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
