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Hi Chang, You command looks fine to me and it does sound like your output matrix has the correct size. I'm not sure what your question is regarding the "If I give a volumetric seed mask and use --meshspace=freesurfer --seedref=orig.nii.g,the size of the connectivity matrix is WxN where W is the number of voxels in seed. and it creates automatically another file fdt.log:". Again your output matrix seems to have the correct size. In this case it appears that all your masks are volumes and not surfaces, so you don't actually have to define --meshspace. To answer your original questions: 1. It sounds like you want to find any regions that streamlines from your ROI are going to. Avoid masks remove any streamlines from the analysis which cross these mask, so you would typically not want to include them in such an analysis. If you were interested in a specific white matter tract, you could use avoid masks to remove any alternative streamline routes. 2. To determine which WM regions the STS/STG connects to, you would use a volumetric mask for target2 (as you did). If you were more interested in which cortical GM regions the STS/STG connects to you could instead provide for example the white/gray matter boundary (lh.white.gii). Good luck, Michiel On 24/06/2016 10:01, HAO, Chang wrote: > Dear FSL list, > Sorry for bothering you but I haven't received any answer about my > confusion yet. > The size of the connectivity matrix I got is MxN where M is the number > of vertex in vertices of seed region in seed surfacic mask and N is > the number of points in target. I suppose this is correct, right? > > If I give a volumetric seed mask and use --meshspace=freesurfer > --seedref=orig.nii.g,the size of the connectivity matrix is WxN where > W is the number of voxels in seed. and it creates automatically > another file fdt.log: > set tool probtrackx > set probtrack(usereference_yn) 1 > set probtrack(xfm) ...freesurfer_regist/freesurfer2fa.mat > set probtrack(useSurface) 1 > set probtrack(meshspace) freesurfer > set probtrack(surfref).../orig.nii.gz > set probtrack(bedpost_dir).../raw_dwi.bedpostX > set probtrack(xfm).../freesurfer_regist/freesurfer2fa.mat > set probtrack(mode) seedmask > set probtrack(exclude_yn) 0 > set probtrack(usereference_yn) 1 > set probtrack(verbose_yn) 0 > set probtrack(loopcheck_yn) 1 > set probtrack(modeuler_yn) 0 > set probtrack(curvature) 0.2 > set probtrack(nsteps) 2000 > set probtrack(steplength) 0.5 > set probtrack(nparticles) 2000 > set probtrack(fibthresh) 0.01 > set probtrack(distthresh) 0.0 > set probtrack(sampvox) 0.0 > set probtrack(oneway_yn) 1 > set probtrack(wayorder_yn) 0 > set probtrack(waycond) AND > set probtrack(reference) .../freesurfer_seg/lh_STS+STG.nii.gz > set probtrack(output).../tracto > > ---------- Forwarded message ---------- > From: *HAO, Chang* <[log in to unmask] > <mailto:[log in to unmask]>> > Date: 2016-06-23 15:35 GMT+02:00 > Subject: probtrackx using freesurfer surface > To: "[log in to unmask] <mailto:[log in to unmask]>" > <[log in to unmask] <mailto:[log in to unmask]>> > > > Dear FSL experts, > > I'm trying to use surface in probtrackx and compute the connection > probabilities from my seedROI (superior temporal STS/STG) to the rest > of the brain with the option -omatrix2 > > the seed surface is difined as bellow: > # create the seed suaface mask: > mri_annotation2label --subject AHS22 --hemi lh --annotation > aparc.a2009s --outdir ./label/aparc.a2009s > echo $labeldir/lh.bankssts.label lh.middletemporal.label > lh.superiortemporal.label lh.transversetemporal.label > > LH_listOfBigstsstg.txt > label2surf -s $Subdir/surface/lh.white.gii -o > $Subdir/freesurfer_seg/lh.big_STS_STG.gii -l > $subdir/label/LH_listOfBigstsstg.txt > > The target is the rest of the brain excluding the ventricels. I've > created this target mask in volume (Nifti) using published altas.( > named: target.nii.gz) > > My questions are: > 1. should I use -avoid by giving the surface which is created with the > list of exclusion (ventricles+seed)? > 2. the input of target2 in this case should be a surface of a > volumetric mask ? can I use the target.nii.gz for -target2? or project > onto surface (mri_vol2surf) > > Thank you in advance >