Yes that fits with what Juan and I have seen so far—no problems with our 2mm data, but sudden weirdness with 2.4mm data. We’ll try version 3.22 and let you know if we have further issues. Thanks
__________________________ gaurav patel gauravpa...@gmail.com www.neurofreak.net > On Nov 8, 2017, at 10:24 PM, Harms, Michael <mha...@wustl.edu> wrote: > > > 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: > mha...@wustl.edu > > From: <hcp-users-boun...@humanconnectome.org> on behalf of Marta Moreno > <mmorenoort...@icloud.com> > Date: Wednesday, November 8, 2017 at 5:23 PM > To: "Glasser, Matthew" <glass...@wustl.edu> > Cc: "Sanchez, Juan (NYSPI)" <juan.sanc...@nyspi.columbia.edu>, > "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > 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 <glass...@wustl.edu> 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: <hcp-users-boun...@humanconnectome.org> on behalf of "Sanchez, Juan >> (NYSPI)" <juan.sanc...@nyspi.columbia.edu> >> Date: Wednesday, November 8, 2017 at 3:41 PM >> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>, >> "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>, >> "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>, >> "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>, >> "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>, >> "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>, >> "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >> 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 >> 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. 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 > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
