Hi, No. I believe the switch to using FSL’s ‘mcflirt’ as the “default” motion correction was around release 3.15. I’d suggest you switch to using the latest release in the 3.x line, which is 3.22.
For additional context, since the original post referenced the ABCD study, I assume that the effect you observed (poor motion correction) was with 2.4 mm BOLD data. We observed that exact same effect on 2.4 mm resolution data when using MotionCorrection_FLIRTbased.sh as the motion correction. The reasons for this are not entirely clear, but it is the reason which is why we switched the fMRIVolume pipeline to use standard FSL ‘mcflirt’ as the motion correcton with release 3.15. Interestingly, the motion correction is fine when using the legacy MotionCorrection_FLIRTbased.sh correction applied to the 2.0 mm HCP BOLD data. Cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: [email protected] From: <[email protected]> on behalf of Marta Moreno <[email protected]> Date: Wednesday, November 8, 2017 at 5:23 PM To: "Glasser, Matthew" <[email protected]> Cc: "Sanchez, Juan (NYSPI)" <[email protected]>, "[email protected]" <[email protected]> Subject: Re: [HCP-Users] mcflirt_acc in ABCD Is the version 3.4.0 the latest version of the pipelines which default to FSL mcflirt? Thanks, -L Sent from my iPhone On Nov 8, 2017, at 4:55 PM, Glasser, Matthew <[email protected]<mailto:[email protected]>> wrote: 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]<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 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
