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
