[HCP-Users] San Diego NIAAA T32 Postdoc Position Opening

[Eileen Moore]

San Diego NIAAA T32 Postdoc Position Opening Announcement

A postdoctoral position in alcohol research is available now through an NIAAA 
T32 institutional training grant between SDSU and UCSD in San Diego, CA. 
Postdoctoral appointees are supported for twelve-month, full-time appointments 
with the ability to receive up to two years of support based upon acceptable 
progress during their initial year. Qualified candidates must be U.S. citizens 
(or permanent resident or noncitizen national of the U.S.) and have completed 
their doctoral degree requirements in the clinical and behavioral sciences. 
Specific areas of alcohol research include fetal alcohol spectrum disorders, 
adolescent and adult alcohol/substance use disorders, risk and protective 
factors for alcoholism, alcohol and brain disease, neurobiological/behavioral 
effects of alcoholism, neuropsychological function, structural and functional 
neuroimaging, interventions, and psychiatric and medical comorbidity. Fellows 
will conduct research with their mentor, including comprehensive literature 
reviews and participation in data collection and analysis. Fellows are expected 
to become involved in manuscript and grant writing, to participate in alcohol 
research training program seminars, and present at national meetings (e.g., 
Research Society on Alcoholism). 

Faculty mentors include Drs. Edward Riley (Director), Susan Tapert 
(co-Director), Robert Anthenelli, Kara Bagot, Sandra A. Brown, Mariana Cherner, 
Cindy Ehlers, Jay Giedd, Igor Grant, Joanna Jacobus, Terry Jernigan, Ksenija 
Marinkovic, Sarah Mattson, David Moore, Mark Myers, Sonya Norman, Marc 
Schuckit, Andrea Spadoni, Michael Taylor, Jennifer Thomas, Ryan Trim, Tamara 
Wall, and Matt Worley. 

To apply please complete the online form (http://niaaa-t32.sdsu.edu/apply/) and 
submit your CV, personal statement, and the names of three references to Edward 
Riley's assistant, Jill Vander Velde, at vand...@mail.sdsu.edu.
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] HCP-Users Digest, Vol 64, Issue 2

[Timothy Coalson]

I believe you need to use the "bin_macosx64" folder as the path to
wb_command on mac, so try this as CARET7DIR:

/Applications/workbench/bin_macosx64

Tim


On Mon, Mar 5, 2018 at 3:03 PM, Kwan-Jin Jung  wrote:

