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/${subjectID}/experiments/${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/${subjectID}/experiments/${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
>
>
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