gz rh.S_front_inf.nii.gz
error.log lh.G_oc-temp_med-Parahip.nii.gz lh.S_collat_transv_post.nii.gz rh.BA2_exvivo.label rh.G_occipital_sup.label rh.S_front_middle.label
lh.BA1_exvivo.label lh.G_occipital_middle.label lh.S_front_inf.label rh.BA2_exvivo.thresh.label rh.G_occipital_sup.nii.gz rh.S_front_middle.nii.gz
lh.BA1_exvivo.thresh.label lh.G_occipital_middle.nii.gz lh.S_front_inf.nii.gz rh.BA3a_exvivo.label rh.G_orbital.label rh.S_front_sup.label
lh.BA2_exvivo.label lh.G_occipital_sup.label lh.S_front_middle.label rh.BA3a_exvivo.thresh.label rh.G_orbital.nii.gz rh.S_front_sup.nii.gz
lh.BA2_exvivo.thresh.label lh.G_occipital_sup.nii.gz lh.S_front_middle.nii.gz rh.BA3b_exvivo.label rh.G_pariet_inf-Angular.label rh.S_interm_prim-Jensen.label
lh.BA3a_exvivo.label lh.G_orbital.label lh.S_front_sup.label rh.BA3b_exvivo.thresh.label rh.G_pariet_inf-Angular.nii.gz rh.S_interm_prim-Jensen.nii.gz
lh.BA3a_exvivo.thresh.label lh.G_orbital.nii.gz lh.S_front_sup.nii.gz rh.BA44_exvivo.label rh.G_pariet_inf-Supramar.label rh.S_intrapariet&P_trans.label
lh.BA3b_exvivo.label lh.G_pariet_inf-Angular.label lh.S_interm_prim-Jensen.label rh.BA44_exvivo.thresh.label rh.G_pariet_inf-Supramar.nii.gz rh.S_intrapariet&P_trans.nii.gz
lh.BA3b_exvivo.thresh.label lh.G_pariet_inf-Angular.nii.gz lh.S_interm_prim-Jensen.nii.gz rh.BA45_exvivo.label rh.G_parietal_sup.label rh.S_oc-temp_lat.label
lh.BA44_exvivo.label lh.G_pariet_inf-Supramar.label lh.S_intrapariet&P_trans.label rh.BA45_exvivo.thresh.label rh.G_parietal_sup.nii.gz rh.S_oc-temp_lat.nii.gz
lh.BA44_exvivo.thresh.label lh.G_pariet_inf-Supramar.nii.gz lh.S_intrapariet&P_trans.nii.gz rh.BA4a_exvivo.label rh.G_postcentral.label rh.S_oc-temp_med&Lingual.label
lh.BA45_exvivo.label lh.G_parietal_sup.label lh.S_oc-temp_lat.label rh.BA4a_exvivo.thresh.label rh.G_postcentral.nii.gz rh.S_oc-temp_med&Lingual.nii.gz
lh.BA45_exvivo.thresh.label lh.G_parietal_sup.nii.gz lh.S_oc-temp_lat.nii.gz rh.BA4p_exvivo.label rh.G_precentral.label rh.S_oc_middle&Lunatus.label
lh.BA4a_exvivo.label lh.G_postcentral.label lh.S_oc-temp_med&Lingual.label rh.BA4p_exvivo.thresh.label rh.G_precentral.nii.gz rh.S_oc_middle&Lunatus.nii.gz
lh.BA4a_exvivo.thresh.label lh.G_postcentral.nii.gz lh.S_oc-temp_med&Lingual.nii.gz rh.BA6_exvivo.label rh.G_precuneus.label rh.S_oc_sup&transversal.label
lh.BA4p_exvivo.label lh.G_precentral.label lh.S_oc_middle&Lunatus.label rh.BA6_exvivo.thresh.label rh.G_precuneus.nii.gz rh.S_oc_sup&transversal.nii.gz
lh.BA4p_exvivo.thresh.label lh.G_precentral.nii.gz lh.S_oc_middle&Lunatus.nii.gz rh.BA_exvivo.annot rh.G_rectus.label rh.S_occipital_ant.label
lh.BA6_exvivo.label lh.G_precuneus.label lh.S_oc_sup&transversal.label rh.BA_exvivo.thresh.annot rh.G_rectus.nii.gz rh.S_occipital_ant.nii.gz
lh.BA6_exvivo.thresh.label lh.G_precuneus.nii.gz lh.S_oc_sup&transversal.nii.gz rh.G&S_cingul-Ant.label rh.G_subcallosal.label rh.S_orbital-H_Shaped.label
lh.BA_exvivo.annot lh.G_rectus.label lh.S_occipital_ant.label rh.G&S_cingul-Ant.nii.gz rh.G_subcallosal.nii.gz rh.S_orbital-H_Shaped.nii.gz
