Re: [HCP-Users] Pittsburgh Sleep Quality Index Component Scores

[Elam, Jennifer]

Hi Ely,

The PSQI Component scores are already available in ConnectomeDB. We don't have 
plans to release the MMSE component scores.


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 Ely, Benjamin 

Sent: Wednesday, February 28, 2018 6:33:40 PM
To: Burgess, Gregory
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Pittsburgh Sleep Quality Index Component Scores

Hi Greg and co,

What’s the status on the planned release of PSQI component scores? Also, are 
there plans to release the MMSE (aka Mini) component scores?

Thank you!
-Ely

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[HCP-Users] HCP Young Adult Genetics Data Released on dbGaP!!

[Elam, Jennifer]

News from the Human Connectome Project (HCP)
March 2, 2018
The Human Connectome Project (HCP) WU-Minn consortium is pleased to announce 
the release of all SNP Genotypes collected for HCP-Young Adult (HCP-YA) 
subjects on dbGaP:

Mapping the Human Connectome - Structure, Function, and Heritability: Healthy 
Young Adults (Age 22-35 Years) Including Twins and their Non-Twin Siblings
dbGaP Study Accession: phs001364.v1.p1
https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001364.v1.p1
The dbGaP data comprises array and imputed genotyping and a limited number of 
phenotypic variables (self reported sex, age, twin status, and family IDs) 
collected for 1142 of our 1206 released HCP-YA participants, including 149 
pairs of genetically-confirmed monozygotic twins (298 participants) and 94 
pairs of genetically-confirmed dizygotic twins (188 participants). Other open 
and restricted access subject variables are available in 
ConnectomeDB.

dbGaP download of the HCP-YA data requires authorized access through a data 
access request initiated after logging into dbGaP with an eRA 
Commons PI account. 
General instructions for submitting a successful data access 
request
 for dbGaP are linked from the blue box on the study page.
You will need to submit as part of the request:

  *   A research statement and a nontechnical summary statement describing your 
planned use of the data.
  *   The name of the institutional signing official who will certify the terms 
of use assurances on behalf of your institution.
  *   A list of all internal investigators at your institution who will share 
access to the data for the proposed research.
  *   A list of external collaborating investigators.
  *   The name of the information technology (IT) Director for your institution.
  *   Local Institutional Review Board (IRB) approval for use.

Once you are logged in and click Create/Begin a New Research Project, on the 
Choose Datasets tab of the Project Request page, under Primary Disease select 
"Connectome" to find the HCP dataset. Then proceed with your application.

Best,
WU-Minn HCP Consortium

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


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

[Gaurav Patel]

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
>>> To: Timothy Coalson , "Glasser, Matthew"
>>>
>>> Cc: "Erin W. E. Dickie" ,
>>>"hcp-users@humanconnectome.org" 
>>> Message-ID:
>>> 
>>> <1cf06fac1128cf49ab6143a2d6a10f859345e...@hhcexchmb04.hhcsystem.org>
>>> Content-Type: text/plain; charset="utf-8"
>>> 
>>> Hi Tim,
>>> 
>>> Thanks.  That?s clear and sounds like a really reasonable approach.
>>> 
>>> Can you point me towards the exact files I?d need to reference and
>>> maybe suggest which function calls I?ll need to use to do the
>>> 

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

[Glasser, Matthew]

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"  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
>> To: Timothy Coalson , "Glasser, Matthew"
>> 
>> Cc: "Erin W. E. Dickie" ,
>> "hcp-users@humanconnectome.org" 
>> Message-ID:
>> 
>><1cf06fac1128cf49ab6143a2d6a10f859345e...@hhcexchmb04.hhcsystem.org>
>> Content-Type: text/plain; charset="utf-8"
>> 
>> Hi Tim,
>> 
>> Thanks.  That?s clear and sounds like a really reasonable approach.
>> 
>> Can you point me towards the exact files I?d need to reference and
>>maybe suggest which function calls I?ll need to use to do the
>>volume-to-surface mapping you describe?  I?ll whip up a quick script to
>>loop through about 120 datasets from this R01 project and let you know
>>how well it works.
>> 
>> Mike
>> 
>> 
>> From: Timothy Coalson [mailto:tsc...@mst.edu]
>> Sent: Friday, February 23, 2018 6:49 PM
>> To: Glasser, Matthew
>> Cc: Stevens, Michael; Erin W. E. Dickie; hcp-users@humanconnectome.org
>> Subject: Re: 

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

[Gaurav Patel]

