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: <[email protected]<mailto:[email protected]>> on behalf of "Sanchez, Juan (NYSPI)" <[email protected]<mailto:[email protected]>> Date: Wednesday, November 8, 2017 at 3:41 PM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> 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 [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
