Re: [HCP-Users] Intermediate freesurfer files not available through CREST?

2018-09-25 Thread Elam, Jennifer 
This wiki page might help: 
https://wiki.humanconnectome.org/display/PublicData/How+To+Access+Subject+Data+via+REST

How To Access Subject Data via REST - Connectome Data 
...
wiki.humanconnectome.org
For the HCP 1200 Release, unprocessed and processed data for a subject can be 
accessed via REST calls apart from using other modes such as Connectome In a 
Box, Aspera, Amazon AWS.. In order to access data for a subject, you will need 
to register at https://db.humanconnectome.org To get data via REST, in a 
script, you could use tools like curl. Data organization

Best,

Jenn

Jennifer Elam, Ph.D.
Scientific Outreach, Human Connectome Project
Washington University School of Medicine
Department of Neuroscience, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
e...@wustl.edu
www.humanconnectome.org



From: hcp-users-boun...@humanconnectome.org 
 on behalf of Harms, Michael 

Sent: Tuesday, September 25, 2018 10:22:40 AM
To: Nicola Toschi; hcp-users@humanconnectome.org >> hcp-users
Subject: Re: [HCP-Users] Intermediate freesurfer files not available through 
CREST?


They should be.

Have you searched the list for previous recipes for REST calls into the CREST 
resource?  It may be simply that your path isn't correct.
The FS data folder structure begins at /T1w/, so you probably 
want something like /T1w//surf/lh.white


--
Michael Harms, Ph.D.

---

Associate Professor of Psychiatry

Washington University School of Medicine

Department of Psychiatry, Box 8134

660 South Euclid Ave.Tel: 314-747-6173

St. Louis, MO  63110  Email: mha...@wustl.edu

On 9/25/18, 9:56 AM, "Nicola Toschi"  wrote:

Hi Michael,

thank you for your reply.

I am working with the whole S1200 release would actually much prefer to
fetch only the files I need (namely surfaces, thickness, area, curvature
and jacobian - more or less) in a targeted way (not least because of
data footprint issue on compute clusters).

Are those files available via CREST?

Thank you!

nicola


On 09/25/2018 03:17 PM, Harms, Michael wrote:
> Hi,
> You can obtain the entire FreeSurfer output via the Structural Extended 
> packages.  Perhaps that would be an easier way for you to proceed?
>
> Cheers,
> -MH
>
> --
> Michael Harms, Ph.D.
>
> ---
>
> Associate Professor of Psychiatry
>
> Washington University School of Medicine
>
> Department of Psychiatry, Box 8134
>
> 660 South Euclid Ave.Tel: 314-747-6173
>
> St. Louis, MO  63110  Email: mha...@wustl.edu
>
> On 9/24/18, 6:25 PM, "hcp-users-boun...@humanconnectome.org on behalf of 
> Nicola Toschi"  tos...@med.uniroma2.it> wrote:
>
> Hello List,
>
> I am trying to retrieve the files present in the 'surf' directory of the
> freesurfer reconstruction via CREST. However, when trying to retrieve
> (e.g) lh.white I always end up with a file containing only error messages.
>
> I would be grateful for any pointers. below is an example of my curl
> call after opening a session.
>
> curl --cookie JSESSIONID= -O
> https://db.humanconnectome.org/data/archive/projects/HCP_1200/subjects/100307/experiments/100307_CREST/resources/100307_CREST/files/T1w/surf/lh.white
>
> Thank you very much in advance!
>
> Nicola
>
>
> ---
> This email has been checked for viruses by Avast antivirus software.
> https://www.avast.com/antivirus
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> 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.




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
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Intermediate freesurfer files not available through CREST?

2018-09-25 Thread Harms, Michael 

They should be.

Have you searched the list for previous recipes for REST calls into the CREST 
resource?  It may be simply that your path isn't correct.
The FS data folder structure begins at /T1w/, so you probably 
want something like /T1w//surf/lh.white


--
Michael Harms, Ph.D.

---

Associate Professor of Psychiatry

Washington University School of Medicine

Department of Psychiatry, Box 8134

660 South Euclid Ave.Tel: 314-747-6173

St. Louis, MO  63110  Email: mha...@wustl.edu

On 9/25/18, 9:56 AM, "Nicola Toschi"  wrote:

Hi Michael,

thank you for your reply.

I am working with the whole S1200 release would actually much prefer to
fetch only the files I need (namely surfaces, thickness, area, curvature
and jacobian - more or less) in a targeted way (not least because of
data footprint issue on compute clusters).

Are those files available via CREST?

