Re: [HCP-Users] Transformation matrices of HCP 500 Subject Release

2015-12-02 Thread Harms, Michael

Hi,
You should be able to obtain the files via REST calls into the database.
See previous post in the list archives for an example of how to do so.

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 12/2/15 1:58 PM, "Kim, Joo-won"  wrote:

Dear HCP,

Thank you for the HCP data. I have a request.

Could you release the transformation matrices from unprocessed images to
ACPC aligned images of the HCP 500 Subjects Release? I would like to
analyze both averaged and individual scans, but when I ran the
PreFreeSurfer, the ACPC-aligned images were shifted a little bit compared
to those in the released data. Specifically, could you provide the
following files corresponding to the subjects in the attachment?

T1w/AverageT1wImages/ToHalfTrans000?.mat or
T1w/AverageT1wImages/ImToHalf000?.nii.gz
T1w/xfms/acpc.mat
T2w/AverageT2wImages/ToHalfTrans000?.mat or
T2w/AverageT2wImages/ImToHalf000?.nii.gz
T2w/xfms/acpc.mat
T2w/T2wToT1wReg/T2w2T1w.mat

Best,
Joo-won


--
Joo-won Kim

Postdoctoral Fellow
Translational and Molecular Imaging Institute
Department of Radiology
Icahn School of Medicine at Mount Sinai

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Re: [HCP-Users] Transformation matrices of HCP 500 Subject Release

2015-12-02 Thread Hodge, Michael

Joo-won,

We've recently created a "CREST" experiment for each released subject that 
should give you access to intermediate/non-relased files in the database via 
REST and for which you know the paths.

Here's an example for subject 100307 for one of the files you're interested in:

curl -s -k --cookie JSESSIONID=$DBSESSION 
https://db.humanconnectome.org/data/projects/HCP_500/subjects/100307/experiments/100307_CREST/resources/100307_CREST/files/T1w/AverageT1wImages/ImToHalf0001.nii.gz

The JSESSIONID variable can be set via the following:

DBSESSION=`curl -s -u username:password -X GET 
https://db.humanconnectome.org/data/JSESSIONID`;echo $DBSESSION

Regards,

Mike


From: hcp-users-boun...@humanconnectome.org 
<hcp-users-boun...@humanconnectome.org> on behalf of Harms, Michael 
<mha...@wustl.edu>
Sent: Wednesday, December 2, 2015 2:25 PM
To: Kim, Joo-won; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Transformation matrices of HCP 500 Subject Release

Hi,
You should be able to obtain the files via REST calls into the database.
See previous post in the list archives for an example of how to do so.

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 12/2/15 1:58 PM, "Kim, Joo-won" <joo-won@mssm.edu> wrote:

Dear HCP,

Thank you for the HCP data. I have a request.

Could you release the transformation matrices from unprocessed images to
ACPC aligned images of the HCP 500 Subjects Release? I would like to
analyze both averaged and individual scans, but when I ran the
PreFreeSurfer, the ACPC-aligned images were shifted a little bit compared
to those in the released data. Specifically, could you provide the
following files corresponding to the subjects in the attachment?

T1w/AverageT1wImages/ToHalfTrans000?.mat or
T1w/AverageT1wImages/ImToHalf000?.nii.gz
T1w/xfms/acpc.mat
T2w/AverageT2wImages/ToHalfTrans000?.mat or
T2w/AverageT2wImages/ImToHalf000?.nii.gz
T2w/xfms/acpc.mat
T2w/T2wToT1wReg/T2w2T1w.mat

Best,
Joo-won


--
Joo-won Kim

Postdoctoral Fellow
Translational and Molecular Imaging Institute
Department of Radiology
Icahn School of Medicine at Mount Sinai

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strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

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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.

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