Thanks a lot for your prompt reply, Doug and Bruce. I did collect field maps and just tried epidewarp.fsl, but I met with the following error "FSL Version is 5.0.6, must be 3.X or 4.X". I've searched the email archives and found a message about epidewarp.fsl that works with FSL 5 from Doug, however the link seems to be invalid now ( ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl). Would you please update the link of this file? Thank you in advance.
Best regards, Bingjiang If you did collect field maps, you can use epidewarp.fsl to create a voxel shift map (the only output of epidewarp.fsl that you need; you'll need to FSL to run that program), then use bbregister with the --vsm option to register your func to the struct, then use mri_vol2vol with the --vsm option to map your functional time courses to the anatomical space, then use mri_segstats with the --avgwf (or --avgwfvol) option to get the average time courses for each ROI (or you can do this in matlab easily enough too) doug On 7/21/15 9:29 AM, Bruce Fischl wrote: > Hi Bingjiang > > did you acquire any field maps? If so, you can them to undistort the EPIs > > cheers > Bruce > > > On Tue, 21 Jul 2015, Bingjiang Lyu wrote: > >> Dear all, >> I've got the automaticlly parcellated 'aparc.a2009s+aseg.nii' file for >> individual T1 image, and I want to calculate functional connectivity between >> each pair of the brain regions. I normalized both the T1 and EPI images to >> standard MNI space using SPM12, however, the normalized structural and >> functional images didn't match very well due to the distortion of >> susceptibility artifacts, especially for the inferior temporal and orbital >> frontal cortex (Please see the attached pictures). Could anyone give some >> suggestions on better co-registration of the normalized structural and >> functional images? Thanks a lot in advance. >> >> Best regards, >> Bingjiang >> >> -- >> Bingjiang LyuPhD student >> Center for MRI Research >> Peking University >> Beijing, China >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Bingjiang Lyu PhD student Center for MRI Research Peking University Beijing, China
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