Hi Jennifer,
Thank you very much for the reply. Is there a list of the
problematic data that helps users avoid them? I am sorry that I did
not notice this thread.
Thanks,
Frank
On Fri, Oct 30, 2015 at 12:08 PM, Jennifer Elam <el...@pcg.wustl.edu> wrote:
> Hi Frank,
>
> Thanks for the catch. We found the problem with 103515 several weeks ago and
> posted this message to HCP-Users:
>
>
>
> From: hcp-users-boun...@humanconnectome.org
> [mailto:hcp-users-boun...@humanconnectome.org] On Behalf Of Jennifer Elam
>
> Sent: Tuesday, October 13, 2015 4:19 PM
>
> To: hcp-users@humanconnectome.org
>
> Subject: [HCP-Users] Preprocessed Diffusion Data for 103515 incomplete
>
>
>
> We have recently discovered that the preprocessed diffusion data for subject
> 103515, released in Q1 (June 2013) and available since then is
> incomplete/corrupted and should not be used. This is evidenced by the fact
> that the preprocessed diffusion package is <400MB, when it should be 1.22GB.
>
>
>
> It appears that the diffusion preprocessing for that subject skipped an
> important middle pipeline and that accounts for the missing data. Since
> 103515 is a Q1 Release subject, the preprocessed diffusion data for this
> subject has been incomplete since our first Q1 data release and affects all
> HCP distributions via ConnectomeDB, Connectome in a Box, and Amazon S3.
>
>
>
> We are reprocessing the subject and will rerelease the diffusion data for
> 103515 along with the upcoming 900 Subjects +MEG3 Release. At that time,
> Connectome in a Box and Amazon S3 distributions will be updated with the fix
> as well.
>
> Sorry for any inconvenience this has caused. We have added a note about this
> subject on our Data Issues and Fixes wiki page
> (https://wiki.humanconnectome.org/x/EIDDAQ).
>
>
>
> Best,
>
> Jenn
>
>
>
> For 173132, we posted to the list and put this entry in the Data Issues and
> Fixes wiki page (https://wiki.humanconnectome.org/x/EIDDAQ):
>
>
>
> ยท Diffusion data for subject 173132 corrupted
> A problem with the early stages of the v3.1 (500 Subjects) preprocessing of
> diffusion data released for subject 173132 has been found. Diffusion data
> for this subject downloaded from June 6, 2014-October 31, 2014 (or
> distributed in Connectome in a Box drives dated 20140805 or earlier) should
> not be used.
>
> Completed fix: Diffusion data for subject 173132 has been completely
> reprocessed and the fixed version is available in ConnectomeDB as of
> 10/31/14. These files will need to be replaced for 500 Subjects Connectome
> in a Box dated 20140805 or earlier. The reprocessed files are included in
> 500 Subjects Connectome in a Box versions dated 20141203 and later.
>
>
>
> For our QC process in HCP, we do have an extensive QC process, on the
> scan-level data especially, which is detailed in Marcus et al. 2013 and in
> the Post Session 1 section of the HCP Reference Manual Standard Operating
> Procedure Appendix 4.
>
>
>
> When we do find a problem, we work to fix it and update the database ASAP.
> If we are preparing for a data release, we typically roll the fix into the
> updated data in the release, as we will do with the preprocessed diffusion
> packages for 103515.
>
>
>
> 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
>
> el...@pcg.wustl.edu
>
> www.humanconnectome.org
>
>
>
> ___
>
>
>
> 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
>
> el...@pcg.wustl.edu
>
> www.humanconnectome.org
>
>
>
>
>
> -Original Message-
> From: hcp-users-boun...@humanconnectome.org
> [mailto:hcp-users-boun...@humanconnectome.org] On Behalf Of Fang-Cheng Yeh
> Sent: Friday, October 30, 2015 10:19 AM
> To: hcp-users@humanconnectome.org
> Subject: [HCP-Users] Another corrupted diffusion MRI data set found (Subject
> #103515)
>
>
>
> Dear HCP experts,
>
>
>
> The preproc diffusion data in subject #103515 seems to contain empty
> values in some DWI acquisitions. It seems that the preproc failed in this
> subject? (The unproc data look okay)
>
>
>
> I tried to download and check the preproc
