Thank you Matt & Michael. I initially thought this might be listed on the known issues page ( https://wiki.humanconnectome.org/display/PublicData/HCP+Data+Release+Updates%3A+Known+Issues+and+Planned+fixes). It might be useful to list subjects with incomplete brain coverage there. Yet I also see how the responsibility could be left to the investigators who are using the data, who should in all cases properly look at the images they are using.
Thank you for all your work, and the sharing of this amazing resource. - Julien On Mon, Dec 19, 2016 at 7:56 AM, Harms, Michael <[email protected]> wrote: > > Yes, there is a giant nod of the head around frames 900-906 for the > REST1_LR run of 101107. The fMRI preprocessing pipeline is set up such > that the final brain mask requires that data be available in a given brain > voxel for *every* time point. If that isn’t the case, that voxel gets > masked out. > > The vast majority of subjects have complete brain coverage. But the issue > of how to communicate the instances of incomplete brain coverage in a large > dataset (such as HCP) is a complicated one. If you have suggestions, we’d > be happy to hear them. > > 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] > > From: <[email protected]> on behalf of "Glasser, > Matthew" <[email protected]> > Date: Friday, December 16, 2016 at 9:38 PM > To: Julien Dubois <[email protected]>, "[email protected]" < > [email protected]> > Subject: Re: [HCP-Users] Subject 101107: different brain mask for > rfMRI_REST1_LR and rfMRI_REST1_RL? > > Check the raw data for that run and see if the head didn’t move out of the > FOV. > > Peace, > > Matt. > > From: <[email protected]> on behalf of Julien Dubois < > [email protected]> > Date: Friday, December 16, 2016 at 1:02 PM > To: "[email protected]" <[email protected]> > Subject: [HCP-Users] Subject 101107: different brain mask for > rfMRI_REST1_LR and rfMRI_REST1_RL? > > Hi, > > I was just working with some of the HCP volume data and noticed that > subject 101107 had a chunk of ventral prefrontal cortex missing in the > rfMRI_REST1_LR.nii.gz volume (in MNINonLinear/Results/rfMRI_REST1_LR). > > Interestingly, the brain mask for rfMRI_REST1_RL.nii.gz seems different > (more inclusive). I thought that the brain masking was based on the > anatomicals (T1w and T2w), and was therefore the same across functional > scans? > > Either I misunderstood the brain masking procedure, or there is an issue > in the minimally preprocessed data for 101107. Screenshot of REST1_LR and > REST1_RL volumes, side by side, attached. > > Thanks! > - Julien > > _______________________________________________ > 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. > > _______________________________________________ > 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. > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
