So, what did the result from 'mcflirt' motion correction look like? Was that well-corrected?
I addition to running the HCP Pipeline without the SBRef (i.e., using the first 10 frames as the motion correction target), it would be informative to run using the middle time point as the motion correction target (which is what 'mcflirt' is doing internally). That would help separate whether the "improvement" is specific to using 'mcflirt', or if it is more a function of the precise motion correction target used in this case. 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 On 10/28/14 12:19 PM, "Book, Gregory" <gregory.b...@hhchealth.org> wrote: >Hi Michael, >The animated gif has the raw timeseries >(SubjID/unprocessed/3T/resting/analysis_3T_resting.nii.gz) on top and the >end result of the HCP processing on the bottom >(SubjID/MNINonLinear/Results/resting/resting.nii.gz). Some of the big >motions are from volumes 450-600. The voxel size of the raw image is >3x3x3 and the final resolution set in the >GenericfMRIVolumeProcessingPipeline script is 3x3x3. > >I can try running it again without the sbref image and see what happens. >-G > > >-----Original Message----- >From: Harms, Michael [mailto:mha...@wustl.edu] >Sent: Tuesday, October 28, 2014 11:40 AM >To: Book, Gregory; Greg Burgess; Xu, Junqian >Subject: Re: [HCP-Users] GenericfMRIVolumeProcessingPipelineBatch motion >correction > > >Hi Greg, >I'm a little confused by what you are showing in your gif. Is the >"original" (top) the uncorrected (raw) time series, and the "final" >(bottom) the result following 'mcflirt' motion correction? If so, why is >there no frontal lobe susceptibility artifact present in the bottom set? > >Or, is the top the result from 'mcflirt', and the bottom the result from >the HCP Pipeline using the SBRef as the Scout? If that is the case, I >think it would be informative if you could run the data through the HCP >Pipeline, but not supply an explicit motion correction reference image, >in which case (as Greg Burgess noted) the mcflirt_acc.sh script will >default to using the average of the first 10 frames as the motion >correction target. > >Also, when you say that the SBRef looks fine, did you overlay the SBRef >and the BOLD timeseries, and compare the two directly? > >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 > > > > >On 10/28/14 7:45 AM, "Book, Gregory" <gregory.b...@hhchealth.org> 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:gcburg...@gmail.com] >>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: burge...@pcg.wustl.edu >> >>On Oct 24, 2014, at 1:10 PM, Xu, Junqian <junqian...@mssm.edu> 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 >>>><gregory.b...@hhchealth.org> 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 >>>> 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 >>>> >>> >>> _______________________________________________ >>> HCP-Users mailing list >>> 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 > > >________________________________ >The materials in this message are private and may contain Protected >Healthcare Information or other information of a sensitive nature. 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