Use the DICOM viewer I mentioned earlier and the specified field.

Matt.

From: Marc Dubin <[email protected]<mailto:[email protected]>>
Date: Saturday, July 21, 2018 at 11:13 PM
To: "Harms, Michael" <[email protected]<mailto:[email protected]>>
Cc: Matt Glasser <[email protected]<mailto:[email protected]>>, 
"[email protected]<mailto:[email protected]>" 
<[email protected]<mailto:[email protected]>>
Subject: [HCP-Users] Generating Field Maps for PreFreeSurferPipelineBatch.sh 
input


Thanks…..for some reason DwellTime isn’t listed in my json files (attached).

On 21 Jul 2018, at 23:59, Harms, Michael wrote:
Hi,
Use a DICOM reader to check the value of (0019,1018).  Or, IIRC, the value is 
extracted as “DwellTime” in the BIDS json returned by ‘dcm2niix’.

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: 
[email protected]<mailto:[email protected]>
From: Marc Dubin <[email protected]<mailto:[email protected]>>
Date: Saturday, July 21, 2018 at 10:28 PM
To: "Harms, Michael" <[email protected]<mailto:[email protected]>>
Cc: "Glasser, Matthew" <[email protected]<mailto:[email protected]>>, 
"[email protected]<mailto:[email protected]>" 
<[email protected]<mailto:[email protected]>>
Subject: [HCP-Users] Generating Field Maps for PreFreeSurferPipelineBatch.sh 
input


Hi Matt,

Do you know how to find the following? I was unable to find them in the 
dcm2niix json file or in the Matlab metadata structure. I just want to be sure 
my values are the same as the default values listed below.

Thanks!

Marc
DICOM field (0019,1018) in s or "NONE" if not used
    T1wSampleSpacing="0.0000074"

    # DICOM field (0019,1018) in s or "NONE" if not used
    T2wSampleSpacing="0.0000021"

On 19 Jul 2018, at 22:55, Harms, Michael wrote:

As defined in the text comment, “ReconMatrixPE” is just the size (dimension) of 
your images in the PE direction.  You don’t need to attempt to “derive” it from 
fields in the DICOM – just check your converted NIFTI itself!

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: 
[email protected]<mailto:[email protected]>
From: Marc Dubin <[email protected]<mailto:[email protected]>>
Date: Thursday, July 19, 2018 at 9:46 PM
To: "Glasser, Matthew" <[email protected]<mailto:[email protected]>>
Cc: "Harms, Michael" <[email protected]<mailto:[email protected]>>, 
"[email protected]<mailto:[email protected]>" 
<[email protected]<mailto:[email protected]>>
Subject: [HCP-Users] Generating Field Maps for PreFreeSurferPipelineBatch.sh 
input


I used the Matlab DICOM viewer and got BWPPPE as a private field, but did not 
see a field for ReconMatrixPE (is the latter a field in the DICOM header or 
computed from fields?)

Thanks again!

On 19 Jul 2018, at 22:36, Glasser, Matthew wrote:
I would just pull the numbers directly from the indicated DICOM fields using a 
DICOM header viewer such as this one:

https://wiki.xnat.org/xnat-tools/dicombrowser<https://urldefense.proofpoint.com/v2/url?u=https-3A__wiki.xnat.org_xnat-2Dtools_dicombrowser&d=DwMF-g&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=C9S_n0bF0p6dJ48M-Lgp1b9KBLxvTD5zOml7nDJ1vZU&m=GqesNQY9bpJn68E36-I5WBDQNXo9kEZLUS292SO3PoE&s=7rBFGJ2tD4GOT8JdpYtKkt7yMEQXReaOMxgQNWKQIQs&e=>

And then compute using the indicated formulas.  Unfortunately it seems one of 
the field names has been deleted and now it is confusing, but here is what it 
used to say:

https://github.com/Washington-University/HCPpipelines/commit/ca8c80ac7a615f8b8ebbd889b5f396bdcd788db8#diff-1bec2a8a1f62ce72a23680add2b08468<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Washington-2DUniversity_HCPpipelines_commit_ca8c80ac7a615f8b8ebbd889b5f396bdcd788db8-23diff-2D1bec2a8a1f62ce72a23680add2b08468&d=DwMF-g&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=C9S_n0bF0p6dJ48M-Lgp1b9KBLxvTD5zOml7nDJ1vZU&m=GqesNQY9bpJn68E36-I5WBDQNXo9kEZLUS292SO3PoE&s=Z7LvjnrPy7s1J_JJiIMB0ztIa8zp_99rxBH-bXfEb8k&e=>

Matt.