Yes…we’ve 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
> To: Timothy Coalson , "Glasser, Matthew"
> 
> Cc: "Erin W. E. Dickie" ,
> "hcp-users@humanconnectome.org" 
> Message-ID:
> <1cf06fac1128cf49ab6143a2d6a10f859345e...@hhcexchmb04.hhcsystem.org>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi Tim,
> 
> Thanks.  That?s clear and sounds like a really reasonable approach.
> 
> Can you point me towards the exact files I?d need to reference and maybe 
> suggest which function calls I?ll need to use to do the volume-to-surface 
> mapping you describe?  I?ll whip up a quick script to loop through about 120 
> datasets from this R01 project and let you know how well it works.
> 
> Mike
> 
> 
> From: Timothy Coalson [mailto:tsc...@mst.edu]
> Sent: Friday, February 23, 2018 6:49 PM
> To: Glasser, Matthew
> Cc: Stevens, Michael; Erin W. E. Dickie; hcp-users@humanconnectome.org
> Subject: Re: [HCP-Users] Best Approach for using old volumetric data to pick 
> parcels-of-interest
> 
> This is an email from Outside HHC. USE CAUTION opening attachments or links 
> from unknown senders.
> 
> Surface-based methods may boost your statistical power enough (by better 
> alignment, exclusion of irrelevant tissue, and smoothing that 

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

[Sanchez, Juan (NYSPI)]

They do!

From: Glasser, Matthew 
Sent: Friday, March 2, 2018 2:25:47 PM
To: Sanchez, Juan (NYSPI); hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] 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.


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:


  1.  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
To: Timothy Coalson >, "Glasser, Matthew"
>
Cc: "Erin W. E. Dickie" 
>,
"hcp-users@humanconnectome.org" 
>
Message-ID:

<1cf06fac1128cf49ab6143a2d6a10f859345e...@hhcexchmb04.hhcsystem.org>
Content-Type: text/plain; charset="utf-8"

Hi Tim,

Thanks.  That?s clear and sounds like a really reasonable approach.

Can you point me towards the exact files I?d need to reference and maybe 
suggest which function calls I?ll need to use to do the volume-to-surface 
mapping you describe?  I?ll whip up a quick script to loop through about 120 
datasets from 

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

[Glasser, Matthew]

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:


  1.  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
To: Timothy Coalson >, "Glasser, Matthew"
>
Cc: "Erin W. E. Dickie" 
>,
"hcp-users@humanconnectome.org" 
>
Message-ID:

<1cf06fac1128cf49ab6143a2d6a10f859345e...@hhcexchmb04.hhcsystem.org>
Content-Type: text/plain; charset="utf-8"

Hi Tim,

Thanks.  That?s clear and sounds like a really reasonable approach.

Can you point me towards the exact files I?d need to reference and maybe 
suggest which function calls I?ll need to use to do the volume-to-surface 
mapping you describe?  I?ll whip up a quick script to loop through about 120 
datasets from this R01 project and let you know how well it works.

Mike


From: Timothy Coalson [mailto:tsc...@mst.edu]
Sent: Friday, February 23, 2018 6:49 PM
To: Glasser, Matthew
Cc: Stevens, Michael; Erin W. E. Dickie; 
hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Best Approach for using old volumetric data to pick 
parcels-of-interest

This is 

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

[Sanchez, Juan (NYSPI)]

Dear Kwan-Jin Jung

I had rthe same problems when I installed the 3_22 HCP Pipleines

Here is what we did:


  1.  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.


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To subscribe or unsubscribe via the World Wide Web, visit
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When replying, please edit your Subject line so it is more specific
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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
To: Timothy Coalson , "Glasser, Matthew"

Cc: "Erin W. E. Dickie" ,
"hcp-users@humanconnectome.org" 
Message-ID:
<1cf06fac1128cf49ab6143a2d6a10f859345e...@hhcexchmb04.hhcsystem.org>
Content-Type: text/plain; charset="utf-8"

Hi Tim,

Thanks.  That?s clear and sounds like a really reasonable approach.

Can you point me towards the exact files I?d need to reference and maybe 
suggest which function calls I?ll need to use to do the volume-to-surface 
mapping you describe?  I?ll whip up a quick script to loop through about 120 
datasets from this R01 project and let you know how well it works.

Mike


From: Timothy Coalson [mailto:tsc...@mst.edu]
Sent: Friday, February 23, 2018 6:49 PM
To: Glasser, Matthew
Cc: Stevens, Michael; Erin W. E. Dickie; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Best Approach for using old volumetric data to pick 
parcels-of-interest

This is an email from Outside HHC. USE CAUTION opening attachments or links 
from unknown senders.

Surface-based methods may boost your statistical power enough (by better 
alignment, exclusion of irrelevant tissue, and smoothing that doesn't cross 
sulcal banks, if you decide you need smoothing) that you may not need to rely 
as much on existing ROIs.  Parcel-based statistics have a lot of power, because 
the multiple comparisons are orders of magnitude smaller, spatially independent 
noise averages out, and the signal averages together.  We believe that a lot of 
old data would benefit from reanalysis using surfaces.

