Hi Joelle, The r227 is the newer, improved version. On the HCP Issues wiki <https://wiki.humanconnectome.org/pages/viewpage.action?pageId=29589520> :
Image reconstruction algorithm versions Two versions of the image reconstruction algorithm applied to dMRI and fMRI data have been used in HCP to date: version r177 for subjects scanned in Q1 through mid-Q3, version r227 for subjects scanned mid-Q3 and after. We were able to retroactively recon all dMRI data using the newer r227 version. However, for the fMRI data, this was not possible and data reconstructed with both r177 and r227 versions remain in ConnectomeDB. The reconstruction version makes a notable signature on the data that can make a large difference in fMRI data analysis. Users wanting to use only data with the same reconstruction algorithm applied in their analyses can filter data on the ConnectomeDB dashboard by fMRI reconstruction version (in the Study Completion category). See Ramifications of Image Reconstruction Version Differences <https://wiki.humanconnectome.org/x/RQBJB> for more details. 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 From: Joelle Zimmermann [mailto:[email protected]] Sent: Monday, November 30, 2015 4:54 PM To: Jennifer Elam Cc: [email protected] Subject: Re: [HCP-Users] Demographic and behavioral subject data Hi Jennifer, Thanks a lot for your help, that's really useful. With regard to the reconstruction - I just wanted to clarify, and apologies if this is in the manual but I did not find it - When I filter by 'Study Completion' > 'Image Reconstruction' > 3T MR fMRI recon, I have 2 options - r177 and r227. Which is the more recent/ considered 'better' reconstruction method? I suspect that the r227 is better if I am interested in using both diffusion MRI data and fMRI data, as the r227 is available for both, whereas r177 is only available for fMRI data, and not for dMRI. Is that correct? Thanks, Joelle On Mon, Nov 30, 2015 at 1:48 PM, Jennifer Elam <[email protected]> wrote: Hi Joelle, Here are the HCP Inclusion Criteria: Inclusion Criteria: No significant history of psychiatric disorder, substance abuse, neurological, or cardiovascular disease -No person report of diagnosis by a treating physician -No hospitalization No pharmacologic or behavioral treatment (12 months duration or longer) by a specialty-trained physician (psychiatrist, neurologist, cardiologist) or therapist (e.g., psychologist, social worker) -Childhood ADHD with no current treatment is allowed -Transient childhood seizures allowed (clarify what type) -Migraines allowed if not taking daily psychoactive medications Age 22 to 35 Ability to give valid informed consent MMSE score of 24 or above Here are the HCP Exclusion Criteria: Two or more non-provoked (e.g., not due to fever) seizures or a diagnosis of epilepsy Any genetic disorder, such as Cystic Fibrosis Use of daily prescription medications for migraines in the past month Multiple Sclerosis, Cerebral Palsy Brain tumor or Stroke Currently on chemotherapy or immunomodulatory agents, or history of radiation or chemotherapy that could affect the brain Sickle Cell Disease Thyroid Hormone Treatment in the past month Treatment for Diabetes in the past month (do not exclude for gestational or diet controlled diabetes) Head Injury If: LOC>30 minutes or Amnesia >24 hours Change in Mental Status >24 hours or CT findings consistent with TBI 3 or more concussive (mild) TBIs Premature Birth (Born >37 weeks for non-twins, born <34 weeks for twins. If weeks unknown, less than 5 lbs. at birth for non-twins. Current Pregnancy Unsafe metal or devices in the body (Cardiac Pacemaker, cochlear implant, aneurism clip) Moderate to Severe Claustrophobia Hope that helps. 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 From: Joelle Zimmermann [mailto:[email protected]] Sent: Monday, November 30, 2015 11:12 AM To: Jennifer Elam Cc: [email protected] Subject: Re: [HCP-Users] Demographic and behavioral subject data Hi Michael and Jennifer, Thank you both for your help, much appreciated. One remaining question - is there currently any cutoff for cognitive scores (i.e. for the MMSE for ex) for subjects being included in the 500 release dataset? Can't find mention of it in the ref manual, so Im guessing probably not. Thanks, Joelle On Mon, Nov 30, 2015 at 11:49 AM, Jennifer Elam <[email protected]> wrote: Hi Joelle, All the HCP subjects are considered healthy young adults with no diagnosed cognitive abnormalities. They do, of course, have a range of abilities and scores on the behavioral tests we conduct. There is a lot of information in Chapter 1 of the current 500 Subjects Reference Manual <http://humanconnectome.org/documentation/S500/HCP_S500+MEG2_Release_Reference_Manual.pdf> for navigating the behavioral data and for filtering subjects—please check it out. There is also a “Download CSV button” at the upper right of the subject Dashboard that will allow you to download all the open access behavioral data in one spreadsheet. Look at the sections of the Reference Manual on Restricted access data to see if you need to apply for access to that data for your purposes. As detailed in the Introduction section of the Reference Manual, subjects that were originally acquired or released in different quarters/releases can be combined in analyses because we ran all subjects through the same analysis pipelines as of the 500 subjects release (as long as you are using data currently in ConnectomeDB, the S500 Connectome in a Box, or S500 S3 Bucket data). Again, as stated in the Ref Manual Introduction, one thing you should be aware of is that the fMRI data collected in Q1 and part of Q2 was reconstructed with a slightly different reconstruction algorithm than subsequent data. You can filter on Study Completion>Image Reconstruction Info: 3T MR>3T MR fMRI Recon Version, if you think it might make a difference to your analyses. In the upcoming 900 Subjects release (coming within the next couple of weeks!), the new subject data will also be comparable to the 500 Subject release data. Pipeline changes since the S500 release have been mostly minor and have only added to the data available (more details to come). 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 From: [email protected] [mailto:[email protected]] On Behalf Of Joelle Zimmermann Sent: Monday, November 30, 2015 10:27 AM To: [email protected] Subject: [HCP-Users] Demographic and behavioral subject data Hello everyone, I want to pick a group of subjects from the 500 subjects +MEG2 for which I will perform (rsfMRI and dMRI) analysis. These should be young, healthy, subjects that have no abnormalities and cognitively able. Does anyone have any pointers about how I can go weeding out subjects? Under "Subject Information" of all subjects, I can see a list of all subjects, where I can see age, release and gender. And when I click on the subject, I find a bunch of behavioral tests and their results for that subject. Should subjects from different releases be combined? Which is the most recent release? Are there certain scores for cognitive assessments that are considered to weed out the cognitively able, healthy subjects? Is this data available somewhere in a spreadsheet form, without having to go into each subject and scrolling though their various assessment scores? Anything would help. Thanks, Joelle _______________________________________________ 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