> Hi Gaurav,
>
> Thank you.
> I updated the workbench, but I got the same error as before: "CORTEX_LEFT
> does not exist."
>
> Without changing “${CARET7DIR}/wb_command” to “open -a
> ${CARET7DIR}/wb_command” in FreeSurferHiresPial.sh, the wb_command cannot
> start:
> "/Users/kjjung/bin/HCP/FreeSurfer/scripts/FreeSurferHiresPial.sh: line
> 92: /Applications/workbench/macosx64_apps/wb_command: No such file or
> directory"
>
> Can you guide me once again?
>
> Kwan-Jin Jung
> HMRC, IALS, UMASS Amherst
> Phone: 413-577-0538 <(413)%20577-0538>
>
>
>
> On Mar 2, 2018, at 2:45 PM, Gaurav Patel  wrote:
>
> Well, I guess that would be us every time we update our local
> installation.  We’ll let you know how it goes
> 
> gaurav patel
> gauravpa...@gmail.com
> pateldsclab.net
>
> On Mar 2, 2018, at 2:30 PM, Glasser, Matthew  wrote:
>
> Hi Gaurav,
>
> I guess they are supported on mac for now, but I don¹t know that anyone is
> actively testing them for macŠ
>
> Matt.
>
> On 3/2/18, 1:28 PM, "Gaurav Patel"  gauravpa...@gmail.com> wrote:
>
> YesŠwe¹ve been 3.4 for many years without problems, and 3.22 only
> required those minor changes.  We recently verified that it was easy to
> install and run on macs when we expanded the network of mac pros we use
> to run the HCP pipelines
> 
> gaurav patel
> gauravpa...@gmail.com
> pateldsclab.net
>
> On Mar 2, 2018, at 2:25 PM, Glasser, Matthew  wrote:
>
> So you are saying that the Pipelines work fine on the Mac for you aside
> from this cp issue?
>
> Matt.
>
> From:  on behalf of "Sanchez,
> Juan (NYSPI)" 
> Date: Friday, March 2, 2018 at 1:24 PM
> To: "hcp-users@humanconnectome.org" 
> Subject: Re: [HCP-Users] HCP-Users Digest, Vol 64, Issue 2
>
> Dear
> Kwan-Jin Jung
>
> I had rthe same problems when I installed the 3_22 HCP Pipleines
> Here is what we did:
>
>
> €
> syntax in
> scripts:
> Just remove the "--preserve=timestamps" from all of the Pipeline
> scripts
> 2. workbench:
>
> Get the "dev_latest" zip file that says "mac64" from here:
>
> http://brainvis.wustl.edu/workbench/
>
> From: hcp-users-boun...@humanconnectome.org
>  on behalf of
> hcp-users-requ...@humanconnectome.org
> 
> Sent: Friday, March 2, 2018 1:00:01 PM
> To: hcp-users@humanconnectome.org
> Subject: HCP-Users Digest, Vol 64, Issue 2
>
> ATTENTION: This email came from an external source. Do not open
> attachments or click on links from unknown senders or unexpected emails.
>
>
> Send HCP-Users mailing list submissions to
>   hcp-users@humanconnectome.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>   http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> or, via email, send a message with subject or body 'help' to
>   hcp-users-requ...@humanconnectome.org
>
> You can reach the person managing the list at
>   hcp-users-ow...@humanconnectome.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of HCP-Users digest..."
>
>
> Today's Topics:
>
>  1. Re: Best Approach for using old volumetric data to pick
> parcels-of-interest (Stevens, Michael)
>  2. Movement regressor missing (Linnman, Clas,Ph.D.)
>  3. Re: Movement regressor missing (Glasser, Matthew)
>  4. Error in FreeSurfer processing "recon-all.v6.hires: command
> not found" (Pubuditha Abeyasinghe)
>  5. Re: Error in FreeSurfer processing "recon-all.v6.hires:
> command not found" (Glasser, Matthew)
>  6. Re: Error in FreeSurfer processing "recon-all.v6.hires:
> command not found" (Timothy B. Brown)
>  7. Re: Best Approach for using old volumetric data to pick
> parcels-of-interest (Timothy Coalson)
>  8. Re: ROI cluster centers to surface grayordinates (Timothy Coalson)
>  9. Re: Best Approach for using old volumetric data to pick
> parcels-of-interest (Erin W. E. Dickie)
> 10. Re: Correct interpretation of NIH battery test
> 'Words-in-Noise' in HCP subjects (Robert Becker)
> 11. Split dtseries (A R)
> 12. Re: Split dtseries (Glasser, Matthew)
> 13. Change of FreeSurferHiresPial.sh for MacBook IOS (Kwan-Jin Jung)
> 14. Re: Change of FreeSurferHiresPial.sh for MacBook IOS
> (Glasser, Matthew)
>
>
> --
>
> Message: 1
> Date: Thu, 1 Mar 2018 19:22:32 +
> From: "Stevens, Michael" 
> Subject: Re: [HCP-Users] Best Approach for using old volumetric data
>   to pick parcels-of-interest
> 

Re: [HCP-Users] Is surface myelin map the same as the volume T1w/T2 map?

[Glasser, Matthew]

No that would be without _BC and I don’t know what the 2mmResample is.

Peace,

Matt.

From: 
>
 on behalf of Xavier Guell Paradis >
Date: Monday, March 5, 2018 at 4:57 PM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] Is surface myelin map the same as the volume T1w/T2 map?

Dear HCP experts,
Is S1200.All.MyelinMap_BC_MSMAll.32k_fs_LR.dscalar.nii calculated in the same 
way as the S1200_AverageT1wDividedByT2w_2mmResample.nii, with the only 
difference that one file is surface and the other is volume?

Thank you very much,
Xavier.

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] Is surface myelin map the same as the volume T1w/T2 map?

[Xavier Guell Paradis]

Dear HCP experts,
Is S1200.All.MyelinMap_BC_MSMAll.32k_fs_LR.dscalar.nii calculated in the same 
way as the S1200_AverageT1wDividedByT2w_2mmResample.nii, with the only 
difference that one file is surface and the other is volume?