However, our paper is mainly focused on specificity and continuous data.  If 
you have a binary volume ROI and you only need a rough guess of it on the 
surface, you can get approximate answers, in a way that should reduce false 
negatives (and give more false positives) from the surface/volume transition 
problems.  You can map the ROI to the anatomical MNI surfaces of a group of 
subjects, and take the max across subjects.  Each individual may miss the 
expected group ribbon location in any given location, but it is very likely 
that every point in the expected group ribbon location will 

Re: [HCP-Users] Change of FreeSurferHiresPial.sh for MacBook IOS

[Glasser, Matthew]

Google finds this: 

https://www.mail-archive.com/hcp-users@humanconnectome.org/msg01081.html

Matt. 

On 3/2/18, 1:06 PM, "Kwan-Jin Jung"  wrote:

>Hi Matthew,
>
>Thank you.
>It is a long list:
>linux-vdso.so.1 =>  (0x7ffece4f)
>libz.so.1 => /usr/local/lib/libz.so.1 (0x7fafe4dd9000)
>libcrypt.so.1 => /lib/x86_64-linux-gnu/libcrypt.so.1
>(0x7fafe4ba1000)
>libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2
>(0x7fafe499d000)
>libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
>(0x7fafe478)
>libnetcdf.so.6 => /usr/lib/x86_64-linux-gnu/libnetcdf.so.6
>(0x7fafe443f000)
>libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
>(0x7fafe40bd000)
>libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x7fafe3db4000)
>libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1
>(0x7fafe3b92000)
>libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1
>(0x7fafe397c000)
>libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x7fafe35b2000)
>/lib64/ld-linux-x86-64.so.2 (0x7fafe4ff3000)
>libhdf5_hl.so.6 => /usr/lib/x86_64-linux-gnu/libhdf5_hl.so.6
>(0x7fafe3392000)
>libhdf5.so.6 => /usr/lib/x86_64-linux-gnu/libhdf5.so.6
>(0x7fafe2ef5000)
>libcurl.so.4 => /usr/lib/x86_64-linux-gnu/libcurl.so.4
>(0x7fafe2c86000)
>libsz.so.2 => /usr/lib/x86_64-linux-gnu/libsz.so.2
>(0x7fafe2a83000)
>libidn.so.11 => /usr/lib/x86_64-linux-gnu/libidn.so.11
>(0x7fafe285)
>librtmp.so.1 => /usr/lib/x86_64-linux-gnu/librtmp.so.1
>(0x7fafe2634000)
>libssl.so.1.0.0 => /lib/x86_64-linux-gnu/libssl.so.1.0.0
>(0x7fafe23cb000)
>libcrypto.so.1.0.0 => /lib/x86_64-linux-gnu/libcrypto.so.1.0.0
>(0x7fafe1f87000)
>libgssapi_krb5.so.2 =>
>/usr/lib/x86_64-linux-gnu/libgssapi_krb5.so.2 (0x7fafe1d3d000)
>liblber-2.4.so.2 => /usr/lib/x86_64-linux-gnu/liblber-2.4.so.2
>(0x7fafe1b2e000)
>libldap_r-2.4.so.2 =>
>/usr/lib/x86_64-linux-gnu/libldap_r-2.4.so.2 (0x7fafe18dd000)
