Re: [HCP-Users] group comparison

[nailin yao]

Thank you MH! That's exactly what I want to know.

Best,
Nailin

2016-12-15 16:20 GMT-05:00 Harms, Michael :

>
> Hi,
> Please keep the exchange on the HCP-Users list, so that responses can be
> captured as part of the thread on the list.
>
> Anderson can confirm, but I believe that if you are supplying the optional
> “area file” as part of the -s argument to PALM, then you don’t really need
> an average midthickness surface, because the surface file is just used to
> discern the topology of the mesh (which is the same for the 32k_fs_LR mesh
> across all subjects).   In which case you could use the midthickness
> surface for any subject, or the 32k sphere.  For the area file, you would
> still want to provide the average vertex area (“va”) file across subjects,
> and that can be computed as outlined in Example 10 of the PALM wiki.
>
> 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 <(314)%20747-6173>
> St. Louis, MO  63110 Email: mha...@wustl.edu
>
> From: nailin yao 
> Date: Thursday, December 15, 2016 at 12:45 PM
> To: Michael Harms 
> Subject: Re: [HCP-Users] group comparison
>
> Hi MH,
>
> How can I generate the mean midthickness.surf.gii for my subjects? I tried
> cifti-merge, but the error says: ERROR: error reading NIfTI file
> /home/fas/glahn/ny87/scratch60/Connectivity_Study/S0039JRF/MNINonLinear/
> fsaverage_LR32k/S0039JRF.R.midthickness.32k_fs_LR.surf.gii:
> /home/fas/glahn/ny87/scratch60/Connectivity_Study/S0039JRF/MNINonLinear/
> fsaverage_LR32k/S0039JRF.R.midthickness.32k_fs_LR.surf.gii is not a valid
> NIfTI file
>
> Thanks!
>
> Best,
> Nailin
>
> 2016-12-15 13:11 GMT-05:00 Harms, Michael :
>
>>
>> Do you mean for each individual subject?  They are in the
>> $subj/T1w/fsaverage_LR32k directory (assuming you want the version on the
>> 32k mesh).
>>
>> 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 <(314)%20747-6173>
>> St. Louis, MO  63110Email: mha...@wustl.edu
>>
>> From:  on behalf of nailin yao <
>> ynai...@gmail.com>
>> Date: Thursday, December 15, 2016 at 11:44 AM
>> To: NEUROSCIENCE tim 
>> Cc: "hcp-users@humanconnectome.org" ,
>> "Dierker, Donna" 
>> Subject: Re: [HCP-Users] group comparison
>>
>> Hi Tim,
>>
>> Do you know where can I find midthickness.surf.gii file for palm CIFTI
>> usage? Thanks!
>>
>> Best,
>> Nailin
>>
>> 2016-12-09 16:00 GMT-05:00 Timothy Coalson :
>>
>>> The -metric-reduce command outputs a metric file.  You should alter the
>>> wb_command line so that the output file has extension .func.gii.
>>>
>>> Tim
>>>
>>>
>>> On Fri, Dec 9, 2016 at 1:38 PM, nailin yao  wrote:
>>>
 Hi,

 I'm trying to run "palm -i data_L.func.gii -d design.mat -t design.con
 -o results_L_cort -T -tfce2D -s L_midthickness.surf.gii L_area.dscalar.nii
 -logp " according to PALM website. In the file preparation, the
 L_midthick_va.func.gii file looks fine in wb_view, but the
 L_area.dscalar.nii which generated by "wb_command -metric-reduce
 L_midthick_va.func.gii MEAN L_area.dscalar.nii " cannot be open in wb_view.
 Both of the files are attached, do you know why?

 Thank you!
 Nailin​
  L_area.dscalar.nii
 
 ​​
  L_midthick_va.func.gii
 
 ​

 2016-11-30 13:43 GMT-05:00 Glasser, Matthew :

> Perhaps you have to add .func.gii instead of .gii to the extension
> names for wb_view to know what kind of file it is.  Do you actually need 
> to
> do the CIFTI separate part though?  I thought PALM supported CIFTI files
> natively now.
>
> Peace,
>
> Matt.
>
> From: nailin yao 
> Date: Wednesday, November 30, 2016 at 11:35 AM
> To: Matt Glasser 
> Cc: "Dierker, Donna" , "hcp-users@humanconnectome.org"
> 
>
> Subject: Re: [HCP-Users] group comparison
>
> Hi Matt,
>
> The result is generated by the command:
>
> wb_command -cifti-separate data.dtseries.nii COLUMN (-volume-all
> data_sub.nii) -metric CORTEX_LEFT data_L.func.gii -metric CORTEX_RIGHT
> data_R.func.gii
>
> palm -i data_L.func.gii -i data_R.func.gii -d design.mat -t design.con
> -o results -corrmod -logp
>
> And the result files are :
>
> results_dpv_tstat_fwep_m1_c1.gii
>
> results_dpv_tstat_fwep_m1_c2.gii
>
> results_dpv_tstat_fwep_m2_c1.gii
>
> results_dpv_tstat_fwep_m2_c2.gii
>>

[HCP-Users] data release

[Christopher Weise]

Dear HCP team,

thanks for all your great work! I was wondering if you have a time i mind for 
the next data new release (S1200)?

