Re: [HCP-Users] Gradient nonlinearity correction on Prisma

[Philip A Cook]

Success - HCP-gradunwarp version 1.0.3 runs without errors.

Thanks

> On May 10, 2017, at 1:50 PM, Philip A Cook  wrote:
> 
> Thanks Michael, we have release 1.0.2. I will try 1.0.3
> 
> 
>> On May 9, 2017, at 5:27 PM, Harms, Michael  wrote:
>> 
>> 
>> The Prisma coefficient file contains more harmonics than the original
>> gradient_unwarp.py could handle.
>> Although, I thought that we had fixed that in the version that we are
>> hosting on github…
>> (Tim Brown?)
>> 
>> --
>> 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 5/9/17, 3:57 PM, "hcp-users-boun...@humanconnectome.org on behalf of
>> Philip A Cook" > coo...@mail.med.upenn.edu> wrote:
>> 
>> Hi,
>> 
>> I was trying to do gradient nonlinearity correction as part of the
>> structural pre-processing pipeline, which failed. Calling
>> gradient_unwarp.py independently produces the same error:
>> 
>> gradient_unwarp.py T1w.nii.gz trilinear.nii.gz siemens -g coeff.grad -n
>> 
>> gradient_unwarp.py fails to read the file, the output is:
>> 
>> gradunwarp-INFO: Parsing coeff.grad for harmonics coeffs
>> Traceback (most recent call last):
>> File "/share/apps/python/Python-2.7.9/bin/gradient_unwarp.py", line 122,
>> in 
>>   grad_unwarp.run()
>> File "/share/apps/python/Python-2.7.9/bin/gradient_unwarp.py", line 91,
>> in run
>>   self.args.gradfile)
>> File
>> "/share/apps/python/Python-2.7.9/lib/python2.7/site-packages/gradunwarp/cor
>> e/coeffs.py", line 30, in get_coefficients
>>   return get_siemens_grad(cfile)
>> File
>> "/share/apps/python/Python-2.7.9/lib/python2.7/site-packages/gradunwarp/cor
>> e/coeffs.py", line 194, in get_siemens_grad
>>   R0_m, max_ind = grad_file_parse(gfile, txt_var_map)
>> File
>> "/share/apps/python/Python-2.7.9/lib/python2.7/site-packages/gradunwarp/cor
>> e/coeffs.py", line 159, in grad_file_parse
>>   txt_var_map['Alpha_z'][x,y] = float(line.split()[-2])
>> IndexError: index 15 is out of bounds for axis 0 with size 14
>> 
>> We have gradunwarp installed from
>> 
>> https://github.com/Washington-University/gradunwarp
>> 
>> I can successfully correct T1w images from Lifespan pilot data, using the
>> Skyra .grad file:
>> 
>> gradient_unwarp.py T1w.nii.gz trilinear.nii.gz siemens -g
>> coeff_SC72C_Skyra.grad -n
>> 
>> So I think the gradunwarp install is OK. I think the Prisma coeff file is
>> also correct, as we've checked it against the same file from another
>> scanner. Has anyone managed to do the GDC with Prisma coeffs?
>> 
>> 
>> Thanks
>> 
>> 
>> 
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[HCP-Users] Announcing UK-dHCP first data release

[Saad Jbabdi]

Hi All,

On behalf of the UK Developing Human Connectome Project consortium:

We would like to announce the first preliminary release of data as part of the 
Developing Human Connectome Project (dHCP) – an ERC-funded collaboration 
between King’s College London, Imperial College London and Oxford University.

This is the project’s first open access data release which consist of images of 
40 representative term neonatal subjects. The imaging data includes structural 
imaging, structural connectivity data (diffusion MRI) and functional 
connectivity data (resting-state fMRI). This preliminary data release comes 
with minimal accompanying meta data: gender, age at birth and age at scan. More 
specific information about the available data can be found in the accompanying 
data release notes. To access the data please follow this 
link (**). You will be required to 
agree to a simple data sharing agreement.

We invite colleagues in the field to explore and feedback on the value and 
characteristics of the image dataset. The image data are processed using 
analysis pipelines that are subject to further development.

The project to date has successfully completed 584 neonatal scans and further 
data is still being collected, including fetal imaging (imaging babies before 
birth). Future data releases will consist of comprehensive image data with 
accompanying clinical, neurodevelopmental and genetics information.


Best wishes

Saad Jbabdi


(**) https://data.developingconnectome.org/app/template/Login.vm



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Re: [HCP-Users] Coding of Tier 1 Data

[Elam, Jennifer]

Hi Judita,

Sorry for the confusion in the data dictionary-- I added this information there.


For "Menstrual_BirthControlCode" What birth control, progesterone, or fertility 
drugs is the participant using? 1=OC's for contraception, 2=OC's primarily for 
menstrual regulation, 3=estradiol for menstrual regulation, 4=progesterone for 
menstrual regulation, 5=fertility therapy, 6=other, 7=unknown  (Asked of female 
participants only).


For "Menstrual_CycleLength" Average length of participant's menstrual cycles in 
days. (Asked of female participants only).


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 Judita Huber 

Sent: Wednesday, May 10, 2017 6:44:50 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Coding of Tier 1 Data

Dear HCP users,

I have two questions regarding the meaning of codes in Tier 1 restricted data.

Specifically, I don't understand the codes for the variable 
"Menstrual_BirthControlCode" (codes 1-6). I checked in the HCP Data Dictionary 
and didn't find anything there (in fact, in the description column it is 
written "What are the codes?").

Furthermore, for the data on "Menstrual_CycleLength", what are the units? Or do 
these numbers code for a certain length?

I would be grateful for your help, thank you very much in advance for your 
answer!

Kind regards,
Judita





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[HCP-Users] Coding of Tier 1 Data

[Judita Huber]

Dear HCP users,

I have two questions regarding the meaning of codes in Tier 1 restricted
data.

Specifically, I don't understand the codes for the variable
"Menstrual_BirthControlCode" (codes 1-6). I checked in the HCP Data
Dictionary and didn't find anything there (in fact, in the description
column it is written "What are the codes?").

Furthermore, for the data on "Menstrual_CycleLength", what are the units?
Or do these numbers code for a certain length?

I would be grateful for your help, thank you very much in advance for your
answer!

Kind regards,
Judita

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