>libaec.so.0 => /usr/lib/x86_64-linux-gnu/libaec.so.0
>(0x7fafe16d5000)
>libgnutls.so.30 => /usr/lib/x86_64-linux-gnu/libgnutls.so.30
>(0x7fafe13a5000)
>libhogweed.so.4 => /usr/lib/x86_64-linux-gnu/libhogweed.so.4
>(0x7fafe1172000)
>libnettle.so.6 => /usr/lib/x86_64-linux-gnu/libnettle.so.6
>(0x7fafe0f3c000)
>libgmp.so.10 => /usr/lib/x86_64-linux-gnu/libgmp.so.10
>(0x7fafe0cbc000)
>libkrb5.so.3 => /usr/lib/x86_64-linux-gnu/libkrb5.so.3
>(0x7fafe09ea000)
>libk5crypto.so.3 => /usr/lib/x86_64-linux-gnu/libk5crypto.so.3
>(0x7fafe07bb000)
>libcom_err.so.2 => /lib/x86_64-linux-gnu/libcom_err.so.2
>(0x7fafe05b7000)
>libkrb5support.so.0 =>
>/usr/lib/x86_64-linux-gnu/libkrb5support.so.0 (0x7fafe03ac000)
>libresolv.so.2 => /lib/x86_64-linux-gnu/libresolv.so.2
>(0x7fafe0191000)
>libsasl2.so.2 => /usr/lib/x86_64-linux-gnu/libsasl2.so.2
>(0x7fafdff76000)
>libgssapi.so.3 => /usr/lib/x86_64-linux-gnu/libgssapi.so.3
>(0x7fafdfd35000)
>libp11-kit.so.0 => /usr/lib/x86_64-linux-gnu/libp11-kit.so.0
>(0x7fafdfad1000)
>libtasn1.so.6 => /usr/lib/x86_64-linux-gnu/libtasn1.so.6
>(0x7fafdf8be000)
>libkeyutils.so.1 => /lib/x86_64-linux-gnu/libkeyutils.so.1
>(0x7fafdf6ba000)
>libheimntlm.so.0 => /usr/lib/x86_64-linux-gnu/libheimntlm.so.0
>(0x7fafdf4b1000)
>libkrb5.so.26 => /usr/lib/x86_64-linux-gnu/libkrb5.so.26
>(0x7fafdf227000)
>libasn1.so.8 => /usr/lib/x86_64-linux-gnu/libasn1.so.8
>(0x7fafdef85000)
>libhcrypto.so.4 => /usr/lib/x86_64-linux-gnu/libhcrypto.so.4
>(0x7fafded52000)
>libroken.so.18 => /usr/lib/x86_64-linux-gnu/libroken.so.18
>(0x7fafdeb3c000)
>libffi.so.6 => /usr/lib/x86_64-linux-gnu/libffi.so.6
>(0x7fafde934000)
>libwind.so.0 => /usr/lib/x86_64-linux-gnu/libwind.so.0
>(0x7fafde70b000)
>libheimbase.so.1 => /usr/lib/x86_64-linux-gnu/libheimbase.so.1
>(0x7fafde4fc000)
>libhx509.so.5 => /usr/lib/x86_64-linux-gnu/libhx509.so.5
>(0x7fafde2b1000)
>libsqlite3.so.0 => /usr/lib/x86_64-linux-gnu/libsqlite3.so.0
>(0x7fafddfdc000)
>
>
>Kwan-Jin Jung, Ph.D.
>S230J, HMRC, Life Science Laboratories
>UMASS Amherst
>Office: 413-577-0538
>Website: http://www.umass.edu/ials/hmrc
>
>
>
>-Original Message-
>From: Glasser, Matthew [mailto:glass...@wustl.edu]
>Sent: Friday, March 02, 2018 2:00 PM
>To: Kwan-Jin Jung ; hcp-users@humanconnectome.org
>Subject: Re: [HCP-Users] Change of FreeSurferHiresPial.sh for MacBook IOS
>
>Well you will actually have to run the command on the file to get a
>meaningful output.  Sometimes FreeSurfer has shell wrappers for binaries,
>so you’ll need to be sure that isn’t the case for mris_make_surfaces, but
>I 