lh.BA_exvivo.thresh.annot lh.G_rectus.nii.gz lh.S_occipital_ant.nii.gz rh.G&S_cingul-Mid-Ant.label rh.G_temp_sup-G_T_transv.label rh.S_orbital_lateral.label
lh.G&S_cingul-Ant.label lh.G_subcallosal.label lh.S_orbital-H_Shaped.label rh.G&S_cingul-Mid-Ant.nii.gz rh.G_temp_sup-G_T_transv.nii.gz rh.S_orbital_lateral.nii.gz
lh.G&S_cingul-Ant.nii.gz lh.G_subcallosal.nii.gz lh.S_orbital-H_Shaped.nii.gz rh.G&S_cingul-Mid-Post.label rh.G_temp_sup-Lateral.label rh.S_orbital_med-olfact.label
lh.G&S_cingul-Mid-Ant.label lh.G_temp_sup-G_T_transv.label lh.S_orbital_lateral.label rh.G&S_cingul-Mid-Post.nii.gz rh.G_temp_sup-Lateral.nii.gz rh.S_orbital_med-olfact.nii.gz
lh.G&S_cingul-Mid-Ant.nii.gz lh.G_temp_sup-G_T_transv.nii.gz lh.S_orbital_lateral.nii.gz rh.G&S_frontomargin.label rh.G_temp_sup-Plan_polar.label rh.S_parieto_occipital.label
lh.G&S_cingul-Mid-Post.label lh.G_temp_sup-Lateral.label lh.S_orbital_med-olfact.label rh.G&S_frontomargin.nii.gz rh.G_temp_sup-Plan_polar.nii.gz rh.S_parieto_occipital.nii.gz
lh.G&S_cingul-Mid-Post.nii.gz lh.G_temp_sup-Lateral.nii.gz lh.S_orbital_med-olfact.nii.gz rh.G&S_occipital_inf.label rh.G_temp_sup-Plan_tempo.label rh.S_pericallosal.label
lh.G&S_frontomargin.label lh.G_temp_sup-Plan_polar.label lh.S_parieto_occipital.label rh.G&S_occipital_inf.nii.gz rh.G_temp_sup-Plan_tempo.nii.gz rh.S_pericallosal.nii.gz
lh.G&S_frontomargin.nii.gz lh.G_temp_sup-Plan_polar.nii.gz lh.S_parieto_occipital.nii.gz rh.G&S_paracentral.label rh.G_temporal_inf.label rh.S_postcentral.label
lh.G&S_occipital_inf.label lh.G_temp_sup-Plan_tempo.label lh.S_pericallosal.label rh.G&S_paracentral.nii.gz rh.G_temporal_inf.nii.gz rh.S_postcentral.nii.gz
lh.G&S_occipital_inf.nii.gz lh.G_temp_sup-Plan_tempo.nii.gz lh.S_pericallosal.nii.gz rh.G&S_subcentral.label rh.G_temporal_middle.label rh.S_precentral-inf-part.label
lh.G&S_paracentral.label lh.G_temporal_inf.label lh.S_postcentral.label rh.G&S_subcentral.nii.gz rh.G_temporal_middle.nii.gz rh.S_precentral-inf-part.nii.gz
lh.G&S_paracentral.nii.gz lh.G_temporal_inf.nii.gz lh.S_postcentral.nii.gz rh.G&S_transv_frontopol.label rh.Lat_Fis-ant-Horizont.label rh.S_precentral-sup-part.label
lh.G&S_subcentral.label lh.G_temporal_middle.label lh.S_precentral-inf-part.label rh.G&S_transv_frontopol.nii.gz rh.Lat_Fis-ant-Horizont.nii.gz rh.S_precentral-sup-part.nii.gz
lh.G&S_subcentral.nii.gz lh.G_temporal_middle.nii.gz lh.S_precentral-inf-part.nii.gz rh.G_Ins_lg&S_cent_ins.label rh.Lat_Fis-ant-Vertical.label rh.S_suborbital.label
lh.G&S_transv_frontopol.label lh.Lat_Fis-ant-Horizont.label lh.S_precentral-sup-part.label rh.G_Ins_lg&S_cent_ins.nii.gz rh.Lat_Fis-ant-Vertical.nii.gz rh.S_suborbital.nii.gz
lh.G&S_transv_frontopol.nii.gz lh.Lat_Fis-ant-Horizont.nii.gz lh.S_precentral-sup-part.nii.gz rh.G_cingul-Post-dorsal.label rh.Lat_Fis-post.label rh.S_subparietal.label
lh.G_Ins_lg&S_cent_ins.label lh.Lat_Fis-ant-Vertical.label lh.S_suborbital.label rh.G_cingul-Post-dorsal.nii.gz rh.Lat_Fis-post.nii.gz rh.S_subparietal.nii.gz
