Hi Estrid, When I look this list of subjects up in ConnectomeDB, I get the following:
Subject Release 298051 Q2 397760 Q2 414229 Q2 499566 Q1 654754 Q2 672756 Q1 What "Release" means in ConnectomeDB is the HCP Data Release in which this subject's data was first released. Since all these subjects were first released in the Q1-Q3 releases, they were part of the Q3 data you downloaded in Feb 2014. I am not sure what you mean by the Q4 and Q5 directories of the 500 Subjects release, I'm CC'ing Michael Hileman who works on putting Connectome in a Box together to see if he can clarify that for you. Best, Jenn Jennifer Elam, Ph.D. Outreach Coordinator, Human Connectome Project Washington University School of Medicine Department of Anatomy and Neurobiology, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 [email protected] www.humanconnectome.org -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Estrid Jakobsen Sent: Thursday, September 11, 2014 11:20 AM To: Michael Harms Cc: [email protected] Subject: Re: [HCP-Users] Subject directories missing from connectome in a box Hi Michael, Thanks again. I am only using data from the Q3 release for this particular analysis, and will exclude subject 727654. Perhaps you can clarify another issue regarding the different release versions. Is it possible that some subjects, which are listed in the Q4 and Q5 directories of the 500 subjects release, were included in the Q3 release? The following subjects were downloaded from connectomeDB in February 2014 along with many other Q1-3 subjects, and are listed as belonging to Q4 and Q5 in the 500 subjects release data: 298051 397760 414229 499566 654754 672756 I'm a bit confused as to how the Q label in the directory structure relates to the release names, as "Q3 release" seems to imply that it should only contain subjects from Q1-3. Best, Estrid **************** Estrid Jakobsen PhD Student, IMPRS NeuroCom Department of Neurophysics Max Planck Research Group Neuroanatomy and Connectivity Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig +49 341 9940-2423 ----- Original Message ----- From: "Michael Harms" <[email protected]> To: "Estrid Jakobsen" <[email protected]>, "Michael Harms" <[email protected]> Cc: [email protected] Sent: Thursday, September 11, 2014 5:25:54 PM Subject: Re: [HCP-Users] Subject directories missing from connectome in a box Hi Estrid, First, we highly recommend that users do not mix subjects between data releases that were processed using different pipelines, which is the case for the "500 Subject" and earlier "Q3" releases. Subject 727654 was not included in the 500 Subject release for the reason that I outlined. So, if you are conducting an analysis using the 500 Subject release data, then you should not have a 727654, nor should you include that subject's data from the Q3 release. If you are conducting an analysis using only Q3 release data, then I'd exclude ANY fMRI data from that subject from your Q3 analysis if possible, because that subject's data was released with an intermediate recon version that we didn't intend to release as were in the process of switching the recon version for the fMRI scans. 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: [email protected] On 9/11/14 10:13 AM, "Estrid Jakobsen" <[email protected]> wrote: >Thanks for the information. The issues and fixes page suggests that the >reconstruction artifact for subject 727654 only pertains to the emotion >task data >(https://wiki.humanconnectome.org/display/PublicData/HCP+Data+Release+U >pda tes%3A+Known+Issues+and+Planned+fixes). Is this correct, or would >you recommend excluding this subject from all analyses (e.g. >resting-state)? > >Thanks again! > >**************** >Estrid Jakobsen >PhD Student, IMPRS NeuroCom >Department of Neurophysics >Max Planck Research Group Neuroanatomy and Connectivity Max Planck >Institute for Human Cognitive and Brain Sciences, Leipzig >+49 341 9940-2423 > >----- Original Message ----- >From: "Michael Harms" <[email protected]> >To: "Estrid Jakobsen" <[email protected]>, >[email protected] >Sent: Thursday, September 11, 2014 4:06:51 PM >Subject: Re: [HCP-Users] Subject directories missing from connectome in >a box > > >Hi, >The omission of those 4 subjects from the 500 subject release was >intentional. > >For the first 3 of those subjects, they didn't have gradient-echo >fieldmaps to accompany the structurals. The GE fieldmaps are not >mandatory for running the structurals through the HCP pipelines, but we >didn't get the process for handling those exceptions automated in time >for the 500 subject release. > >For 727654, we need to "retro-recon" that subject's functional runs. >The data from that subject ideally would not have been released in >earlier releases. > >We anticipate that all 4 of those subjects will "return" when the next >batch of subjects gets released sometime in Spring 2015. > >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: [email protected] > > > > >On 9/11/14 6:39 AM, "Estrid Jakobsen" <[email protected]> wrote: > >>Dear all, >> >>We recently received the updated "connectome in a box" with the new >>500 subject release. I've noticed that four subjects, which were >>previously included in data downloaded from connectomeDB, are missing >>from the new data. I was wondering if these subjects have been removed >>on purpose (although I can't find any information on the website >>suggesting this), or if they are likely to be missing due to an error >>while transferring the data to and from the hard drive. >> >>The missing subjects are: >>111009 >>111514 >>429040 >>727654 >> >>Any further information would be much appreciated. >>Best, >> >>Estrid >> >>**************** >>Estrid Jakobsen >>PhD Student, IMPRS NeuroCom >>Department of Neurophysics >>Max Planck Research Group Neuroanatomy and Connectivity Max Planck >>Institute for Human Cognitive and Brain Sciences, Leipzig >>+49 341 9940-2423 >>_______________________________________________ >>HCP-Users mailing list >>[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. 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 [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
