Re: [HCP-Users] GenericfMRIVolumeProcessingPipelineBatch motion correction

[Harms, Michael]

Yes, you can use that output in subsequent stats processing. Regarding the motion, you need to compare against the uncorrected time series at the same time points.  Was there very large motion at those time points?  Large motion that occurs in the middle of a volume acquisition is impossible to correct fully, as that frame is inherently corrupted.  So, you may be seeing the remnants of that. Also, what is the quality of the "SBRef" that you are using as the registration target for the motion correction?  If that itself is severely corrupted (because the subject moved considerably at the very start of the scan) we have seen that that can have detrimental effects on not only the quality of the reconstruction of the whole BOLD time series, but also the stability of the motion correction itself. 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: mha...@wustl.edu From: <Book>, Gregory <gregory.b...@hhchealth.org> Date: Friday, October 24, 2014 8:36 AM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] GenericfMRIVolumeProcessingPipelineBatch motion correction I processed some of our fMRI own data through the HCP pipelines and now I’m looking at the AnalysisDir/MNINonLinear/Results/taskname/taskname.nii.gz file. I’m assuming this is the 4D file which should be motion corrected, undistorted, and skull stripped. And that this file should be able to be used directly in stats processing without any further steps?   However, I still see significant motion when viewing the 4D file in a cine view. The brain mask is constant, but the image under the mask moves. Did the mcflirt step not work, or is this normal?   The animated .gif can be seen here: http://olinnidb.org/preview.gif The major motion occurs around volumes 150 and 200-250. -G   _________________________________________________ Gregory Book Senior Technology Manager Olin Neuropsychiatry Research Center, Institute of Living, Hartford Hospital 200 Retreat Avenue Hartford, CT 06106 Tel: 860-545-7267 Fax: 860-545-7797 gregory.b...@hhchealth.org http://nidb.sourceforge.net   This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure, or distribution is prohibited. If you are not the intended recipient, or an employee or agent responsible for delivering the message to the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message, including any attachments. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org 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 HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users