lh.G_Ins_lg&S_cent_ins.nii.gz lh.Lat_Fis-ant-Vertical.nii.gz lh.S_suborbital.nii.gz rh.G_cingul-Post-ventral.label rh.MT_exvivo.label rh.S_temporal_inf.label
lh.G_cingul-Post-dorsal.label lh.Lat_Fis-post.label lh.S_subparietal.label rh.G_cingul-Post-ventral.nii.gz rh.MT_exvivo.thresh.label rh.S_temporal_inf.nii.gz
lh.G_cingul-Post-dorsal.nii.gz lh.Lat_Fis-post.nii.gz lh.S_subparietal.nii.gz rh.G_cuneus.label rh.Pole_occipital.label rh.S_temporal_sup.label
lh.G_cingul-Post-ventral.label lh.MT_exvivo.label lh.S_temporal_inf.label rh.G_cuneus.nii.gz rh.Pole_occipital.nii.gz rh.S_temporal_sup.nii.gz
lh.G_cingul-Post-ventral.nii.gz lh.MT_exvivo.thresh.label lh.S_temporal_inf.nii.gz rh.G_front_inf-Opercular.label rh.Pole_temporal.label rh.S_temporal_transverse.label
lh.G_cuneus.label lh.Pole_occipital.label lh.S_temporal_sup.label rh.G_front_inf-Opercular.nii.gz rh.Pole_temporal.nii.gz rh.S_temporal_transverse.nii.gz
lh.G_cuneus.nii.gz lh.Pole_occipital.nii.gz lh.S_temporal_sup.nii.gz rh.G_front_inf-Orbital.label rh.S_calcarine.label rh.Unknown.label
lh.G_front_inf-Opercular.label lh.Pole_temporal.label lh.S_temporal_transverse.label rh.G_front_inf-Orbital.nii.gz rh.S_calcarine.nii.gz rh.V1_exvivo.label
lh.G_front_inf-Opercular.nii.gz lh.Pole_temporal.nii.gz lh.S_temporal_transverse.nii.gz rh.G_front_inf-Triangul.label rh.S_central.label rh.V1_exvivo.thresh.label
lh.G_front_inf-Orbital.label lh.S_calcarine.label lh.Unknown.label rh.G_front_inf-Triangul.nii.gz rh.S_central.nii.gz rh.V2_exvivo.label
lh.G_front_inf-Orbital.nii.gz lh.S_calcarine.nii.gz lh.V1_exvivo.label rh.G_front_middle.label rh.S_cingul-Marginalis.label rh.V2_exvivo.thresh.label
lh.G_front_inf-Triangul.label lh.S_central.label lh.V1_exvivo.thresh.label rh.G_front_middle.nii.gz rh.S_cingul-Marginalis.nii.gz rh.aparc.DKTatlas.annot
lh.G_front_inf-Triangul.nii.gz lh.S_central.nii.gz lh.V2_exvivo.label rh.G_front_sup.label rh.S_circular_insula_ant.label rh.aparc.a2009s.annot
lh.G_front_middle.label lh.S_cingul-Marginalis.label lh.V2_exvivo.thresh.label rh.G_front_sup.nii.gz rh.S_circular_insula_ant.nii.gz rh.aparc.annot
lh.G_front_middle.nii.gz lh.S_cingul-Marginalis.nii.gz lh.aparc.DKTatlas.annot rh.G_insular_short.label rh.S_circular_insula_inf.label rh.cortex.label
lh.G_front_sup.label lh.S_circular_insula_ant.label lh.aparc.a2009s.annot rh.G_insular_short.nii.gz rh.S_circular_insula_inf.nii.gz rh.entorhinal_exvivo.label
lh.G_front_sup.nii.gz lh.S_circular_insula_ant.nii.gz lh.aparc.annot rh.G_oc-temp_lat-fusifor.label rh.S_circular_insula_sup.label rh.entorhinal_exvivo.thresh.label
lh.G_insular_short.label lh.S_circular_insula_inf.label lh.cortex.label rh.G_oc-temp_lat-fusifor.nii.gz rh.S_circular_insula_sup.nii.gz rh.perirhinal_exvivo.label
lh.G_insular_short.nii.gz lh.S_circular_insula_inf.nii.gz lh.entorhinal_exvivo.label rh.G_oc-temp_med-Lingual.label rh.S_collat_transv_ant.label rh.perirhinal_exvivo.thresh.label
