Matt

No, I don't think so. By the way, on a side note, it seems that applying afni's 3dcopy can restore the sform matrix that we talked about.

Yes, I have the average image from the EPI. Thanks

Thanks Nick, I'm afraid I lost you there, would you please elaborate more? or point me to an example? Matt

Hi Nick, You are right. I did these two lines of motion correction for one subject and although in fsleyes and ITK-SNAP (it only works on the first volume) the orientations are OK, but sform matrix is not showing. So, there is some effect here. If I skip the motion correction in ANTs, can we proceed to next step using the files pre-processed in FSL? P.S. Interestingly, the template that I created, seems to have not affected and all the matrices are ok. Thanks, Matt

Hi Nick, You are right. I did these two lines of motion correction of one subject and although in fsleyes and ITK-SNAP (it only works on the first volume) the orientations are OK, but sform matrix is not showing. So, there is some effect here. If I skip the motion correction in ANTs, can we proceed to next step using the files pre-processed in FSL? P.S. Interestingly, the template that I created, seems to have not affected and all the matrices are ok. Thanks, Matt

Hi Nick, You are right. I did these two lines of motion correction of one subject and although in fsleyes and ITK-SNAP (it only works on the first volume) the orientations are OK, but sform matrix is not showing. So, there is some effect here. If I skip the motion correction in ANTs, can we proceed to next step using the files preprocessed inFSL? P.S. Interestingly, the template that I created, seems to have not affected and all the matrices are ok. Thanks, Matt

Hi Nick, You are right. I did these two lines of motion correction of one subject and although in fsleyes and ITK-SNAP (it only works on the first volume) the orientations are OK, but sform matrix is not showing. So, there is some effect here. If I skip the motion correction in ANTs, can we proceed to next step using the files FSL? P.S. Interestingly, the template that I created, seems to have not affected and all the matrices are ok. Thanks, Matt

Oh, I see... then this could cause a problem down the line. I want to run group ICA on the final registered EPI files. On the other hand, FSL's registration would not give the best outcome, so I like to use ANTs for registration. Any work around you might think of? Thanks!