I think it is okay to over write for those pipelines. For the structural pipelines you cannot rerun FreeSurfer after running PostFreeSurfer.
Matt. From: Timothy Hendrickson <[email protected]<mailto:[email protected]>> Date: Tuesday, February 21, 2017 at 4:26 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: "Harms, Michael" <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] Variation in HCP Minimal Preprocessing Pipeline Differences Across Releases Darn. Alright I will reprocess the fMRI and DTI data. It sounds like the structural pipeline has not been changed so I would not have to reprocess that right? I am curious are the pipelines associated with the fMRI and DTI data smart enough to overwrite data files or do I have to totally delete files and start over? -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Office: 612-624-6441 Mobile: 507-259-3434 (texts okay) On Tue, Feb 21, 2017 at 3:34 PM, Glasser, Matthew <[email protected]<mailto:[email protected]>> wrote: I had a look over this and there are some important changes for fMRIVolume (change in the way bias field correction is done) and potentially also some changes in the diffusion pipeline. While it would probably work fine, I would recommend rerunning if it isn’t too painful. Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of Timothy Hendrickson <[email protected]<mailto:[email protected]>> Date: Tuesday, February 21, 2017 at 11:07 AM To: "Harms, Michael" <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] Variation in HCP Minimal Preprocessing Pipeline Differences Across Releases I can see that several changes/additions have been made to 3.21, but I asked whether there is a difference in just the minimal preprocessing pipelines (i.e. PreFreeSurfer, FreeSurfer, PostFreeSurfer, fMRIVolume, fMRISurface, and Diffusion) between 3.4.0 and 3.21. I can ask this a different way, do MSMAll, DeDriftAndResample, PostFix, RestingStateStats, ICAFIX, and TaskfMRIAnalysis scripts rely specifically on data preprocessed from a particular version? My impression was that perhaps MSMAll, DeDriftAndResample, PostFix, RestingStateStats, ICAFIX, and TaskfMRIAnalysis act on top of minimally preprocessed data. Is this wrong? -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Office: 612-624-6441<tel:(612)%20624-6441> Mobile: 507-259-3434<tel:(507)%20259-3434> (texts okay) On Tue, Feb 21, 2017 at 10:59 AM, Harms, Michael <[email protected]<mailto:[email protected]>> wrote: There have been a lot of changes/additions from 3.4.0 to 3.21. If you are starting a new study, it would be preferable for you to start with the latest version. cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173<tel:(314)%20747-6173> St. Louis, MO 63110Email: [email protected]<mailto:[email protected]> From: <[email protected]<mailto:[email protected]>> on behalf of Timothy Hendrickson <[email protected]<mailto:[email protected]>> Date: Tuesday, February 21, 2017 at 9:38 AM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] Variation in HCP Minimal Preprocessing Pipeline Differences Across Releases Hello, I have been using version 3.4.0 of the HCP Minimal Preprocessing Pipeline to process my HCP compatible data. I've used 3.4.0 to run the structural (PreFreeSurfer, FreeSurfer, PostFreeSurfer), fMRI (fMRIVolume, and fMRISurface), and diffusion sub-pipelines. I have now downloaded version 3.21 and notice several additional sub-pipelines such as MSMAll, DeDriftAndResample, PostFix, RestingStateStats, ICAFIX, and TaskfMRIAnalysis to name a few. I am curious whether I can use minimally preprocessed data from 3.4.0 and shoehorn it into the additional sub-pipelines just mentioned. I am hoping I can get away with not reprocessing all of my data through the minimal preprocessing! Thank you! -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Office: 612-624-6441<tel:(612)%20624-6441> Mobile: 507-259-3434<tel:(507)%20259-3434> (texts okay) _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> 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. 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