Thank you!

nicola


On 09/25/2018 03:17 PM, Harms, Michael wrote:
> Hi,
> You can obtain the entire FreeSurfer output via the Structural Extended 
> packages.  Perhaps that would be an easier way for you to proceed?
>
> Cheers,
> -MH
>
> --
> Michael Harms, Ph.D.
>
> ---
>
> Associate Professor of Psychiatry
>
> Washington University School of Medicine
>
> Department of Psychiatry, Box 8134
>
> 660 South Euclid Ave.Tel: 314-747-6173
>
> St. Louis, MO  63110  Email: mha...@wustl.edu
>
> On 9/24/18, 6:25 PM, "hcp-users-boun...@humanconnectome.org on behalf of 
> Nicola Toschi"  tos...@med.uniroma2.it> wrote:
>
> Hello List,
>
> I am trying to retrieve the files present in the 'surf' directory of the
> freesurfer reconstruction via CREST. However, when trying to retrieve
> (e.g) lh.white I always end up with a file containing only error messages.
>
> I would be grateful for any pointers. below is an example of my curl
> call after opening a session.
>
> curl --cookie JSESSIONID= -O
> https://db.humanconnectome.org/data/archive/projects/HCP_1200/subjects/100307/experiments/100307_CREST/resources/100307_CREST/files/T1w/surf/lh.white
>
> Thank you very much in advance!
>
> Nicola
>
>
> ---
> This email has been checked for viruses by Avast antivirus software.
> https://www.avast.com/antivirus
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> 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.




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
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Intermediate freesurfer files not available through CREST?

2018-09-25 Thread Nicola Toschi 
Hi Michael,

thank you for your reply.

I am working with the whole S1200 release would actually much prefer to 
fetch only the files I need (namely surfaces, thickness, area, curvature 
and jacobian - more or less) in a targeted way (not least because of 
data footprint issue on compute clusters).

Are those files available via CREST?

Thank you!

nicola


On 09/25/2018 03:17 PM, Harms, Michael wrote:
> Hi,
> You can obtain the entire FreeSurfer output via the Structural Extended 
> packages.  Perhaps that would be an easier way for you to proceed?
>
> Cheers,
> -MH
>
> --
> Michael Harms, Ph.D.
>
> ---
>
> Associate Professor of Psychiatry
>
> Washington University School of Medicine
>
> Department of Psychiatry, Box 8134
>
> 660 South Euclid Ave.Tel: 314-747-6173
>
> St. Louis, MO  63110  Email: mha...@wustl.edu
>
> On 9/24/18, 6:25 PM, "hcp-users-boun...@humanconnectome.org on behalf of 
> Nicola Toschi"  tos...@med.uniroma2.it> wrote:
>
> Hello List,
>
> I am trying to retrieve the files present in the 'surf' directory of the
> freesurfer reconstruction via CREST. However, when trying to retrieve
> (e.g) lh.white I always end up with a file containing only error messages.
>
> I would be grateful for any pointers. below is an example of my curl
> call after opening a session.
>
> curl --cookie JSESSIONID= -O
> https://db.humanconnectome.org/data/archive/projects/HCP_1200/subjects/100307/experiments/100307_CREST/resources/100307_CREST/files/T1w/surf/lh.white
>
> Thank you very much in advance!
>
> Nicola
>
>
> ---
> This email has been checked for viruses by Avast antivirus software.
> https://www.avast.com/antivirus
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> 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
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Intermediate freesurfer files not available through CREST?

2018-09-25 Thread Harms, Michael 

Hi,
You can obtain the entire FreeSurfer output via the Structural Extended 
packages.  Perhaps that would be an easier way for you to proceed?

Cheers,
-MH

--
Michael Harms, Ph.D.

---

Associate Professor of Psychiatry

Washington University School of Medicine

Department of Psychiatry, Box 8134

660 South Euclid Ave.Tel: 314-747-6173

St. Louis, MO  63110  Email: mha...@wustl.edu

On 9/24/18, 6:25 PM, "hcp-users-boun...@humanconnectome.org on behalf of 
Nicola Toschi"  wrote:

Hello List,

I am trying to retrieve the files present in the 'surf' directory of the
freesurfer reconstruction via CREST. However, when trying to retrieve
(e.g) lh.white I always end up with a file containing only error messages.

I would be grateful for any pointers. below is an example of my curl
call after opening a session.

curl --cookie JSESSIONID= -O
https://db.humanconnectome.org/data/archive/projects/HCP_1200/subjects/100307/experiments/100307_CREST/resources/100307_CREST/files/T1w/surf/lh.white

Thank you very much in advance!

Nicola


---
This email has been checked for viruses by Avast antivirus software.
https://www.avast.com/antivirus

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
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
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users