Thank you very much,
Xavier.

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] contrast in human connectome 3T structural MRI

[Glasser, Matthew]

Indeed this contrast mechanism is used to make MR angiograms of the head
without using contrast.

Peace,

Matt.

On 3/5/18, 12:44 PM, "Xu, Junqian"  wrote:

>Hi Jamila,
>
>These variable bright arteries in the T1w MPRAGE images are probably due
>to the time-of-flight (TOF) effects of those ³fresh" arterial blood
>flowing into the brain after the inverse pulse.
>
>http://mriquestions.com/time-of-flight-effects.html
>
>Regards
>Gordon
>
>> On Mar 5, 2018, at 9:15 AM, Glasser, Matthew  wrote:
>> 
>> No gadolinium contrast was used in the HCP.  Sometimes blood will
>>appear bright on T1w scans for reasons other than gadolinium contrast.
>> 
>> Peace,
>> 
>> Matt.
>> 
>> From:  on behalf of Jamila
>>Ahdidan 
>> Date: Monday, March 5, 2018 at 2:53 AM
>> To: "hcp-users@humanconnectome.org" 
>> Subject: [HCP-Users] contrast in human connectome 3T structural MRI
>> 
>> Hi,
>> 
>> I have noticed that many if not all the structural MRIs of the HCP show
>>signs of contrast in the subjects blood. Is that correct? Have you
>>scanned the participants without using contrast as this disturbs the
>>segmentation?
>> 
>> Thank you.
>> 
>> Best regards / Cordialement / De bedste hilsner
>> 
>> Jamila Ahdidan
>> PhD, Partner, CSO
>> Brainreader ApS
>> Emil Møllers Gade 41
>> 8700 Horsens - DK
>> tel: +45 5050 5544
>> email: jam...@brainreader.net
>> skype: jamila_ahdidan
>> website: www.brainreader.net
>> ___
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>> ___
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] contrast in human connectome 3T structural MRI

[Xu, Junqian]

Hi Jamila,

These variable bright arteries in the T1w MPRAGE images are probably due to the 
time-of-flight (TOF) effects of those “fresh" arterial blood flowing into the 
brain after the inverse pulse.

http://mriquestions.com/time-of-flight-effects.html 

Regards
Gordon

> On Mar 5, 2018, at 9:15 AM, Glasser, Matthew  wrote:
> 
> No gadolinium contrast was used in the HCP.  Sometimes blood will appear 
> bright on T1w scans for reasons other than gadolinium contrast.
> 
> Peace,
> 
> Matt.
> 
> From:  on behalf of Jamila Ahdidan 
> 
> Date: Monday, March 5, 2018 at 2:53 AM
> To: "hcp-users@humanconnectome.org" 
> Subject: [HCP-Users] contrast in human connectome 3T structural MRI
> 
> Hi,
> 
> I have noticed that many if not all the structural MRIs of the HCP show signs 
> of contrast in the subjects blood. Is that correct? Have you scanned the 
> participants without using contrast as this disturbs the segmentation?
> 
> Thank you.
> 
> Best regards / Cordialement / De bedste hilsner
> 
> Jamila Ahdidan
> PhD, Partner, CSO
> Brainreader ApS
> Emil Møllers Gade 41
> 8700 Horsens - DK
> tel: +45 5050 5544
> email: jam...@brainreader.net
> skype: jamila_ahdidan
> website: www.brainreader.net
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] question about mother vs. non-mothers in the HCP 1200

[Elam, Jennifer]

Hi Osama,

We did not ask the participants specifically about whether they were parents, 
but in the Restricted data there is a variable called "Menstrual_Explain" where 
the female participants can give an explanation for why their current cycles 
are irregular in length. About 25 participants cite having a baby recently and 
breastfeeding for this variable, so that could give you a list of mothers. 
However, there is no variable that confirms that a female participant is *not* 
a mother.


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 Glasser, Matthew 

Sent: Monday, March 5, 2018 8:19:33 AM
To: Osama Abdullah; hcp-users@humanconnectome.org
Cc: Nikos Nikiforakis
Subject: Re: [HCP-Users] question about mother vs. non-mothers in the HCP 1200

I don’t know that Gs and Ps were asked about unfortunately.

