Re: [HCP-Users] Integration of FIX cleanup with the minimal preprocessing pipeline

[Glasser, Matthew]

Hi Julien, We simply ran melodic + FIX on the MNI space volume results of each resting state run (i.e. the outputs of the minimal preprocessing pipelines).  The cleanup was then applied to both the volume timeseries and the CIFTI timeseries.  Look in the FIX distribution for a shell script hcp_fix that accomplishes everything. Peace, Matt. From: Julien Dubois <jdub...@caltech.edu> Date: Monday, December 15, 2014 at 2:07 PM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] Integration of FIX cleanup with the minimal preprocessing pipeline Dear HCP Could you give the details of how you integrated the FIX cleanup with the minimal processing pipelines, to generate the cleaned rsBOLD data?  More specifically, MELODIC should be applied in native space after motion correction and correction of distortions with the fieldmap. It seems that the relevant output volume may not be saved by the minimal processing pipeline (unless my assumption that I should work in native space is wrong). Also, FIX requires that "full registration" is run within MELODIC. This of course would mean doing the work twice, since the minimal preprocessing pipeline does the registrations. Before I make all the necessary modifications to the code to incorporate MELODIC exploration and FIX clean up, can you let me know the gist of how you did it (since you did it...)? Thanks! - Julien _______________________________________________ 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 nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users