Re: [HCP-Users] Only 40 preprocessed diffusion data in Q2 and Q1 reproc?

[Harms, Michael]

The newer recon algorithm is already incorporated into the ICE code of the R009a "development release" of the multi-band sequence, available at: http://www.cmrr.umn.edu/multiband/ It is not part of the R008 "long-term stable release" however. See the Release Notes, Version Changes of the R009a release for more details. 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 St. Louis, MO  63110 Email: mha...@wustl.edu From: Timothy Verstynen <timot...@gmail.com> Date: Monday, September 9, 2013 7:38 AM To: "Harms, Michael" <mha...@wustl.edu> Cc: Fang-Cheng Yeh <frank....@gmail.com>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Only 40 preprocessed diffusion data in Q2 and Q1 reproc? Thanks for the clarification Michael.  One follow up question, given the heavy development work being done, will the recon algorithms be publicly released as well (apologies if they already are and I'm being naive) in case anyone wants to compare data from the same diffusion WIP sequence from a non-HCP scanner? Very much appreciate the help on this. Cheers, --Tim On Sun, Sep 8, 2013 at 11:49 PM, Harms, Michael <mha...@wustl.edu> wrote: Hi, No, calling the unprocessed and preprocessed dMRI data from Q1/Q2 "unusable" would be too strong a statement.  That data is still very high quality.  It is more an issue that you probably should not mix dMRI data from the different recons, because they will have somewhat different noise properties.  Namely, the new recon algorithm yield "crisper" (less smooth) images.  We understand that changing the recon is a rather major thing, but in this particular case, after considerable discussion, we felt that the new recon was sufficiently improved to merit the change.  The further we get into data acquisition, the more of a hurdle it is to "retro recon" (and then re-process) the existing data, so the odds of us making another change to the recon down the road are relatively low.  It would require a major improvement in recon quality in order for us to even consider something like that again. 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 St. Louis, MO  63110 Email: mha...@wustl.edu From: Timothy Verstynen <timot...@gmail.com> Date: Sunday, September 8, 2013 8:06 PM To: "Harms, Michael" <mha...@wustl.edu>, Fang-Cheng Yeh <frank....@gmail.com> Subject: Fwd: [HCP-Users] Only 40 preprocessed diffusion data in Q2 and Q1 reproc? Dear Michael, Thanks for getting back to us. I have a few quick clarification questions. Am I understanding you correctly that the dMRI data released with Q1 & Q2 are essentially unusable? Is this a pipeline optimization problem or an acquisition issue that resulted in the change? Does HCP have a plan to have a stable recon or will there be continuous recon algo development happening throughout the project. Best, --Tim ---------- Forwarded message ---------- From: Fang-Cheng Yeh <frank....@gmail.com> Date: Sun, Sep 8, 2013 at 4:56 PM Subject: Fwd: [HCP-Users] Only 40 preprocessed diffusion data in Q2 and Q1 reproc? To: Timothy Verstynen <timot...@gmail.com> ---------- Forwarded message ---------- From: Harms, Michael <mha...@wustl.edu> Date: Sun, Sep 8, 2013 at 9:36 AM Subject: Re: [HCP-Users] Only 40 preprocessed diffusion data in Q2 and Q1 reproc? To: "Glasser, Matthew" <glass...@wusm.wustl.edu>, Fang-Cheng Yeh <frank....@gmail.com>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Cc: "Marcus, Dan" <dmar...@wustl.edu>, "Harms, Michael" <mha...@wustl.edu> The impeding Q3 release will have a set of (approximately) 40 different subjects of preprocessed dMRI data. You probably should not mix these 40 (in analysis) with the previous set of 40.  We are in the process of "retro reconning" all the dMRI for the subjects that won't be in the Q3 release, and preprocessed data for all of them should be part of the Q4 release in about 3 months. 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 St. Louis, MO  63110                    Email: mha...@wustl.edu On 9/8/13 2:16 AM, "Glasser, Matthew" <glass...@wusm.wustl.edu> wrote: >This was because the diffusion data were going to be "retro reconned," >meaning that the MR reconstruction into images was going to be performed >again with a better algorithm.  I don't know the status of releasing new >diffusion data, but perhaps Dan or Mike knows. > >Peace, > >Matt. > >On 9/5/13 12:47 PM, "Fang-Cheng Yeh" <frank....@gmail.com> wrote: > >>Hi, >> >>    Our team bought the "Commectone in a box" and found that there are >>only 40 subjects with preprocessed diffusion data, whereas there are >>128 subjects having "unprocessed" diffusion data. It seems that some >>subjects do not have their diffusion data preprocessed. Any reason for >>not doing the preprocessing on their diffusion data? >> >>    I checked out the Q2 documents and there seems no answer to this >>discrepancy. >> >>Best regards, >>Frank >>_______________________________________________ >>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. -- Timothy Verstynen Ph.D. Assistant Professor Dept. of Psychology & Center for the Neural Basis of Cognition Carnegie Mellon University Pittsburgh, PA 15213 www.cognitiveaxon.com   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. -- Timothy Verstynen Ph.D. Assistant Professor Dept. of Psychology & Center for the Neural Basis of Cognition Carnegie Mellon University Pittsburgh, PA 15213 www.cognitiveaxon.com   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