Cheers

Chris
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Re: [HCP-Users] pconn.nii plot

[nailin yao]

Hi Tim,

I don't quite get it. What I want to do is to plot
output_correlation.pconn.nii file as a 180*180 correlation color matrix for
viewing . If wb_command can achieve this, may I know the exact wb_command I
can use to generate the scene file or image file? Or is there any tabs on
wb_view can execute this? Thanks!

Best,
Nailin

2016-12-15 17:41 GMT-05:00 Timothy Coalson :

> If you make a scene file that shows the plot, wb_command -show-scene can
> make a capture of it to an image file.  However, you'll need to use some
> tricks to be able to swap out the data file if you want to capture multiple
> plots without manually creating more scenes.
>
> If you want to make a figure that includes such plots, take a look at the
> tile tabs and annotations features in wb_view, as it can manage a lot of
> the multipanel, arrows, external images, and text figure layout that is
> often done with photoshop or other image editing software.  These can be
> saved to scene files for ease of later tweaking or fixing with reprocessed
> data.
>
> Tim
>
>
> On Wed, Dec 14, 2016 at 11:45 AM, nailin yao  wrote:
>
>> Hi,
>>
>> Do you know if wb_command can directly plot the color matrix of pconn.nii
>> file? Thank you!
>>
>> Best,
>> Nailin
>>
>> --
>> Nailin Yao,  PhD
>>
>> Postdoctoral Associate
>> Department of Psychiatry, Yale University
>>
>> ___
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>
>
>


-- 
Nailin Yao,  PhD

Postdoctoral Associate
Department of Psychiatry, Yale University

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[HCP-Users] Subject 101107: different brain mask for rfMRI_REST1_LR and rfMRI_REST1_RL?

[Julien Dubois]

Hi,

I was just working with some of the HCP volume data and noticed that
subject 101107 had a chunk of ventral prefrontal cortex missing in the
rfMRI_REST1_LR.nii.gz volume (in MNINonLinear/Results/rfMRI_REST1_LR).

Interestingly, the brain mask for rfMRI_REST1_RL.nii.gz seems different
(more inclusive). I thought that the brain masking was based on the
anatomicals (T1w and T2w), and was therefore the same across functional
scans?

Either I misunderstood the brain masking procedure, or there is an issue in
the minimally preprocessed data for 101107. Screenshot of REST1_LR and
REST1_RL volumes, side by side, attached.

Thanks!
- Julien

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Re: [HCP-Users] data release

[Elam, Jennifer]

Hi Chris,

We are currently working on finishing up processing for the 1200 Subjects 
Release (~1100 with image data) and, if all goes well, we plan to release the 
data in January 2017.


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 Christopher Weise 

Sent: Friday, December 16, 2016 10:31:50 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] data release

Dear HCP team,

thanks for all your great work! I was wondering if you have a time i mind for 
the next data new release (S1200)?

Cheers

Chris
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[HCP-Users] Two jobs avail: Data Science and Machine Learning in the NIMH IRP

[Thomas, Adam (NIH/NIMH) [E]]

Full details here: https://github.com/nih-fmrif/mlc_job_ad
And here:  https://github.com/nih-fmrif/ADS_job_ad

HIRING: Machine learning in neuroimaging researcher

Who we are:

The National Institute of Mental Health (NIMH) is the lead federal agency for 
research on mental disorders. NIMH is one of the 27 Institutes and Centers that 
make up the National Institutes of Health (NIH), which is responsible for all 
federally funded biomedical research in US. NIH is part of the U.S. Department 
of Health and Human Services (HHS). The NIH is a highly rated employer at 
glassdoor.com with very competitive salary and benefits packages.

The Machine Learning Core (MLC) is a new group created to support the use of 
machine learning methods in analyzing human neuroimaging data, collected within 
the NIMH Intramural Research Program (IRP) or from functional and anatomic 
imaging databases worldwide. The MLC will both develop new methods and provide 
education and support to NIMH IRP researchers using machine learning approaches.

What you will do:

You and the team will be responsible for assisting NIMH IRP investigators in 
using machine learning methods to answer clinical and scientific questions. Key 
areas of work include biomarkers to help diagnose mental health and neurologic 
disorders, as well as the development of models of mental processes in healthy 
subjects. You will help devise research approaches using prediction models that 
combine imaging and non-imaging data, and leverage structured knowledge 
resources (databases, scientific literature, etc) to generate explanations and 
hypotheses.