Re: [HCP-Users] Change of FreeSurferHiresPial.sh for MacBook IOS

[Kwan-Jin Jung]

Hi Matthew,

Thank you.
It is a long list:
linux-vdso.so.1 =>  (0x7ffece4f)
libz.so.1 => /usr/local/lib/libz.so.1 (0x7fafe4dd9000)
libcrypt.so.1 => /lib/x86_64-linux-gnu/libcrypt.so.1 
(0x7fafe4ba1000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x7fafe499d000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 
(0x7fafe478)
libnetcdf.so.6 => /usr/lib/x86_64-linux-gnu/libnetcdf.so.6 
(0x7fafe443f000)
libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 
(0x7fafe40bd000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x7fafe3db4000)
libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1 
(0x7fafe3b92000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 
(0x7fafe397c000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x7fafe35b2000)
/lib64/ld-linux-x86-64.so.2 (0x7fafe4ff3000)
libhdf5_hl.so.6 => /usr/lib/x86_64-linux-gnu/libhdf5_hl.so.6 
(0x7fafe3392000)
libhdf5.so.6 => /usr/lib/x86_64-linux-gnu/libhdf5.so.6 
(0x7fafe2ef5000)
libcurl.so.4 => /usr/lib/x86_64-linux-gnu/libcurl.so.4 
(0x7fafe2c86000)
libsz.so.2 => /usr/lib/x86_64-linux-gnu/libsz.so.2 (0x7fafe2a83000)
libidn.so.11 => /usr/lib/x86_64-linux-gnu/libidn.so.11 
(0x7fafe285)
librtmp.so.1 => /usr/lib/x86_64-linux-gnu/librtmp.so.1 
(0x7fafe2634000)
libssl.so.1.0.0 => /lib/x86_64-linux-gnu/libssl.so.1.0.0 
(0x7fafe23cb000)
libcrypto.so.1.0.0 => /lib/x86_64-linux-gnu/libcrypto.so.1.0.0 
(0x7fafe1f87000)
libgssapi_krb5.so.2 => /usr/lib/x86_64-linux-gnu/libgssapi_krb5.so.2 
(0x7fafe1d3d000)
liblber-2.4.so.2 => /usr/lib/x86_64-linux-gnu/liblber-2.4.so.2 
(0x7fafe1b2e000)
libldap_r-2.4.so.2 => /usr/lib/x86_64-linux-gnu/libldap_r-2.4.so.2 
(0x7fafe18dd000)
libaec.so.0 => /usr/lib/x86_64-linux-gnu/libaec.so.0 
(0x7fafe16d5000)
libgnutls.so.30 => /usr/lib/x86_64-linux-gnu/libgnutls.so.30 
(0x7fafe13a5000)
libhogweed.so.4 => /usr/lib/x86_64-linux-gnu/libhogweed.so.4 
(0x7fafe1172000)
libnettle.so.6 => /usr/lib/x86_64-linux-gnu/libnettle.so.6 
(0x7fafe0f3c000)
libgmp.so.10 => /usr/lib/x86_64-linux-gnu/libgmp.so.10 
(0x7fafe0cbc000)
libkrb5.so.3 => /usr/lib/x86_64-linux-gnu/libkrb5.so.3 
(0x7fafe09ea000)
libk5crypto.so.3 => /usr/lib/x86_64-linux-gnu/libk5crypto.so.3 
(0x7fafe07bb000)
libcom_err.so.2 => /lib/x86_64-linux-gnu/libcom_err.so.2 
(0x7fafe05b7000)
libkrb5support.so.0 => /usr/lib/x86_64-linux-gnu/libkrb5support.so.0 
(0x7fafe03ac000)
libresolv.so.2 => /lib/x86_64-linux-gnu/libresolv.so.2 
(0x7fafe0191000)
libsasl2.so.2 => /usr/lib/x86_64-linux-gnu/libsasl2.so.2 
(0x7fafdff76000)
libgssapi.so.3 => /usr/lib/x86_64-linux-gnu/libgssapi.so.3 
(0x7fafdfd35000)
libp11-kit.so.0 => /usr/lib/x86_64-linux-gnu/libp11-kit.so.0 
(0x7fafdfad1000)
libtasn1.so.6 => /usr/lib/x86_64-linux-gnu/libtasn1.so.6 
(0x7fafdf8be000)
libkeyutils.so.1 => /lib/x86_64-linux-gnu/libkeyutils.so.1 
(0x7fafdf6ba000)
libheimntlm.so.0 => /usr/lib/x86_64-linux-gnu/libheimntlm.so.0 
(0x7fafdf4b1000)
libkrb5.so.26 => /usr/lib/x86_64-linux-gnu/libkrb5.so.26 
(0x7fafdf227000)
libasn1.so.8 => /usr/lib/x86_64-linux-gnu/libasn1.so.8 
(0x7fafdef85000)
libhcrypto.so.4 => /usr/lib/x86_64-linux-gnu/libhcrypto.so.4 
(0x7fafded52000)
libroken.so.18 => /usr/lib/x86_64-linux-gnu/libroken.so.18 
(0x7fafdeb3c000)
libffi.so.6 => /usr/lib/x86_64-linux-gnu/libffi.so.6 
(0x7fafde934000)
libwind.so.0 => /usr/lib/x86_64-linux-gnu/libwind.so.0 
(0x7fafde70b000)
libheimbase.so.1 => /usr/lib/x86_64-linux-gnu/libheimbase.so.1 
(0x7fafde4fc000)
libhx509.so.5 => /usr/lib/x86_64-linux-gnu/libhx509.so.5 
(0x7fafde2b1000)
libsqlite3.so.0 => /usr/lib/x86_64-linux-gnu/libsqlite3.so.0 
(0x7fafddfdc000)


Kwan-Jin Jung, Ph.D.
S230J, HMRC, Life Science Laboratories
UMASS Amherst
Office: 413-577-0538
Website: http://www.umass.edu/ials/hmrc



-Original Message-
From: Glasser, Matthew [mailto:glass...@wustl.edu] 
Sent: Friday, March 02, 2018 2:00 PM
To: Kwan-Jin Jung ; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Change of FreeSurferHiresPial.sh for MacBook IOS

Well you will actually have to run the command on the file to get a meaningful 
output.  Sometimes FreeSurfer has shell wrappers for binaries, so you’ll need 
to be sure that isn’t the case for mris_make_surfaces, but I don’t think it is.

Peace,

Matt.

