Hi Yeun, You would not want to use MIGP for this and this isn’t for running melodic directly on CIFTI files. If you are acquiring no more than a total of 1652 frames of fMRI per subject, you shouldn’t have any issues with that version that I can think of. Tim Brown might have further thoughts though.
Matt. From: Yeun Kim <yeun...@gmail.com<mailto:yeun...@gmail.com>> Date: Wednesday, July 26, 2017 at 5:04 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>, "Brown, Tim" <tbbr...@wustl.edu<mailto:tbbr...@wustl.edu>> Subject: Re: [HCP-Users] hcp_fix.for_fix1.06a 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<mailto: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<mailto:yeun...@gmail.com>> Date: Friday, July 21, 2017 at 1:38 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto: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<mailto: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<mailto: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<mailto:yeun...@gmail.com>> Date: Thursday, July 20, 2017 at 4:33 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto: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<mailto:glass...@wustl.edu>> wrote: The latest of everything will work for most applications. Peace, Matt. From: Yeun Kim <yeun...@gmail.com<mailto:yeun...@gmail.com>> Date: Wednesday, July 19, 2017 at 7:20 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto: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<mailto: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<mailto:yeun...@gmail.com>> Date: Wednesday, July 19, 2017 at 7:14 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto: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<mailto:glass...@wustl.edu>> wrote: What is this in reference to? Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Yeun Kim <yeun...@gmail.com<mailto:yeun...@gmail.com>> Date: Wednesday, July 19, 2017 at 7:04 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto: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<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
