What is the resolution of this fMRI data? I seem to recall someone else had trouble with the motion correction pipeline on lower resolution data. It may be that we need to allow an option for mcflirt in the pipelines if the default method doesn¹t work for someone.
Peace, Matt. On 10/28/14, 7:45 AM, "Book, Gregory" <[email protected]> wrote: >Hi Greg, >I ran some more subjects and I checked the resulting image for one of >them. This subject had 0.6mm total displacement over the 900 volumes, no >spikes, all smooth constant displacement through the timeseries. I used >mcflirt to do that registration. In this image >http://olinnidb.org/overlay.gif the final 4D image has motion that the >original, raw 4D image does not. The original image is on top, the final >image on the bottom. The final image moves around more than the raw >image, so I'm wondering if this is really an effect of motion or >something else in our data? Our SBRef images look fine. >Also does it matter that the processed image is moving. Can it still be >used for stats, or is this something we need to fix before attempting >stats? >-Greg > >-----Original Message----- >From: Greg Burgess [mailto:[email protected]] >Sent: Saturday, October 25, 2014 11:25 AM >To: Xu, Junqian >Cc: Book, Gregory; HCP Users >Subject: Re: [HCP-Users] GenericfMRIVolumeProcessingPipelineBatch motion >correction > >I agree with Mike and Gordon. Our best guess right now is that the motion >correction registration target (i.e., SBRef) is corrupted, and that is >affecting the efficacy of motion correction. Previous testing in healthy >normal adults suggested that the SBRef was the best motion correction >target. But, we've seen that the SBRef can be corrupted by motion during >the SBRef collection (immediately prior to the MB scan volumes) in high >motion individuals (e.g., kids, clinical populations). In those cases, >it's possible that a different motion correction target would yield >better results. > >The mcflirt_acc.sh script in the HCP pipelines allows for alternate >"Scout" images (like the mean image or mid-volume), or in the absence of >a motion correction reference image the scripts will create a reference >image from the average of the first 10 frames. > >Even with a good motion correction target, large motions may not be >completely corrected. From your image, it appears that all of the other >frames were adequately corrected. There was no absolute displacement that >was uncorrected. Only the timepoints of large displacement were >inadequately corrected. To salvage data of this sort, you should >seriously consider using frame censoring (aka "scrubbing") or motion >outlier regressors (a la fsl_motion_outliers) in your subsequent analysis. > >--Greg > >____________________________________________________________________ >Greg Burgess, Ph.D. >Staff Scientist, Human Connectome Project Washington University School of >Medicine Department of Anatomy and Neurobiology >Phone: 314-362-7864 >Email: [email protected] > >On Oct 24, 2014, at 1:10 PM, Xu, Junqian <[email protected]> wrote: > >> Greg, >> >> We've observed very similar issue in our Sinai non-compliant subject >>data. I briefly discussed the issue with Greg Burgess at WU, which >>didn't lead to a conclusive solution. I think it may be worthwhile for >>us to put the troublesome motion correction data together and >>cross-check our examination methods to get to the bottom of this issue. >> >> Gordon >> >>> On Oct 24, 2014, at 9:36 AM, Book, Gregory >>><[email protected]> wrote: >>> >>> 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 >>> [email protected] >>> 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. 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