You will also develop new methods to address the unique research needs in our 
environment. You will have the resources of the NIH HPC Cluster at your 
disposal as well as additional help from the AWS cloud. All tools and code will 
be open source and freely distributed.

The MLC will provide education and outreach to further the use of machine 
learning across the NIMH IRP. You will be involved in designing and teaching 
courses on basic methods and data analysis. You will help run data analysis 
clinics and consults to help identify research needs, and mentor junior 
researchers in joint projects.

Who you are:

We are seeking candidates with practical machine learning experience, e.g. 
training of classification and regression models, statistical testing of 
results, interpretation and visualization of key aspects of models. Beyond 
this, we would like knowledge of optimization and statistics, insofar as they 
bear on machine learning method development.

Experience working with neuroimaging data (MRI, as well as MEG/EEG) will be 
considered very favorably, in particular the generation of quantitative 
measures to use as features (e.g. activation maps, functional and structural 
connectivity, scalar maps, cortical structure volumes, etc.).

Finally, you should have demonstrable experience coding in languages currently 
used in data-intensive, scientific computing such as Python, MATLAB or R (and 
relevant data processing libraries).

How to apply:

Email your resume (your email can serve as a cover letter) to 
mlcore-jobsea...@mail.nih.gov

Questions are welcome. The National Institutes of Health is an equal 
opportunity employer.






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Re: [HCP-Users] pconn.nii plot

[Timothy Coalson]

wb_view is the only way for workbench to set up how to view that matrix.
Load the file, and change the view type to "chart", and select "matrix" for
chart type if it isn't already selected.  As with any other display in
wb_view, you can capture the image with "file->capture image...".

Because you specifically asked about wb_command, and not just how to view
it in general, I mentioned the capability to save this view setup with
wb_view to a scene file, which can then be captured to an image with
wb_command (which can be done in a script, rather than needing to click on
things to capture an image), which can be useful for certain purposes, but
takes some additional setup and trickery to be more useful than just
manually capturing what is shown in wb_view.

Tim


On Fri, Dec 16, 2016 at 11:36 AM, nailin yao  wrote:

> Hi Tim,
>
> I don't quite get it. What I want to do is to plot
> output_correlation.pconn.nii file as a 180*180 correlation color matrix for
> viewing . If wb_command can achieve this, may I know the exact wb_command I
> can use to generate the scene file or image file? Or is there any tabs on
> wb_view can execute this? Thanks!
>
> Best,
> Nailin
>
> 2016-12-15 17:41 GMT-05:00 Timothy Coalson :
>
>> If you make a scene file that shows the plot, wb_command -show-scene can
>> make a capture of it to an image file.  However, you'll need to use some
>> tricks to be able to swap out the data file if you want to capture multiple
>> plots without manually creating more scenes.
>>
>> If you want to make a figure that includes such plots, take a look at the
>> tile tabs and annotations features in wb_view, as it can manage a lot of
>> the multipanel, arrows, external images, and text figure layout that is
>> often done with photoshop or other image editing software.  These can be
>> saved to scene files for ease of later tweaking or fixing with reprocessed
>> data.
>>
>> Tim
>>
>>
>> On Wed, Dec 14, 2016 at 11:45 AM, nailin yao  wrote:
>>
>>> Hi,
>>>
>>> Do you know if wb_command can directly plot the color matrix of
>>> pconn.nii file? Thank you!
>>>
>>> Best,
>>> Nailin
>>>
>>> --
>>> Nailin Yao,  PhD
>>>
>>> Postdoctoral Associate
>>> Department of Psychiatry, Yale University
>>>
>>> ___
>>> HCP-Users mailing list
>>> HCP-Users@humanconnectome.org
>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>
>>
>>
>
>
> --
> Nailin Yao,  PhD
>
> Postdoctoral Associate
> Department of Psychiatry, Yale University
>
>

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Re: [HCP-Users] Subject 101107: different brain mask for rfMRI_REST1_LR and rfMRI_REST1_RL?

[Glasser, Matthew]

Check the raw data for that run and see if the head didn't move out of the FOV.

Peace,

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Julien Dubois mailto:jcrdub...@gmail.com>>
Date: Friday, December 16, 2016 at 1:02 PM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Subject 101107: different brain mask for rfMRI_REST1_LR 
and rfMRI_REST1_RL?

Hi,

I was just working with some of the HCP volume data and noticed that subject 
101107 had a chunk of ventral prefrontal cortex missing in the 
rfMRI_REST1_LR.nii.gz volume (in MNINonLinear/Results/rfMRI_REST1_LR).

Interestingly, the brain mask for rfMRI_REST1_RL.nii.gz seems different (more 
inclusive). I thought that the brain masking was based on the anatomicals (T1w 
and T2w), and was therefore the same across functional scans?

Either I misunderstood the brain masking procedure, or there is an issue in the 
minimally preprocessed data for 101107. Screenshot of REST1_LR and REST1_RL 
volumes, side by side, attached.

Thanks!
- Julien

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