Hi Matt, Great, thanks. I was able to use the multi-run ICA+FIX with MELODIC from FSL 5.0.9-3~nd14.04+1.
Is it correct to use MELODIC from this FSL release (5.0.9-3~nd14.04+1) for HCP multi-run ICA+FIX? We would like to lock down the software versions for our pipelines very soon. According to their change logs, the 5.0.10 version of MELODIC has the following updates: MELODIC can run on CIFTI files; temporal concatenation in MELODIC now defaults to using MIGP. Thank you, Yeun On Fri, Jul 21, 2017 at 1:19 PM, Glasser, Matthew <glass...@wustl.edu> wrote: > Hi Yeun, > > I think you should use multi-run ICA+FIX given the relatively short runs > you have. If your data are all from the same session, I would recommend > cleaning all fMRI runs together (resting state and task). > > As for which version to use, I think using the original is fine, as the > other may have modifications specific to the HCP computer system. I’ve > CCed Tim Brown who made the additional changes in case he has further > comment. > > Matt. > > From: Yeun Kim <yeun...@gmail.com> > Date: Friday, July 21, 2017 at 1:38 PM > > To: Matt Glasser <glass...@wustl.edu> > Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: Re: [HCP-Users] hcp_fix.for_fix1.06a > > To follow up, which script should I work with? hcp_fix_multi_run > or hcp_fix_multi_run.original? > > Thanks, > Yeun > > On Fri, Jul 21, 2017 at 11:13 AM, Yeun Kim <yeun...@gmail.com> wrote: > >> Hi Matt, >> >> We're a Depression-HCP site, using nearly identical sequences as ongoing >> HCP Aging projects. For rs-fMRI: TR = 800ms, 488 volumes, voxel size 2mm^3, >> for 2 runs (one AP, one PA phase encoding). Total time when concatenating >> the two runs is about 13 minutes. Task fMRI runs are the same but shorter >> (300 volumes for CARIT; 338 vol x 2 runs for an in-house task). >> >> On Thu, Jul 20, 2017 at 5:38 PM, Glasser, Matthew <glass...@wustl.edu> >> wrote: >> >>> Hi Yeun, >>> >>> How long are your scans in frames and minutes. What is your acquisition >>> resolution and TR? Using hcp_fix_multi_run might be helpful. >>> >>> Matt. >>> >>> From: Yeun Kim <yeun...@gmail.com> >>> Date: Thursday, July 20, 2017 at 4:33 PM >>> >>> To: Matt Glasser <glass...@wustl.edu> >>> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >>> Subject: Re: [HCP-Users] hcp_fix.for_fix1.06a >>> >>> I've been creating the preprocessing pipeline for CRHD Perturbation of >>> the Treatment of Resistant Depression Connectome by Fast-Acting Therapies. >>> Since it is a longitudinal study, I need all the versions to be consistent >>> for optimal reproducibility. All preprocessing workflows so far have used >>> FSL 5.0.9-3~nd14.04+1. I would like to know if an installation of a newer >>> version is necessary to obtain the modified version of melodic, because >>> this will require re-processing of all data to ensure consistency in data >>> processing. Or, if I can find the modified melodic in another repository >>> separately. >>> >>> Also, we have multiple fMRI scans (2 sets of rs-fMRIs and 2 sets of >>> task-fMRIs). Should we use hcp_fix_multi_run? >>> >>> Thank you, >>> Yeun >>> >>> On Wed, Jul 19, 2017 at 5:21 PM, Glasser, Matthew <glass...@wustl.edu> >>> wrote: >>> >>>> The latest of everything will work for most applications. >>>> >>>> Peace, >>>> >>>> Matt. >>>> >>>> From: Yeun Kim <yeun...@gmail.com> >>>> Date: Wednesday, July 19, 2017 at 7:20 PM >>>> >>>> To: Matt Glasser <glass...@wustl.edu> >>>> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >>>> Subject: Re: [HCP-Users] hcp_fix.for_fix1.06a >>>> >>>> Latest release meaning 5.0.10? Or were the modifications implemented in >>>> previous releases/patches (in 5.0.9)? >>>> >>>> Is the hcp_fix script in http://www.fmrib.ox.ac.uk/~ >>>> steve/ftp/fix.tar.gz (the latest release - version 1.065) the correct >>>> one to use, then? >>>> >>>> >>>> On Wed, Jul 19, 2017 at 5:15 PM, Glasser, Matthew <glass...@wustl.edu> >>>> wrote: >>>> >>>>> I wouldn’t worry about that. Those modifications should be in the >>>>> latest FSL release. >>>>> >>>>> Peace, >>>>> >>>>> Matt. >>>>> >>>>> From: Yeun Kim <yeun...@gmail.com> >>>>> Date: Wednesday, July 19, 2017 at 7:14 PM >>>>> To: Matt Glasser <glass...@wustl.edu> >>>>> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >>>>> Subject: Re: [HCP-Users] hcp_fix.for_fix1.06a >>>>> >>>>> In the script ICAFIX/hcp_fix.for_fix1.06a, it uses the modified >>>>> version of melodic: >>>>> >>>>> Debug "Modified version of melodic in use" >>>>> Debug "melodic located at: ${HOME}/pipeline_tools/fix1.06a/melodic >>>>> used" >>>>> Debug "instead of melodic located at: ${FSLDIR}/bin/melodic" >>>>> Debug "Beginning of melodic version log" >>>>> if [ "${DEBUG}" = "TRUE" ] ; then >>>>> ${HOME}/pipeline_tools/fix1.06a/melodic --version >>>>> fi >>>>> Debug "End of melodic version log" >>>>> >>>>> # "old" melodic command >>>>> #$FSLDIR/bin/melodic -i $fmri -o ${fmri}.ica/filtered_func_data.ica >>>>> -d -250 --nobet --report --Oall --tr=$tr >>>>> # >>>>> >>>>> ${HOME}/pipeline_tools/fix1.06a/melodic -i $fmri -o >>>>> ${fmri}.ica/filtered_func_data.ica -d -250 --nobet --report --Oall >>>>> --tr=$tr >>>>> >>>>> ------------------------------- >>>>> Or should I be using the old melodic? >>>>> >>>>> On Wed, Jul 19, 2017 at 5:05 PM, Glasser, Matthew <glass...@wustl.edu> >>>>> wrote: >>>>> >>>>>> What is this in reference to? >>>>>> >>>>>> Peace, >>>>>> >>>>>> Matt. >>>>>> >>>>>> From: <hcp-users-boun...@humanconnectome.org> on behalf of Yeun Kim < >>>>>> yeun...@gmail.com> >>>>>> Date: Wednesday, July 19, 2017 at 7:04 PM >>>>>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >>>>>> Subject: [HCP-Users] hcp_fix.for_fix1.06a >>>>>> >>>>>> Hi, >>>>>> >>>>>> I cannot find the modified version of melodic in >>>>>> http://www.fmrib.ox.ac.uk/~steve/ftp/fix.tar.gz. >>>>>> >>>>>> Where is the modified melodic? >>>>>> >>>>>> Thank you, >>>>>> Yeun >>>>>> >>>>>> _______________________________________________ >>>>>> 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