On 3/2/18, 12:58 PM, "Kwan-Jin Jung"  wrote:

>Hi Matthew,
>
>jung@FileServer:~/bin/HCP/Examples/Scripts$ ldd mris_make_surfaces
>ldd: ./mris_make_surfaces: No such file or directory

Re: [HCP-Users] Change of FreeSurferHiresPial.sh for MacBook IOS

[Glasser, Matthew]

Well you will actually have to run the command on the file to get a
meaningful output.  Sometimes FreeSurfer has shell wrappers for binaries,
so you’ll need to be sure that isn’t the case for mris_make_surfaces, but
I don’t think it is.

Peace,

Matt.

On 3/2/18, 12:58 PM, "Kwan-Jin Jung"  wrote:

>Hi Matthew,
>
>jung@FileServer:~/bin/HCP/Examples/Scripts$ ldd mris_make_surfaces
>ldd: ./mris_make_surfaces: No such file or directory
>
>
>Kwan-Jin Jung, Ph.D.
>S230J, HMRC, Life Science Laboratories
>UMASS Amherst
>Office: 413-577-0538
>Website: http://www.umass.edu/ials/hmrc
>
>
>
>
>-Original Message-
>From: Glasser, Matthew [mailto:glass...@wustl.edu]
>Sent: Friday, March 02, 2018 1:45 PM
>To: Kwan-Jin Jung ; hcp-users@humanconnectome.org
>Subject: Re: [HCP-Users] Change of FreeSurferHiresPial.sh for MacBook IOS
>
>On Ubuntu 14.04 what happens if you do ldd mris_make_surfaces?
>
>Peace,
>
>Matt.
>
>On 3/2/18, 12:41 PM, "Kwan-Jin Jung"  wrote:
>
>>Hi Matthew,
>>
>>Since the FreeSurfer HCP version is available for MacOS, I assumed that
>>the HCP pipeline is supported in MacOS.
>>
>>The problems with Ubuntu (both 16.04 and 14.04) were about the missing
>>libraries during mris: Libnetcdf.so.6 error during mris_make_surfaces.
>>
>>This was resolved by following the instruction by Tim:
>>https://www.mail-archive.com/hcp-users@humanconnectome.org/msg04837.html.
>>
>>But I have the following message during FreeSurferPielineBatch.mine.sh:
>>"
>>mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale
>>--i orig.mgz --o orig_nu.mgzrecon-all -s 100307 exited with ERRORS at
>>Fri Mar  2 13:21:24 EST 2018"
>>
>>"mris_make_surfaces: symbol lookup error: mris_make_surfaces: undefined
>>symbol: ncerr"
>>
>>On Centos (both 5 and 6), I was getting different errors.
>>
>>At this point I gave up ...
>>
>>On Macbook, it ran without these issues until the 'wb_command' problem.
>>
>>Kwan-Jin Jung, Ph.D.
>>S230J, HMRC, Life Science Laboratories
>>UMASS Amherst
>>Office: 413-577-0538
>>Website: http://www.umass.edu/ials/hmrc
>>
>>
>>
>>-Original Message-
>>From: Glasser, Matthew [mailto:glass...@wustl.edu]
>>Sent: Friday, March 02, 2018 11:16 AM
>>To: Kwan-Jin Jung ; hcp-users@humanconnectome.org
>>Cc: Hae-Min Jung 
>>Subject: Re: [HCP-Users] Change of FreeSurferHiresPial.sh for MacBook
>>IOS
>>
>>I¹m not sure we support the HCP Pipelines on Mac OS X.  You definitely
>>need to be using a bash interpreter.
>>
>>What issues were you having on Ubuntu?
>>
>>Peace,
>>
>>Matt.
>>
>>On 3/2/18, 10:13 AM, "hcp-users-boun...@humanconnectome.org on behalf
>>of Kwan-Jin Jung" >kjj...@umass.edu> wrote:
>>
>>>Hi,
>>>
>>>After I failed to run FreeSurfer pipeline on both Ubuntu and Centos, I
>>>tried it on MacBook.
>>>
>>>It runs without library issues, but it seems to have differences in
>>>shell scripting commands.
>>>
>>>The first example is Œcp¹ which needs to be replaced into Œrsync¹ in
>>>both FreeSurferHiresWhite.sh and FreeSurferHiresPial.sh.
>>>
>>>Then there was another issue in FreeSurferHiresPial.sh at the line #92
>>>of:
>>>"${CARET7DIR}/wb_command -set-structure "$surfdir"/lh.white.surf.gii
>>>CORTEX_LEFT"
>>>
>>>I converted this into:
>>>"open -a ${CARET7DIR}/wb_command -set-structure
>>>"$surfdir"/lh.white.surf.gii CORTEX_LEFT"
>>>
>>>However, I am getting an error of:
>>>"The file /Users/kjjung/MRI/HCP/Practice/CORTEX_LEFT does not exist."
>>>
>>>Does any one know how to fix this issue?
>>>
>>>My MacBook is macOS High Sierra, v10.13.3.
>>>
>>>Kwan-Jin Jung
>>>UMASS Amherst
>>>
>>>___
>>>HCP-Users mailing list
>>>HCP-Users@humanconnectome.org
>>>http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>
>


