Re: [HCP-Users] mcflirt_acc in ABCD
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 >> > __
Re: [HCP-Users] mcflirt_acc in ABCD
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<mailto: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<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Sanchez, Juan (NYSPI)" <juan.sanc...@nyspi.columbia.edu<mailto:juan.sanc...@nyspi.columbia.edu>> Date: Wednesday, November 8, 2017 at 3:41 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto: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<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ___ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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 na
Re: [HCP-Users] mcflirt_acc in ABCD
Tim Brown would have to comment on this as he sets the version numbers, not me. We made this change some time ago however. Matt. From: Marta Moreno <mmorenoort...@icloud.com<mailto:mmorenoort...@icloud.com>> Date: Wednesday, November 8, 2017 at 5:22 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "Sanchez, Juan (NYSPI)" <juan.sanc...@nyspi.columbia.edu<mailto:juan.sanc...@nyspi.columbia.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto: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<mailto: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<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Sanchez, Juan (NYSPI)" <juan.sanc...@nyspi.columbia.edu<mailto:juan.sanc...@nyspi.columbia.edu>> Date: Wednesday, November 8, 2017 at 3:41 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto: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<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ___ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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
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
Re: [HCP-Users] mcflirt_acc in ABCD
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<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Sanchez, Juan (NYSPI)" <juan.sanc...@nyspi.columbia.edu<mailto:juan.sanc...@nyspi.columbia.edu>> Date: Wednesday, November 8, 2017 at 3:41 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto: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<mailto: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
