Hi Sam, It should be possible to get these without a web browser using the XNAT REST API. I’m not expert at using it, but here’s what I found that worked for me.
###In linux, run the following commands: host="https://db.humanconnectome.org”; project="HCP_500”; # for each subject that you want, set the subjectID and create the session identifier subjectID="100307”; session=“${subjectID}_3T”; curl -u username:password -X GET ${host}/data/archive/projects/${project}/subjects/${subjectID}/experiments/${session} | grep -e 'scans.*rfMRI\"' This should give you a set of “id” fields for the rfMRI scans for that participant. obj.categories["scans"].push({id:"206",label:"206 rfMRI"}); obj.categories["scans"].push({id:"208",label:"208 rfMRI"}); obj.categories["scans"].push({id:"406",label:"406 rfMRI"}); obj.categories["scans"].push({id:"408",label:"408 rfMRI"}); Script something to grab the id fields from that output. For each of the id fields, run the following commands: id="206”; ## this is one of the four id’s returned by the command above curl -u username:password -X GET ${host}/data/archive/projects/${project}/subjects/${subjectID}/experiments/${session}/scans/${id} | grep startTime This should return a field that contains the starting time of the scan: <TR><TD>startTime</TD><TD>20:04:46</TD></TR> Hopefully, using these commands as a basis, you can figure out how to write a script that will loop over all of your subjects and scans to give you all of the start times that you need. --Greg ____________________________________________________________________ Greg Burgess, Ph.D. Staff Scientist, Human Connectome Project Washington University School of Medicine Department of Anatomy and Neurobiology Phone: 314-362-7864 Email: [email protected] > On Nov 13, 2014, at 10:34 AM, Jennifer Elam <[email protected]> wrote: > > Hi Samantha, > Sorry for the delay in getting back to you. The time of day of collection > for each MR session/scan for each HCP subject is available in ConnectomeDB. > Here's how to find it: > > -From the splash page or 500 Subjects project page in ConnectomeDB click on > Explore/Browse Subjects to go to the Subject Dashboard. > -If you wish, you can use the data filters to select for subjects, e.g. with > 4 sessions of complete rfMRI data. > -Click on one of the subject ID listed in the columns--this is a link to a > page for that subject. > -Click on the MR Session link on the subject details page. > -Click on the "+" button beside the scan(s) for which you want time info. > -Time should be listed as the first row of details for the scan. > > We do not include dates of collection for privacy reasons, instead Day 1 and > Day 2 are used to distinguish the days of acquisition. Hope this is helpful > and good luck with your analyses. > > 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: Cunningham, Samantha (NIH/NIAAA) [F] > [mailto:[email protected]] > Sent: Wednesday, November 05, 2014 7:04 AM > To: David Van Essen; Jennifer Elam > Subject: RE: Time of Acquisition-- Human Connectome > > Hi Jenn and David-- thank you for your help! I am working on a circadian > rhythm study and was hoping to compare resting-state data between different > times of the day. > > Best, > Sam > > ________________________________ > From: David Van Essen [[email protected]] > Sent: Tuesday, November 04, 2014 10:00 PM > To: Jennifer Elam > Cc: Cunningham, Samantha (NIH/NIAAA) [F] > Subject: Re: Time of Acquisition-- Human Connectome > > Jenn, > > Good point. Please extend your response to hcp-users as others may be > interested. > > David > > On Nov 4, 2014, at 5:43 PM, Jennifer Elam > <[email protected]<mailto:[email protected]>> wrote: > > Hi Samantha, > Page 44 of the current Reference > Manual<http://humanconnectome.org/documentation/S500/HCP_S500_Release_Refere > nce_Manual.pdf> shows a typical participant schedule. However, in order to > make the scheduling work for our subjects (some of whom work full time and > did the scanning at night/on a weekend, for example), we do the scanning at > many different times of day so you can't assume that all the rfMRI scanning > was done from 1-2pm, for example, for all subjects. As David mentioned, > usually rfMRI session 1 (REST 1) is done on Day 1 and REST2 is done on Day > 2. I am checking with our database expert about whether one can reliably > look at the time information for each scan in ConnectomeDB if you want to > roughly match scan times in your analysis. I'll get back to you when I hear > more. > > 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<tel:314-362-9387> > [email protected]<mailto:[email protected]> > www.humanconnectome.org<http://www.humanconnectome.org/> > > From: David Van Essen [mailto:[email protected]] > Sent: Tuesday, November 04, 2014 5:09 PM > To: Cunningham, Samantha (NIH/NIAAA) [F] > Cc: David Van Essen; Jennifer Elam > ([email protected]<mailto:[email protected]>) > Subject: Re: Time of Acquisition-- Human Connectome > > Hello Samantha, > > In general, one pair of rfMRI scans (LR and RL phase encoding) were acquired > on day 1, another pair on day 2. Time of day varied according to the > schedule. > > I am copying Jenn Elam, who may have more detail to provide. Also, I > believe the Reference Manual on the HCP website gives added information. > > Finally, please join hcp-users and post there if you have additional > questions that may be of general interest. > > David > > > On Nov 4, 2014, at 10:40 AM, Cunningham, Samantha (NIH/NIAAA) [F] > <[email protected]<mailto:[email protected]>> wrote: > > > Hi David, > I am currently working with your Human Connectome datasets for a > resting-state fMRI/DTI project and was hoping for your help. I noticed that > the rs-fMRI scans took place over two separate sessions-did these sessions > take place on the same day (and if so, at what times)? Or on a different day > at the same time? > > I am currently using the unprocessed Structural, Diffusion, and Resting > State fMRI 1 datasets from the "WU-Minn HCP Data - 500 Subjects" (40 > Unrelated Subjects) group. Everything was downloaded > fromhttps://db.humanconnectome.org/. > > Thank you for your help! > Samantha > -------------------------------------------------- > Samantha Cunningham, Ph.D. > Postdoctoral Fellow > National Institutes of Health|NIAAA|LNI > [email protected]<mailto:[email protected]> > > > Samantha Cunningham, Ph.D. > Postdoctoral Fellow > National Institutes of Health|NIAAA|LNI > [email protected]<mailto:[email protected]> > > > _______________________________________________ > 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
