Dear FSL and eddy experts,We are trying using the new version of eddy. Out sequence is a multishell forward-reverse sequence with 33 directions @ b=700, 64 directions @ b=1000 and 100 directions @ b=2500, plus 13 b0s for a total of 210 P>>A volumes and 210 A>>P volumes. Our gradient table is a q-ball table.In our CENTOS OS 6, the eddy_openmp seems to work fine and here are the outputs:EC.niiEC.eddy_outlier_reportEC.eddy_parametersAnd also:EC.eddy_rotated_bvecsEC.eddy_movement_rmsEC.eddy_outlier_mapEC.eddy_outlier_n_stdev_mapEC.eddy_post_eddy_shell_alignment_parameters
As per previous posts, we used the -- resamp=lsr option to average the 210 P>>A and the 210 A>>P. So our fslnvols EC.nii is now 210. However, the EC.eddy_rotated_bvecs still has 420 directions. Can you confirm that the best option available now will be to average the 2 main components of this merged and corrected bvec file?
In this regard, future version of eddy are going to offer ?better? solution for this?
Also, we tested the ‘standard’ version of eddy (described as part of FSL 5.0.8) that comes with FSL 5.0.9 package. With this version, we have been able to run the -- resamp=lsr option, but, of course not the –fep option. However, along with EC.nii, EC.eddy_outlier_report and EC.eddy_parameters, we found an extra image:EC.eddy_outlier_free_data.nii
With eddy 5.0.8, the lsr option did not seem to work (i.e., 420 volumes); however EPI distortions were effectively reduced in the EC.nii, but not in the EC.eddy_outlier_free_data.nii. The name of this second output suggests the outliers reported in EC.eddy_outlier_report had been removed. Is this correct? Is there a way to test this? We tried a simple subtraction, but given that the 1st, but not the 2nd , image is ‘corrected’, it was not possible to make any inference. Also, does the –fep option (in eddy_openmp) ‘fill empty planes in x- or y- directions’ after having removed the outliers? In other words, outliers are already removed in the EC.nii output of eddy_openmp?
Any help will be greatly appreciated! Thanks a lot!! Amelia
Amelia Versace, MDLoeffler Building, room 215121 Meyran AvenuePhone: 412.383.8131Email: [log in to unmask]