Peace,

Matt.

From: 
>
 on behalf of Osama Abdullah 
>
Date: Monday, March 5, 2018 at 12:18 AM
To: "hcp-users@humanconnectome.org" 
>
Cc: Nikos Nikiforakis >
Subject: [HCP-Users] question about mother vs. non-mothers in the HCP 1200

Dear HCP'ers,

We are trying to compare brain data for female participants who are mothers vs. 
non-mothers. I have access to the restricted data but couldn't find a field 
that specifies if a female participant gave birth or not.

Does this information exists?

As always thanks for your support and guidance.

Osama

Osama Abdullah, Ph.D.
MRI Physicist – Core Technology Platforms
New York University Abu Dhabi

Computational Research Building (A2), MRI Lab
Abu Dhabi, UAE (EDT + 8 hours)
Office: +971-2-628-4990
Cell:+971-56-679-3378

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] question about mother vs. non-mothers in the HCP 1200

[Glasser, Matthew]

I don’t know that Gs and Ps were asked about unfortunately.

Peace,

Matt.

From: 
>
 on behalf of Osama Abdullah 
>
Date: Monday, March 5, 2018 at 12:18 AM
To: "hcp-users@humanconnectome.org" 
>
Cc: Nikos Nikiforakis >
Subject: [HCP-Users] question about mother vs. non-mothers in the HCP 1200

Dear HCP'ers,

We are trying to compare brain data for female participants who are mothers vs. 
non-mothers. I have access to the restricted data but couldn't find a field 
that specifies if a female participant gave birth or not.

Does this information exists?

As always thanks for your support and guidance.

Osama

Osama Abdullah, Ph.D.
MRI Physicist – Core Technology Platforms
New York University Abu Dhabi

Computational Research Building (A2), MRI Lab
Abu Dhabi, UAE (EDT + 8 hours)
Office: +971-2-628-4990
Cell:+971-56-679-3378

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] contrast in human connectome 3T structural MRI

[Glasser, Matthew]

No gadolinium contrast was used in the HCP.  Sometimes blood will appear bright 
on T1w scans for reasons other than gadolinium contrast.

Peace,

Matt.

From: 
>
 on behalf of Jamila Ahdidan 
>
Date: Monday, March 5, 2018 at 2:53 AM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] contrast in human connectome 3T structural MRI

Hi,

I have noticed that many if not all the structural MRIs of the HCP show signs 
of contrast in the subjects blood. Is that correct? Have you scanned the 
participants without using contrast as this disturbs the segmentation?

Thank you.

Best regards / Cordialement / De bedste hilsner

Jamila Ahdidan
PhD, Partner, CSO
Brainreader ApS
Emil Møllers Gade 41
8700 Horsens - DK
tel: +45 5050 5544
email: jam...@brainreader.net
skype: jamila_ahdidan
website: www.brainreader.net

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] question about mother vs. non-mothers in the HCP 1200

[Osama Abdullah]

Dear HCP'ers,

We are trying to compare brain data for female participants who are mothers
vs. non-mothers. I have access to the restricted data but couldn't find a
field that specifies if a female participant gave birth or not.

Does this information exists?

As always thanks for your support and guidance.

Osama

*Osama Abdullah*, Ph.D.
MRI Physicist – Core Technology Platforms
New York University Abu Dhabi

Computational Research Building (A2), MRI Lab
Abu Dhabi, UAE (EDT + 8 hours)
Office: +971-2-628-4990
Cell:+971-56-679-3378

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] contrast in human connectome 3T structural MRI

[Jamila Ahdidan]

Hi,

I have noticed that many if not all the structural MRIs of the HCP show
signs of contrast in the subjects blood. Is that correct? Have you scanned
the participants without using contrast as this disturbs the segmentation?

Thank you.

Best regards / Cordialement / De bedste hilsner

Jamila Ahdidan
PhD, Partner, CSO
Brainreader ApS
Emil Møllers Gade 41
8700 Horsens - DK
tel: +45 5050 5544 <+45%2050%2050%2055%2044>
email: jam...@brainreader.net
skype: jamila_ahdidan
website: www.brainreader.net

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users