Requesting DICOM files of HCP Early Psychosis dataset

[Haley Wang]

Hi all,

I'm trying to look for some scan parameters of the HCP Early Psychosis data to set up an analysis pipeline. Some parameters require the info from the DICOM file, but the NDA data only has NIFTIs. Would it be possible for someone to share the DICOM files (s/f/dMRI) of one subject? Thank you for your time and help in advance!

Warmly,

Haley

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Haley R. Wang, M.S., M.A.

Doctoral Student in Clinical Psychology

University of California, Los Angeles

Clinical Cognitive Neuroscience Lab

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[Elam, Jennifer]

Hi Haley,

I'm forwarding this request to the HCP-EP investigators in case they are able to provide what you need. It might help to know what you need from the DICOMS, in case there's a work around. For Lifespan HCP we don't share DICOMS due to the PHI contained in them.

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
el...@wustl.edu
www.humanconnectome.org

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From: Haley Wang <hale...@g.ucla.edu>
Sent: Thursday, September 22, 2022 4:20 PM
To: hcp-...@humanconnectome.org <hcp-...@humanconnectome.org>
Subject: [hcp-users] Requesting DICOM files of HCP Early Psychosis dataset

 

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[Haley Wang]

Hi Jennifer,

Thank you so much for your reply! I am looking for information on T1 and T2 sample spacing (which I couldn't find in the scan protocol appendix). Would it also be possible to get the scanners' gradient coefficients files of the resting and diffusion scans from the 4 Siemens scanners of each study site? I hope to use this info for preprocessing. 

Additionally, do the scanner automatically drop the first several frames during resting scans? It would be greatly helpful for me to decide how many frames to omit at the start of each bold run.

Many thanks,

Haley

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[Harms, Michael]

 

Hi,

Check the sidecar json files that accompany the NIFTi’s.  Everything you need to know should be in those.  What the HCPpipelines call “{t1,t2}samplespacing” for PreFreeSurfer will be ‘DwellTime’ in the json’s.

 

The gradient coefficient files are considered proprietary, and we (and others) aren’t allowed to distribute them per our research agreement with Siemens .  But they are the same for a given scanner platform.  i.e., all Prisma’s have the same file.  I’d ask your local Siemens collaboration manager for help in getting the Prisma version.

 

I don’t recall what we did for HCP-EP in terms of dropped frames, but if we did the same as HCP-LS there would be 10 dropped frames for the resting-state.  Look in the OTHER_FILES directory of the fMRI packages for a file with the name ‘InitialFrames’.  Those will be the dropped initial frames.  The number of dropped frames may potentially differ for task-fMRI scans, depending on the design of the task.

 

Cheers,

-MH

 

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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

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[Haley Wang]

Hi Dr. Harms,

This is so helpful! Thank you so much for your time and for all the great information!

Best,

Haley

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[Haley Wang]

Hi all,

Thank you for your help earlier. I also have another question regarding missing T1w. I downloaded the HCP Early Psychosis data release v1.1 from NDA and there are 3 subjs without T1w image (1007, 1011, 3038). I also don't see their folders in the released preprocessed fmri results. I just wanted to check if they are only missing on my end, or if T1w was not collected for the 3 subjs. If you have any additional information on them, it would be greatly appreciated! Thank you for your help!

Best,

Haley

[Reid, Erin]

Hello Haley,

I show that all 3 of those subjects had T1w scans collected so it may be a glitch in your download.

However, both 1007 and 1011 had poor (1.5) rated T1s but 3038's T1 was rated good (3) ... so that shouldn't be the overall issue.

Sincerely,

Erin Reid (she/her) | Sr Research Technician

Department of Neuroscience

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From: Haley Wang <hale...@g.ucla.edu>
Sent: Monday, September 26, 2022 4:32 PM
To: hcp-...@humanconnectome.org <hcp-...@humanconnectome.org>
Cc: sylvai...@etsmtl.ca <sylvai...@etsmtl.ca>; Mike Coleman <m...@bwh.harvard.edu>

Subject: Re: [hcp-users] Requesting DICOM files of HCP Early Psychosis dataset

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Hi all,

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[Haley Wang]

Hi Erin,

Thank you for looking into it, and it's great to know that the T1w images for those subjects exist! I viewed the shared package in NDA again, but somehow I can't find those files in their corresponding folders. Here is a summary of what I see in the NDA package:

	HCPEPRelease		HCPEP11AllData
Subjects	T1w	T2w	T1w	T2w
1007	N	N	N	N
1011	N	Y	N	Y
3038	N	N	N	N
all others	Y	Y	Y	Y

Would it be possible for you to crosscheck to see if it looks similar on your end of NDA? If so, could you add the T1 and T2 images for these 3 people to the package or share it via other methods?  I really appreciate your time and help, Erin!

Best,

Haley

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[Haley Wang]

Hi everyone,

Hope this finds you well. I just wanted to follow up on the question above regarding the missing T1w and T2w of the 3 participants. Thank you so much for your time and help!

Best,

Haley

[Elam, Jennifer]

Hi Haley,

The sessions for those subjects were missing non-normalized scans and the HCP-EP team was not able to provide them to CCF to then share on NDA.  They are missing in the NDA packages you downloaded because of this.

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
el...@wustl.edu
www.humanconnectome.org

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From: Haley Wang <hale...@g.ucla.edu>
Sent: Tuesday, October 4, 2022 11:40 AM
To: hcp-...@humanconnectome.org <hcp-...@humanconnectome.org>
Cc: sylvai...@etsmtl.ca <sylvai...@etsmtl.ca>; Mike Coleman <m...@bwh.harvard.edu>; Katherine Karlsgodt <kkar...@ucla.edu>

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[Haley Wang]

Hi Jennifer,

Thank you for the clarification. I appreciate your help!

Best,

Haley

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