From: Marc Dubin <[email protected]<mailto:[email protected]>>
Date: Thursday, July 19, 2018 at 9:24 PM
To: Matt Glasser <[email protected]<mailto:[email protected]>>
Cc: "Harms, Michael" <[email protected]<mailto:[email protected]>>, 
"[email protected]<mailto:[email protected]>" 
<[email protected]<mailto:[email protected]>>
Subject: [HCP-Users] Generating Field Maps for PreFreeSurferPipelineBatch.sh 
input


Thank you, Matthew!

Is the Size of the reconstructed image in the PE (phase encoding) direction the 
same as the number of phase encoding steps (109 in the case of my scans)?

Marc

On 18 Jul 2018, at 9:11, Glasser, Matthew wrote:
You need to follow the instructions listed to find those DICOM fields and put 
in the values.

b02b0.cnf is fine.

Peace,

Matt.

From: 
<[email protected]<mailto:[email protected]>>
 on behalf of Marc Dubin 
<[email protected]<mailto:[email protected]>>
Date: Tuesday, July 17, 2018 at 11:29 PM
To: "Harms, Michael" <[email protected]<mailto:[email protected]>>
Cc: "[email protected]<mailto:[email protected]>" 
<[email protected]<mailto:[email protected]>>
Subject: [HCP-Users] Generating Field Maps for PreFreeSurferPipelineBatch.sh 
input


Thank you, Michael!

Do you know for this section:

"Effective" Echo Spacing of Spin Echo Field Maps. Specified in seconds.

    # Set to "NONE" if not used.

    # SEEchoSpacing = 1/(BWPPPE * ReconMatrixPE)

    #   where BWPPPE is the "BandwidthPerPixelPhaseEncode" = DICOM field 
(0019,1028) for Siemens, and

    #   ReconMatrixPE = size of the reconstructed SEFM images in the PE 
dimension

    # In-plane acceleration, phase oversampling, phase resolution, phase 
field-of-view, and interpolation

    # all potentially need to be accounted for (which they are in Siemen's 
reported BWPPPE)

    #

    # Example value for when using Spin Echo Field Maps from the HCP-YA

    #   0.000580002668012

SEEchoSpacing="NONE"

How I would know what the appropriate value of SEEchoSpacing would be for my 
data?

Also, is it safe to assume: TopUpConfig="${HCPPIPEDIR_Config}/b02b0.cnf”. ?

Thanks again!

On 18 Jul 2018, at 0:20, Harms, Michael wrote:

Hi,
If you are using SEFMs, you don't need to generate magnitude and phase field 
maps. It is handled internally. See the Batch script in the Examples directory.

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: [email protected]<mailto:[email protected]>
On 7/17/18, 11:12 PM, 
"[email protected]<mailto:[email protected]>
 on behalf of Marc Dubin" 
<[email protected]<mailto:[email protected]>
 on behalf of [email protected]<mailto:[email protected]>> wrote:

Dear All,

I am new to the HCP MR pipelines and was wondering if anyone can provide
guidance on how to generate magnitude and phase field maps for input to
PreFreeSurferPipelineBatch.sh

The files that I currently have from the Siemens 3T scanner are:

SpinEchoFieldMap_PA
SpinEchoFieldMap_AP

Thanks for any suggestions!!

Marc Dubin


Marc Dubin, MD PhD
Assistant Professor of Psychiatry and Neuroscience
Department of Psychiatry and Brain and Mind Research Institute

Weill Cornell Medicine | New York-Presbyterian
Psychiatry-Box 140
525 East 68th Street
New York, NY 10065
T 212.746.5817

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