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN/s3078815/seg3078815$ cat label_order.txt
G_rectus
G_subcallosal
S_suborbital
S_orbital_med-olfact
G_orbital
S_orbital-H_Shaped
G&S_transv_frontopol
G&S_cingul-Ant
G&S_frontomargin
G_front_sup
S_front_sup
S_front_middle
G_front_middle
S_orbital_lateral
S_front_inf
G_front_inf-Triangul
G_front_inf-Orbital
Lat_Fis-ant-Horizont
Lat_Fis-ant-Vertical
S_circular_insula_ant
S_circular_insula_sup
G_insular_short
G_Ins_lg&S_cent_ins
S_precentral-inf-part
G_front_inf-Opercular
S_precentral-sup-part
G_precentral
S_central
G&S_subcentral
Lat_Fis-post
S_circular_insula_inf
G_temp_sup-Plan_polar
Pole_temporal
G_temp_sup-G_T_transv
S_temporal_transverse
G_temp_sup-Plan_tempo
G_temp_sup-Lateral
S_temporal_sup
G_temporal_middle
S_temporal_inf
G_temporal_inf
S_collat_transv_ant
S_collat_transv_post
G_oc-temp_med-Parahip
S_oc-temp_lat
G_oc-temp_lat-fusifor
G_pariet_inf-Supramar
G_postcentral
S_postcentral
G&S_paracentral
G_parietal_sup
S_intrapariet&P_trans
S_interm_prim-Jensen
G_pariet_inf-Angular
S_occipital_ant
G&S_occipital_inf
G_occipital_middle
S_oc_sup&transversal
G_occipital_sup
G_cuneus
S_oc_middle&Lunatus
Pole_occipital
S_oc-temp_med&Lingual
G_oc-temp_med-Lingual
S_calcarine
S_parieto_occipital
G_precuneus
S_subparietal
G_cingul-Post-dorsal
G_cingul-Post-ventral
S_pericallosal
S_cingul-Marginalis
G&S_cingul-Mid-Post
G&S_cingul-Mid-Ant
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN/s3078815/seg3078815$ ls mri
T1.mgz aparc.a2009s+aseg.nii.gz aseg.presurf.mgz filled.mgz norm.mgz rawavg.mgz talairach.log wmparc.mgz
aparc+aseg.mgz aseg.auto.mgz brain.finalsurfs.mgz freesurfer2struct.mat nu.mgz rh.ribbon.mgz talairach_with_skull.log
aparc+aseg.nii.gz aseg.auto_noCCseg.label_intensities.txt brain.mgz junk orig ribbon.mgz transforms
aparc.DKTatlas+aseg.mgz aseg.auto_noCCseg.mgz brainmask.auto.mgz lh.ribbon.mgz orig.mgz segment.dat wm.asegedit.mgz
aparc.DKTatlas+aseg.nii.gz aseg.mgz brainmask.mgz mri_nu_correct.mni.log orig.nii.gz struct2freesurfer.mat wm.mgz
aparc.a2009s+aseg.mgz aseg.presurf.hypos.mgz ctrl_pts.mgz mri_nu_correct.mni.log.bak orig_nu.mgz talairach.label_intensities.txt wm.seg.mgz
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN/s3078815/seg3078815$ ls results
biggest.nii.gz seeds_to_lh.G_pariet_inf-Supramar.nii.gz seeds_to_lh.S_oc-temp_med&Lingual.nii.gz seeds_to_rh.G_front_middle.nii.gz seeds_to_rh.S_circular_insula_inf.nii.gz
coords_for_fdt_matrix1 seeds_to_lh.G_parietal_sup.nii.gz seeds_to_lh.S_oc_middle&Lunatus.nii.gz seeds_to_rh.G_front_sup.nii.gz seeds_to_rh.S_circular_insula_sup.nii.gz
fdt.log seeds_to_lh.G_postcentral.nii.gz seeds_to_lh.S_oc_sup&transversal.nii.gz seeds_to_rh.G_insular_short.nii.gz seeds_to_rh.S_collat_transv_ant.nii.gz
fdt_matrix1.dot seeds_to_lh.G_precentral.nii.gz seeds_to_lh.S_occipital_ant.nii.gz seeds_to_rh.G_oc-temp_lat-fusifor.nii.gz seeds_to_rh.S_collat_transv_post.nii.gz
fdt_paths.nii.gz seeds_to_lh.G_precuneus.nii.gz seeds_to_lh.S_orbital-H_Shaped.nii.gz seeds_to_rh.G_oc-temp_med-Lingual.nii.gz seeds_to_rh.S_front_inf.nii.gz
