Hi Donna, Thank you--this was very helpful! I am now able to extract the time of acquisition.
Best wishes, Sam -----Original Message----- From: Donna Dierker [mailto:[email protected]] Sent: Wednesday, January 21, 2015 3:55 PM To: Cunningham, Samantha (NIH/NIAAA) [F] Cc: Greg Burgess; [email protected] Subject: Re: [HCP-Users] Time of Acquisition-- Human Connectome Hi Samantha, You can't run that command by itself, because the grep command needs both a pattern and at least one file or standard input. Greg's command below had a curl command followed by "|" to pipe the output of that command to the following grep command. You could capture the output of the curl command to a log file, and then provide the log file as an argument to the grep command, if you have trouble running them all as one string, e.g.: > curl -u username:password -X GET > ${host}/data/archive/projects/${project}/subjects/${subjectID}/experim > ents/${session} > curl.${subjectID}.${session}.|og > grep -e 'scans.*rfMRI\"' curl.${subjectID}.${session}.|og Donna On Jan 21, 2015, at 11:37 AM, "Cunningham, Samantha (NIH/NIAAA) [F]" <[email protected]> wrote: > Hi Greg, > Thank you again for the script below. I am trying to implement it to obtain > the acquisition times for some of the scans, but am running into problems > with the following command: > > grep -e 'scans.*rfMRI\"' > > It seems to hang in my terminal-- am I typing the command correctly? > Thank you! > Sam > > > -----Original Message----- > From: Greg Burgess [mailto:[email protected]] > Sent: Friday, November 14, 2014 4:03 PM > To: Cunningham, Samantha (NIH/NIAAA) [F] > Cc: [email protected] > Subject: Re: [HCP-Users] Time of Acquisition-- Human Connectome > > 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/${subjectID}/experim > ents/${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 _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
