Okay good to know. Thank you Matt. -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 4:28 PM, Glasser, Matthew <glass...@wustl.edu> wrote: > 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 <hendr...@umn.edu> > Date: Tuesday, February 21, 2017 at 4:26 PM > To: Matt Glasser <glass...@wustl.edu> > Cc: "Harms, Michael" <mha...@wustl.edu>, "hcp-users@humanconnectome.org" < > hcp-users@humanconnectome.org> > > 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 <(612)%20624-6441> > Mobile: 507-259-3434 <(507)%20259-3434> (texts okay) > > On Tue, Feb 21, 2017 at 3:34 PM, Glasser, Matthew <glass...@wustl.edu> > 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: <hcp-users-boun...@humanconnectome.org> on behalf of Timothy >> Hendrickson <hendr...@umn.edu> >> Date: Tuesday, February 21, 2017 at 11:07 AM >> To: "Harms, Michael" <mha...@wustl.edu> >> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >> 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 <(612)%20624-6441> >> Mobile: 507-259-3434 <(507)%20259-3434> (texts okay) >> >> On Tue, Feb 21, 2017 at 10:59 AM, Harms, Michael <mha...@wustl.edu> >> 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 <(314)%20747-6173> >>> St. Louis, MO 63110Email: mha...@wustl.edu >>> >>> From: <hcp-users-boun...@humanconnectome.org> on behalf of Timothy >>> Hendrickson <hendr...@umn.edu> >>> Date: Tuesday, February 21, 2017 at 9:38 AM >>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >>> 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 <(612)%20624-6441> >>> Mobile: 507-259-3434 <(507)%20259-3434> (texts okay) >>> >>> _______________________________________________ >>> 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 >> >> >> ------------------------------ >> >> 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. >> > > > ------------------------------ > > 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
