I would use the latest version of the pipelines which default to FSL mcflirt because some folks had been seeing this issue.
Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Sanchez, Juan (NYSPI)" <juan.sanc...@nyspi.columbia.edu<mailto:juan.sanc...@nyspi.columbia.edu>> Date: Wednesday, November 8, 2017 at 3:41 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] mcflirt_acc in ABCD Dear all, We are using pipelines version 3.4. Using the TOPUP distortion correction we are getting very good Epi to T1 co-registration, however it seems that there is intermittent motion in the processed data that is not present in the raw data. This is occuring during MotionCorrection_FLIRTbased.sh the fMRI_gdc.nii.gz shows no motion between volumes, however the fMRI_mc shows motion in the entire brain (around a 1mm shift) see attached qc png This error was present using both mcflirt.sh and mcflirt_acc.sh I used fsl mcflirt with these inputs and the motion error was gone. Any suggestions on how to edit the mcflirt_acc.sh or why this may be happening? thanks Juan Sanchez-Pena _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