fdt_seed_classification.txt seeds_to_lh.G_rectus.nii.gz seeds_to_lh.S_orbital_lateral.nii.gz seeds_to_rh.G_oc-temp_med-Parahip.nii.gz seeds_to_rh.S_front_middle.nii.gz
probtrackx.log seeds_to_lh.G_subcallosal.nii.gz seeds_to_lh.S_orbital_med-olfact.nii.gz seeds_to_rh.G_occipital_middle.nii.gz seeds_to_rh.S_front_sup.nii.gz
seeds_to_lh.G&S_cingul-Ant.nii.gz seeds_to_lh.G_temp_sup-G_T_transv.nii.gz seeds_to_lh.S_parieto_occipital.nii.gz seeds_to_rh.G_occipital_sup.nii.gz seeds_to_rh.S_interm_prim-Jensen.nii.gz
seeds_to_lh.G&S_cingul-Mid-Ant.nii.gz seeds_to_lh.G_temp_sup-Lateral.nii.gz seeds_to_lh.S_pericallosal.nii.gz seeds_to_rh.G_orbital.nii.gz seeds_to_rh.S_intrapariet&P_trans.nii.gz
seeds_to_lh.G&S_cingul-Mid-Post.nii.gz seeds_to_lh.G_temp_sup-Plan_polar.nii.gz seeds_to_lh.S_postcentral.nii.gz seeds_to_rh.G_pariet_inf-Angular.nii.gz seeds_to_rh.S_oc-temp_lat.nii.gz
seeds_to_lh.G&S_frontomargin.nii.gz seeds_to_lh.G_temp_sup-Plan_tempo.nii.gz seeds_to_lh.S_precentral-inf-part.nii.gz seeds_to_rh.G_pariet_inf-Supramar.nii.gz seeds_to_rh.S_oc-temp_med&Lingual.nii.gz
seeds_to_lh.G&S_occipital_inf.nii.gz seeds_to_lh.G_temporal_inf.nii.gz seeds_to_lh.S_precentral-sup-part.nii.gz seeds_to_rh.G_parietal_sup.nii.gz seeds_to_rh.S_oc_middle&Lunatus.nii.gz
seeds_to_lh.G&S_paracentral.nii.gz seeds_to_lh.G_temporal_middle.nii.gz seeds_to_lh.S_suborbital.nii.gz seeds_to_rh.G_postcentral.nii.gz seeds_to_rh.S_oc_sup&transversal.nii.gz
seeds_to_lh.G&S_subcentral.nii.gz seeds_to_lh.Lat_Fis-ant-Horizont.nii.gz seeds_to_lh.S_subparietal.nii.gz seeds_to_rh.G_precentral.nii.gz seeds_to_rh.S_occipital_ant.nii.gz
seeds_to_lh.G&S_transv_frontopol.nii.gz seeds_to_lh.Lat_Fis-ant-Vertical.nii.gz seeds_to_lh.S_temporal_inf.nii.gz seeds_to_rh.G_precuneus.nii.gz seeds_to_rh.S_orbital-H_Shaped.nii.gz
seeds_to_lh.G_Ins_lg&S_cent_ins.nii.gz seeds_to_lh.Lat_Fis-post.nii.gz seeds_to_lh.S_temporal_sup.nii.gz seeds_to_rh.G_rectus.nii.gz seeds_to_rh.S_orbital_lateral.nii.gz
seeds_to_lh.G_cingul-Post-dorsal.nii.gz seeds_to_lh.Pole_occipital.nii.gz seeds_to_lh.S_temporal_transverse.nii.gz seeds_to_rh.G_subcallosal.nii.gz seeds_to_rh.S_orbital_med-olfact.nii.gz
seeds_to_lh.G_cingul-Post-ventral.nii.gz seeds_to_lh.Pole_temporal.nii.gz seeds_to_rh.G&S_cingul-Ant.nii.gz seeds_to_rh.G_temp_sup-G_T_transv.nii.gz seeds_to_rh.S_parieto_occipital.nii.gz
seeds_to_lh.G_cuneus.nii.gz seeds_to_lh.S_calcarine.nii.gz seeds_to_rh.G&S_cingul-Mid-Ant.nii.gz seeds_to_rh.G_temp_sup-Lateral.nii.gz seeds_to_rh.S_pericallosal.nii.gz
seeds_to_lh.G_front_inf-Opercular.nii.gz seeds_to_lh.S_central.nii.gz seeds_to_rh.G&S_cingul-Mid-Post.nii.gz seeds_to_rh.G_temp_sup-Plan_polar.nii.gz seeds_to_rh.S_postcentral.nii.gz
seeds_to_lh.G_front_inf-Orbital.nii.gz seeds_to_lh.S_cingul-Marginalis.nii.gz seeds_to_rh.G&S_frontomargin.nii.gz seeds_to_rh.G_temp_sup-Plan_tempo.nii.gz seeds_to_rh.S_precentral-inf-part.nii.gz