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Re: [HCP-Users] Change of FreeSurferHiresPial.sh for MacBook IOS

[Kwan-Jin Jung]

Hi Matthew,

jung@FileServer:~/bin/HCP/Examples/Scripts$ ldd mris_make_surfaces
ldd: ./mris_make_surfaces: No such file or directory


Kwan-Jin Jung, Ph.D.
S230J, HMRC, Life Science Laboratories
UMASS Amherst
Office: 413-577-0538
Website: http://www.umass.edu/ials/hmrc




-Original Message-
From: Glasser, Matthew [mailto:glass...@wustl.edu] 
Sent: Friday, March 02, 2018 1:45 PM
To: Kwan-Jin Jung ; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Change of FreeSurferHiresPial.sh for MacBook IOS

On Ubuntu 14.04 what happens if you do ldd mris_make_surfaces?

Peace,

Matt.

On 3/2/18, 12:41 PM, "Kwan-Jin Jung"  wrote:

>Hi Matthew,
>
>Since the FreeSurfer HCP version is available for MacOS, I assumed that 
>the HCP pipeline is supported in MacOS.
>
>The problems with Ubuntu (both 16.04 and 14.04) were about the missing 
>libraries during mris: Libnetcdf.so.6 error during mris_make_surfaces.
>
>This was resolved by following the instruction by Tim:
>https://www.mail-archive.com/hcp-users@humanconnectome.org/msg04837.html.
>
>But I have the following message during FreeSurferPielineBatch.mine.sh:
>"
>mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale 
>--i orig.mgz --o orig_nu.mgzrecon-all -s 100307 exited with ERRORS at 
>Fri Mar  2 13:21:24 EST 2018"
>
>"mris_make_surfaces: symbol lookup error: mris_make_surfaces: undefined
>symbol: ncerr"
>
>On Centos (both 5 and 6), I was getting different errors.
>
>At this point I gave up ...
>
>On Macbook, it ran without these issues until the 'wb_command' problem.
>
>Kwan-Jin Jung, Ph.D.
>S230J, HMRC, Life Science Laboratories
>UMASS Amherst
>Office: 413-577-0538
>Website: http://www.umass.edu/ials/hmrc
>
>
>
>-Original Message-
>From: Glasser, Matthew [mailto:glass...@wustl.edu]
>Sent: Friday, March 02, 2018 11:16 AM
>To: Kwan-Jin Jung ; hcp-users@humanconnectome.org
>Cc: Hae-Min Jung 
>Subject: Re: [HCP-Users] Change of FreeSurferHiresPial.sh for MacBook 
>IOS
>
>I¹m not sure we support the HCP Pipelines on Mac OS X.  You definitely 
>need to be using a bash interpreter.
>
>What issues were you having on Ubuntu?
>
>Peace,
>
>Matt.
>
>On 3/2/18, 10:13 AM, "hcp-users-boun...@humanconnectome.org on behalf 
>of Kwan-Jin Jung" kjj...@umass.edu> wrote:
>
>>Hi,
>>
>>After I failed to run FreeSurfer pipeline on both Ubuntu and Centos, I 
>>tried it on MacBook.
>>
>>It runs without library issues, but it seems to have differences in 
>>shell scripting commands.
>>
>>The first example is Œcp¹ which needs to be replaced into Œrsync¹ in 
>>both FreeSurferHiresWhite.sh and FreeSurferHiresPial.sh.
>>
>>Then there was another issue in FreeSurferHiresPial.sh at the line #92
>>of:
>>"${CARET7DIR}/wb_command -set-structure "$surfdir"/lh.white.surf.gii 
>>CORTEX_LEFT"
>>
>>I converted this into:
>>"open -a ${CARET7DIR}/wb_command -set-structure 
>>"$surfdir"/lh.white.surf.gii CORTEX_LEFT"
>>
>>However, I am getting an error of:
>>"The file /Users/kjjung/MRI/HCP/Practice/CORTEX_LEFT does not exist."
>>
>>Does any one know how to fix this issue?
>>
>>My MacBook is macOS High Sierra, v10.13.3.
>>
>>Kwan-Jin Jung
>>UMASS Amherst
>>
>>___
>>HCP-Users mailing list
>>HCP-Users@humanconnectome.org
>>http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>


___
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HCP-Users@humanconnectome.org
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Re: [HCP-Users] Change of FreeSurferHiresPial.sh for MacBook IOS

[Glasser, Matthew]

On Ubuntu 14.04 what happens if you do ldd mris_make_surfaces?

