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This method of fMRI distortion correction is implemented in the HCP Pipelines: https://github.com/Washington-University/Pipelines/blob/master/global/scrip ts/TopupPreprocessingAll.sh Peace, Matt. On 5/13/18, 11:14 PM, "FSL - FMRIB's Software Library on behalf of Him anshu" <[log in to unmask] on behalf of [log in to unmask]> wrote: >Dear Matthew, > >Thank you for your response... > >I also feel that with 2X distortion scans acquired using spin echo is >better conditioned than a standard field map. And even I din't acquired >the regularized field map either. Therefore, I have to use 2X distortion >scans to correct susceptibility induced distortions in my fMRI data. For >this, I have tried FSL-topup and used the commands given below. > >Given that I have two short EPIs, each with 3 volumes (A_P and P_A) in >anterior to posterior and posterior to anterior directions. And I need >to correct the distortions of my resting state EPI, which have 200 >volumes and is acquired in P_A direction. > > >fslroi A_P b0_blip_up 0 1 >fslroi P_A b0_blip_down 0 1 >fslmerge -t both_b0 b0_blip_up b0_blip_down >topup --imain=both_b0 --datain=my_acq_param.txt --config=b02b0.cnf >--out=my_topup_results >applytopup --imain=A_P,P_A --inindex=1,2 --datain=my_acq_param.txt >--topup=my_topup_results --out=my_hifi_images > >I can anticipate that my_hifi_images have 3 volumes does not have >susceptibility induced distortions. Kindly suggest that how the >susceptibility induced distortions of my resting state EPI can be >corrected using applytopup? > >Can you suggest some pointers to solve this issue/problem. > >Thanks and Regards >Himanshu Joshi