seeds_to_lh.G_front_inf-Triangul.nii.gz seeds_to_lh.S_circular_insula_ant.nii.gz seeds_to_rh.G&S_occipital_inf.nii.gz seeds_to_rh.G_temporal_inf.nii.gz seeds_to_rh.S_precentral-sup-part.nii.gz
seeds_to_lh.G_front_middle.nii.gz seeds_to_lh.S_circular_insula_inf.nii.gz seeds_to_rh.G&S_paracentral.nii.gz seeds_to_rh.G_temporal_middle.nii.gz seeds_to_rh.S_suborbital.nii.gz
seeds_to_lh.G_front_sup.nii.gz seeds_to_lh.S_circular_insula_sup.nii.gz seeds_to_rh.G&S_subcentral.nii.gz seeds_to_rh.Lat_Fis-ant-Horizont.nii.gz seeds_to_rh.S_subparietal.nii.gz
seeds_to_lh.G_insular_short.nii.gz seeds_to_lh.S_collat_transv_ant.nii.gz seeds_to_rh.G&S_transv_frontopol.nii.gz seeds_to_rh.Lat_Fis-ant-Vertical.nii.gz seeds_to_rh.S_temporal_inf.nii.gz
seeds_to_lh.G_oc-temp_lat-fusifor.nii.gz seeds_to_lh.S_collat_transv_post.nii.gz seeds_to_rh.G_Ins_lg&S_cent_ins.nii.gz seeds_to_rh.Lat_Fis-post.nii.gz seeds_to_rh.S_temporal_sup.nii.gz
seeds_to_lh.G_oc-temp_med-Lingual.nii.gz seeds_to_lh.S_front_inf.nii.gz seeds_to_rh.G_cingul-Post-dorsal.nii.gz seeds_to_rh.Pole_occipital.nii.gz seeds_to_rh.S_temporal_transverse.nii.gz
seeds_to_lh.G_oc-temp_med-Parahip.nii.gz seeds_to_lh.S_front_middle.nii.gz seeds_to_rh.G_cingul-Post-ventral.nii.gz seeds_to_rh.Pole_temporal.nii.gz targets.txt
seeds_to_lh.G_occipital_middle.nii.gz seeds_to_lh.S_front_sup.nii.gz seeds_to_rh.G_cuneus.nii.gz seeds_to_rh.S_calcarine.nii.gz waypoints.txt
seeds_to_lh.G_occipital_sup.nii.gz seeds_to_lh.S_interm_prim-Jensen.nii.gz seeds_to_rh.G_front_inf-Opercular.nii.gz seeds_to_rh.S_central.nii.gz waytotal
seeds_to_lh.G_orbital.nii.gz seeds_to_lh.S_intrapariet&P_trans.nii.gz seeds_to_rh.G_front_inf-Orbital.nii.gz seeds_to_rh.S_cingul-Marginalis.nii.gz
seeds_to_lh.G_pariet_inf-Angular.nii.gz seeds_to_lh.S_oc-temp_lat.nii.gz seeds_to_rh.G_front_inf-Triangul.nii.gz seeds_to_rh.S_circular_insula_ant.nii.gz
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN/s3078815/seg3078815$ cat seeds.txt
label/lh.G_rectus.nii.gz
label/lh.G_subcallosal.nii.gz
label/lh.S_suborbital.nii.gz
label/lh.S_orbital_med-olfact.nii.gz
label/lh.G_orbital.nii.gz
label/lh.S_orbital-H_Shaped.nii.gz
label/lh.G&S_transv_frontopol.nii.gz
label/lh.G&S_cingul-Ant.nii.gz
label/lh.G&S_frontomargin.nii.gz
label/lh.G_front_sup.nii.gz
label/lh.S_front_sup.nii.gz
label/lh.S_front_middle.nii.gz
label/lh.G_front_middle.nii.gz
label/lh.S_orbital_lateral.nii.gz
label/lh.S_front_inf.nii.gz
label/lh.G_front_inf-Triangul.nii.gz
label/lh.G_front_inf-Orbital.nii.gz
label/lh.Lat_Fis-ant-Horizont.nii.gz
label/lh.Lat_Fis-ant-Vertical.nii.gz
label/lh.S_circular_insula_ant.nii.gz
label/lh.S_circular_insula_sup.nii.gz
label/lh.G_insular_short.nii.gz
label/lh.G_Ins_lg&S_cent_ins.nii.gz
label/lh.S_precentral-inf-part.nii.gz
label/lh.G_front_inf-Opercular.nii.gz
label/lh.S_precentral-sup-part.nii.gz
label/lh.G_precentral.nii.gz
label/lh.S_central.nii.gz
label/lh.G&S_subcentral.nii.gz
label/lh.Lat_Fis-post.nii.gz
label/lh.S_circular_insula_inf.nii.gz
label/lh.G_temp_sup-Plan_polar.nii.gz
label/lh.Pole_temporal.nii.gz
