Dear FSL Group, We ran bedpostx and probtrackx2 using a manually chosen seed in the corpus callosum. The result from the reconstruction of the main fiber directions (dyads1.nii) looked good in fslview 4.0.1 (see image here: https://www.dropbox.com/s/04cxezclyzffhoh/fdt.png). However, the fiber path distribution was not as expected (see image here: https://www.dropbox.com/s/nazh8bk5jkxnbnu/directions.png). It seems as if the A-P axis was inverted. This is the pipeline we used:
1. Eddy current and motion correction using <eddy_correct data.nii 0>
2. Rotation of the bvecs after eddy_correct using <fdt_rotate_bvecs bvecs bvecs_rotated data.ecclog>
3. Mask extraction using <bet nodif.nii nodif_brain -f 0.3 -m>
4. Estimation of diffusion parameters using <bedpostx ${data_dir}>
5. Probabilistic fiber tracking using <probtrackx2
--seedref=nodif_brain_mask -o FT_1 -x fdt_coordinates.txt -l --pd -c 0.2 -S 2000 --steplength=0.5 -P 5000 --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 --forcedir --opd -s merged -m nodif_brain_mask --dir=FT_1> We are wondering what the reason could be for the discrepancy between the two results with respect to the orientations. Any help is highly appreciated. Regards,
Lora
