Hi

Can you try unconstrained tracking to see if you get any streamlines from the correct seed surface? (i.e. check that your surface file and the freesurfer2diffusion transforms etc. are all working correctly).  Then you can add the various constraints (i.e. exclusion/inclusion surfaces) and find out at what point you stop getting streamlines - hopefully you’ll be able to tell what’s going on.

Cheers
Saad

> On 3 Mar 2016, at 01:34, Hitoshi Sasaki <[log in to unmask]> wrote:
>
> Dear experts,
>
> I questioned before but no reply came. Please give me some comments.
>
> I want to use the probtrackx2 to get streamlines from big left Superior Temporal Gyri to Broca area.
> First, I made seed, waypoints, exclusions, target masks (volumes from labels)(Freesurfer) but results of probtrackx were not good because of jumping from gyrus to gyrus.
> So I decided to use sufaces (Freesurfer) but probtrackx2 didn't get any streamlines and FA value.
> "surfaces 0" means seed surfaces don't exist?? but very big STG! or did the command of probtrackx2 below have any mistakes?
>
> Terminal says
> Running in seedmask mode
> load seeds
> read gifti
> read scalar data that is float32
> done.
> read gifti
> read scalar data that is float32
> read gifti
> read scalar data that is float32
> Load bedpostx samples
> 1_1
> 1_2
> 1_3
> 2_1
> 2_2
> 2_3
>
> nfibres  : 2
> nsamples : 50
>
> Done loading samples.
> Surface seeds
> surface 0
> libc++abi.dylib: terminating with uncaught exception of type NEWMAT::IndexException
>
>
>
> Below are posted all the commands to generate and process the data.
>
> #make a freesurfer2fa.mat
> tkregister2 --mov mri/orig.mgz --targ mri/rawavg.mgz --regheader --reg junk --fslregout freesurfer2struct.mat --noedit
> convert_xfm -omat struct2freesurfer.mat -inverse freesurfer2struct.mat
> flirt -in dti.nii_FA.nii.gz -ref T1__MPRAGE__Axial_nograppa.nii -omat fa2struct.mat
> convert_xfm -omat struct2fa.mat -inverse fa2struct.mat
> convert_xfm -omat fa2freesurfer.mat -concat struct2freesurfer.mat fa2struct.mat
> convert_xfm -omat freesurfer2fa.mat -inverse fa2freesurfer.mat
>
> #make a surface(.gii)
> mris_convert lh.white lh.white.gii
> mris_convert lh.pial lh.pial.gii
> echo lh.G_front_inf-Opercular.label lh.G_front_inf-Triangul.label > listOfBroca.txt
> echo A.label B.label C.label - - - - - many> listOfLargeSTG.txt
> echo O.label P.label Q.label - - - - - many> listOfExclusion.txt
> label2surf -s lh.white.gii -o lh.Broca.gii -l listOfBroca.txt
> label2surf -s lh.white.gii -o lh.LargeSTG.gii -l listOfLargeSTG.txt
> label2surf -s lh.pial.gii -o lh.exclusion_pial.gii -l listOfExclusion.txt
>
> #make a orig.nii.gz file and nodif_brain_mask(diffusion space)
> mri_convert orig.mgz orig.nii.gz
> /usr/local/fsl5.0.9/fsl/bin/flirt -in $dti_subjects_dir/$D/bedpostx.bedpostX/nodif_brain_mask.nii.gz -ref $dti_subjects_dir/$D/bedpostx.bedpostX/nodif_brain.nii.gz -out $dti_subjects_dir/$D/bedpostx.bedpostX/nodif_brain_mask_diffusion.nii.gz -omat $dti_subjects_dir/$D/bedpostx.bedpostX/xfms/struct2fa.mat -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12  -interp trilinear
>
> #probtrackx2(seed=lh.LargeSTG.gii, exclusion=lh.exclusion_pial.gii, waypoint and target=lh.Broca.gii)
> echo $subjects_dir/$D/t1_bet/lh.Broca.gii > waypoints.txt
> /usr/local/fsl5.0.9/fsl/bin/probtrackx2 -x $subjects_dir/$D/t1_bet/lh.LargeSTG.gii  -l --onewaycondition -c 0.2 -S 2000 --steplength=0.5 -P 5000 --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 --xfm=$subjects_dir/$D/bedpostx.bedpostX/xfms/freesurfer2fa.mat --meshspace=freesurfer -s $subjects_dir/$D/bedpostx.bedpostX/merged --seedref=$subjects_dir/$D/t1_bet/orig.nii.gz --avoid=$subjects_dir/$D/t1_bet/lh.exclusion_pial.gii --stop=$subjects_dir/$D/t1_bet/lh.Broca.gii --forcedir --opd -m $subjects_dir/$D/bedpostx.bedpostX/nodif_brain_mask_diffusion.nii.gz  --dir=$subjects_dir/$D/bedpostx.bedpostX/result --waypoints=$subjects_dir/$D/bedpostx.bedpostX/result_/waypoints.txt  --waycond=AND
>
>
>  Thank you very much for your help.