label/lh.G_temp_sup-G_T_transv.nii.gz
label/lh.S_temporal_transverse.nii.gz
label/lh.G_temp_sup-Plan_tempo.nii.gz
label/lh.G_temp_sup-Lateral.nii.gz
label/lh.S_temporal_sup.nii.gz
label/lh.G_temporal_middle.nii.gz
label/lh.S_temporal_inf.nii.gz
label/lh.G_temporal_inf.nii.gz
label/lh.S_collat_transv_ant.nii.gz
label/lh.S_collat_transv_post.nii.gz
label/lh.G_oc-temp_med-Parahip.nii.gz
label/lh.S_oc-temp_lat.nii.gz
label/lh.G_oc-temp_lat-fusifor.nii.gz
label/lh.G_pariet_inf-Supramar.nii.gz
label/lh.G_postcentral.nii.gz
label/lh.S_postcentral.nii.gz
label/lh.G&S_paracentral.nii.gz
label/lh.G_parietal_sup.nii.gz
label/lh.S_intrapariet&P_trans.nii.gz
label/lh.S_interm_prim-Jensen.nii.gz
label/lh.G_pariet_inf-Angular.nii.gz
label/lh.S_occipital_ant.nii.gz
label/lh.G&S_occipital_inf.nii.gz
label/lh.G_occipital_middle.nii.gz
label/lh.S_oc_sup&transversal.nii.gz
label/lh.G_occipital_sup.nii.gz
label/lh.G_cuneus.nii.gz
label/lh.S_oc_middle&Lunatus.nii.gz
label/lh.Pole_occipital.nii.gz
label/lh.S_oc-temp_med&Lingual.nii.gz
label/lh.G_oc-temp_med-Lingual.nii.gz
label/lh.S_calcarine.nii.gz
label/lh.S_parieto_occipital.nii.gz
label/lh.G_precuneus.nii.gz
label/lh.S_subparietal.nii.gz
label/lh.G_cingul-Post-dorsal.nii.gz
label/lh.G_cingul-Post-ventral.nii.gz
label/lh.S_pericallosal.nii.gz
label/lh.S_cingul-Marginalis.nii.gz
label/lh.G&S_cingul-Mid-Post.nii.gz
label/lh.G&S_cingul-Mid-Ant.nii.gz
label/rh.G_rectus.nii.gz
label/rh.G_subcallosal.nii.gz
label/rh.S_suborbital.nii.gz
label/rh.S_orbital_med-olfact.nii.gz
label/rh.G_orbital.nii.gz
label/rh.S_orbital-H_Shaped.nii.gz
label/rh.G&S_transv_frontopol.nii.gz
label/rh.G&S_cingul-Ant.nii.gz
label/rh.G&S_frontomargin.nii.gz
label/rh.G_front_sup.nii.gz
label/rh.S_front_sup.nii.gz
label/rh.S_front_middle.nii.gz
label/rh.G_front_middle.nii.gz
label/rh.S_orbital_lateral.nii.gz
label/rh.S_front_inf.nii.gz
label/rh.G_front_inf-Triangul.nii.gz
label/rh.G_front_inf-Orbital.nii.gz
label/rh.Lat_Fis-ant-Horizont.nii.gz
label/rh.Lat_Fis-ant-Vertical.nii.gz
label/rh.S_circular_insula_ant.nii.gz
label/rh.S_circular_insula_sup.nii.gz
label/rh.G_insular_short.nii.gz
label/rh.G_Ins_lg&S_cent_ins.nii.gz
label/rh.S_precentral-inf-part.nii.gz
label/rh.G_front_inf-Opercular.nii.gz
label/rh.S_precentral-sup-part.nii.gz
label/rh.G_precentral.nii.gz
label/rh.S_central.nii.gz
label/rh.G&S_subcentral.nii.gz
label/rh.Lat_Fis-post.nii.gz
label/rh.S_circular_insula_inf.nii.gz
label/rh.G_temp_sup-Plan_polar.nii.gz
label/rh.Pole_temporal.nii.gz
label/rh.G_temp_sup-G_T_transv.nii.gz
label/rh.S_temporal_transverse.nii.gz
label/rh.G_temp_sup-Plan_tempo.nii.gz
label/rh.G_temp_sup-Lateral.nii.gz
label/rh.S_temporal_sup.nii.gz
label/rh.G_temporal_middle.nii.gz
label/rh.S_temporal_inf.nii.gz
label/rh.G_temporal_inf.nii.gz
label/rh.S_collat_transv_ant.nii.gz
label/rh.S_collat_transv_post.nii.gz
label/rh.G_oc-temp_med-Parahip.nii.gz
label/rh.S_oc-temp_lat.nii.gz
label/rh.G_oc-temp_lat-fusifor.nii.gz
label/rh.G_pariet_inf-Supramar.nii.gz
