Hi Hossein,
it seems to me that you have forgotten to specify the reference volume to define the seed space (i.e., --seedref option). Looking at your command, I assume that all your masks (i.e., seed, exclusion, stop and waypoints) were defined in standard MNI 2mm space.
One more thing: check that the waypoint condition you really want is indeed ‘OR’ and not ‘AND’.
Cheers,
Matteo
> On 24 Oct 2017, at 17:39, HOSSEIN KARIMI <[log in to unmask]> wrote:
>
> Dear FSL experts,
>
> I'm very new to FSL and I'm trying to track the optic radiations. The code (which I'm copying below) does not produce any errors so I'm assuming it's correct. However, I keep getting a waytotal of zero every time I run it!
>
> I have tried playing with the seed, the target and the way points but I've had no luck. Last thing I did was to use FSL's seed for tracking the left optic radiations (this file "SEED_LGN_LEFT.nii.gz" from here: "https://fsl.fmrib.ox.ac.uk/fslcourse/lectures/practicals/fdt2/index.html"), but this did not work either. I even made this seed bigger using flsmaths but again no luck.
>
> Does anyone happen to know what might be causing this? Any help would be greatly appreciated.
>
> Thank you in advance!
>
> Hossein
>
> probtrackx2 -x $SEEDdir/SEED_LGN_LEFT.nii.gz -l --onewaycondition --modeuler -c 0.2 -S 2000 --steplength=0.2 -P 5000 --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 --xfm=$XFMSdir/stand2diff_warp.nii.gz --invxfm=$XFMSdir/diff2stand_warp.nii.gz --forcedir --opd -s $BEDPOSTdir/merged -m $BEDPOSTdir/nodif_brain_mask.nii.gz --dir=$PROBdir/ORs --out=OR_LH --waypoints=$WAYdir/way_L-OR/waypoints.txt --waycond=OR --stop=$TARGETdir/OR_LH_stopmask.nii.gz --avoid=$EXCLdir/excl_InterHemiFissure_MNI2mm.nii.gz
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