<div dir="ltr"><div dir="auto"><div><div class="gmail_extra">Hello all,</div></div><div class="gmail_extra" dir="auto"><br></div><div class="gmail_extra" dir="auto">I used the following commands to do tractography with camino. Could someone please let me know whether I did it right and if it's correct how can I read that bfloat file in MATLAB? My goal is to have the coordinate of fiber tracts in MATLAB.</div><div class="gmail_extra" dir="auto"><br></div><div class="gmail_extra" dir="auto"><div class="gmail_extra" dir="auto"><b><i>fslmaths $1/$sub/data/data_FA.nii.gz -thr 0.3 -bin $1/$sub/tract/data_FA_thr03.nii.gz</i></b></div><div class="gmail_extra" dir="auto"><b><i>cp $1/$sub/data/nodif_brain_mask_trimmed.nii.gz $1/$sub/tract/nodif_brain_mask_trimmed.nii.gz</i></b></div><div class="gmail_extra" dir="auto"><b><i>TVFromEigenSystem -basename $1/$sub/data/data -type FSL -out $1/$sub/tract/data_tensor.nii.gz<br></i></b></div><div class="gmail_extra" dir="auto"><b><i>/camino/bin/nii2dt -inputfile $1/$sub/tract/data_tensor.nii.gz -bgmask $1/$sub/tract/nodif_brain_mask_trimmed.nii.gz -uppertriangular > $1/$sub/tract/tensor.Bdouble</i></b></div><div class="gmail_extra" dir="auto"><b><i>cat $1/$sub/tract/tensor.Bdouble | track -inputmodel dt -seedfile $1/$sub/tract/data_FA_thr03.nii.gz -outputroot $1/$sub/tract/WB_one_tensor -curvethresh 80 -anisthresh 0.3</i></b></div><div class="gmail_extra" dir="auto"><b><i>camino_to_trackvis -i $1/$sub/tract/WB_one_tensor1.Bfloat -o $1/$sub/tract/WB_one_tensor.trk --nifti $1/$sub/tract/nodif_brain_mask_trimmed.nii.gz --phys-coords</i></b></div><div class="gmail_extra" dir="auto"><b><i><br></i></b></div><div class="gmail_extra">Thank you!</div><div class="gmail_extra">Mahmoud</div></div></div>
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