label/rh.G_postcentral.nii.gz
label/rh.S_postcentral.nii.gz
label/rh.G&S_paracentral.nii.gz
label/rh.G_parietal_sup.nii.gz
label/rh.S_intrapariet&P_trans.nii.gz
label/rh.S_interm_prim-Jensen.nii.gz
label/rh.G_pariet_inf-Angular.nii.gz
label/rh.S_occipital_ant.nii.gz
label/rh.G&S_occipital_inf.nii.gz
label/rh.G_occipital_middle.nii.gz
label/rh.S_oc_sup&transversal.nii.gz
label/rh.G_occipital_sup.nii.gz
label/rh.G_cuneus.nii.gz
label/rh.S_oc_middle&Lunatus.nii.gz
label/rh.Pole_occipital.nii.gz
label/rh.S_oc-temp_med&Lingual.nii.gz
label/rh.G_oc-temp_med-Lingual.nii.gz
label/rh.S_calcarine.nii.gz
label/rh.S_parieto_occipital.nii.gz
label/rh.G_precuneus.nii.gz
label/rh.S_subparietal.nii.gz
label/rh.G_cingul-Post-dorsal.nii.gz
label/rh.G_cingul-Post-ventral.nii.gz
label/rh.S_pericallosal.nii.gz
label/rh.S_cingul-Marginalis.nii.gz
label/rh.G&S_cingul-Mid-Post.nii.gz
label/rh.G&S_cingul-Mid-Ant.nii.gz
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN/s3078815/seg3078815$ ls surf
error.log lh.defect_labels lh.qsphere.nofix lh.smoothwm.S.crv lh.white.H rh.curv rh.jacobian_white rh.smoothwm.H.crv rh.thickness
lh.area lh.inflated lh.smoothwm lh.smoothwm.nofix lh.white.K rh.curv.pial rh.orig rh.smoothwm.K.crv rh.volume
lh.area.mid lh.inflated.H lh.smoothwm.BE.crv lh.sphere lh.white.preaparc rh.defect_borders rh.orig.nofix rh.smoothwm.K1.crv rh.w-g.pct.mgh
lh.area.pial lh.inflated.K lh.smoothwm.C.crv lh.sphere.reg lh.white.preaparc.H rh.defect_chull rh.pial rh.smoothwm.K2.crv rh.white
lh.avg_curv lh.inflated.nofix lh.smoothwm.FI.crv lh.sulc lh.white.preaparc.K rh.defect_labels rh.qsphere.nofix rh.smoothwm.S.crv rh.white.H
lh.curv lh.jacobian_white lh.smoothwm.H.crv lh.thickness rh.area rh.inflated rh.smoothwm rh.smoothwm.nofix rh.white.K
lh.curv.pial lh.orig lh.smoothwm.K.crv lh.volume rh.area.mid rh.inflated.H rh.smoothwm.BE.crv rh.sphere rh.white.preaparc
lh.defect_borders lh.orig.nofix lh.smoothwm.K1.crv lh.w-g.pct.mgh rh.area.pial rh.inflated.K rh.smoothwm.C.crv rh.sphere.reg rh.white.preaparc.H
lh.defect_chull lh.pial lh.smoothwm.K2.crv lh.white rh.avg_curv rh.inflated.nofix rh.smoothwm.FI.crv rh.sulc rh.white.preaparc.K
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN/s3078815/seg3078815$ cat waypoints.txt
anat/wm.lh.nii.gz
anat/wm.rh.nii.gz
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN/s3097367/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s3097367$ ls
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/s3097367/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s3097367$ ls data
bedpostcom_log.tcl bvals bvecs data.nii.gz nodif_brain_mask.nii.gz
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN/s3097367/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s3097367$ ls 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
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN/s3097367/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s3097367$ ls data.bedpostX/xfms/
eye.mat
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