Peace,

Matt.

On 3/2/18, 12:41 PM, "Kwan-Jin Jung"  wrote:

>Hi Matthew,
>
>Since the FreeSurfer HCP version is available for MacOS, I assumed that
>the HCP pipeline is supported in MacOS.
>
>The problems with Ubuntu (both 16.04 and 14.04) were about the missing
>libraries during mris: Libnetcdf.so.6 error during mris_make_surfaces.
>
>This was resolved by following the instruction by Tim:
>https://www.mail-archive.com/hcp-users@humanconnectome.org/msg04837.html.
>
>But I have the following message during FreeSurferPielineBatch.mine.sh:
>"
>mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale
>--i orig.mgz --o orig_nu.mgzrecon-all -s 100307 exited with ERRORS at Fri
>Mar  2 13:21:24 EST 2018"
>
>"mris_make_surfaces: symbol lookup error: mris_make_surfaces: undefined
>symbol: ncerr"
>
>On Centos (both 5 and 6), I was getting different errors.
>
>At this point I gave up ...
>
>On Macbook, it ran without these issues until the 'wb_command' problem.
>
>Kwan-Jin Jung, Ph.D.
>S230J, HMRC, Life Science Laboratories
>UMASS Amherst
>Office: 413-577-0538
>Website: http://www.umass.edu/ials/hmrc
>
>
>
>-Original Message-
>From: Glasser, Matthew [mailto:glass...@wustl.edu]
>Sent: Friday, March 02, 2018 11:16 AM
>To: Kwan-Jin Jung ; hcp-users@humanconnectome.org
>Cc: Hae-Min Jung 
>Subject: Re: [HCP-Users] Change of FreeSurferHiresPial.sh for MacBook IOS
>
>I¹m not sure we support the HCP Pipelines on Mac OS X.  You definitely
>need to be using a bash interpreter.
>
>What issues were you having on Ubuntu?
>
>Peace,
>
>Matt.
>
>On 3/2/18, 10:13 AM, "hcp-users-boun...@humanconnectome.org on behalf of
>Kwan-Jin Jung" kjj...@umass.edu> wrote:
>
>>Hi,
>>
>>After I failed to run FreeSurfer pipeline on both Ubuntu and Centos, I
>>tried it on MacBook.
>>
>>It runs without library issues, but it seems to have differences in
>>shell scripting commands.
>>
>>The first example is Œcp¹ which needs to be replaced into Œrsync¹ in
>>both FreeSurferHiresWhite.sh and FreeSurferHiresPial.sh.
>>
>>Then there was another issue in FreeSurferHiresPial.sh at the line #92
>>of:
>>"${CARET7DIR}/wb_command -set-structure "$surfdir"/lh.white.surf.gii
>>CORTEX_LEFT"
>>
>>I converted this into:
>>"open -a ${CARET7DIR}/wb_command -set-structure
>>"$surfdir"/lh.white.surf.gii CORTEX_LEFT"
>>
>>However, I am getting an error of:
>>"The file /Users/kjjung/MRI/HCP/Practice/CORTEX_LEFT does not exist."
>>
>>Does any one know how to fix this issue?
>>
>>My MacBook is macOS High Sierra, v10.13.3.
>>
>>Kwan-Jin Jung
>>UMASS Amherst
>>
>>___
>>HCP-Users mailing list
>>HCP-Users@humanconnectome.org
>>http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>


___
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HCP-Users@humanconnectome.org
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Re: [HCP-Users] Change of FreeSurferHiresPial.sh for MacBook IOS

[Kwan-Jin Jung]

Hi Matthew,

Since the FreeSurfer HCP version is available for MacOS, I assumed that the HCP 
pipeline is supported in MacOS.

The problems with Ubuntu (both 16.04 and 14.04) were about the missing 
libraries during mris: Libnetcdf.so.6 error during mris_make_surfaces.

This was resolved by following the instruction by Tim: 
https://www.mail-archive.com/hcp-users@humanconnectome.org/msg04837.html.

But I have the following message during FreeSurferPielineBatch.mine.sh:
"
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i 
orig.mgz --o orig_nu.mgzrecon-all -s 100307 exited with ERRORS at Fri Mar  2 
13:21:24 EST 2018"

"mris_make_surfaces: symbol lookup error: mris_make_surfaces: undefined symbol: 
ncerr"

On Centos (both 5 and 6), I was getting different errors.

At this point I gave up ...

On Macbook, it ran without these issues until the 'wb_command' problem.

Kwan-Jin Jung, Ph.D.
S230J, HMRC, Life Science Laboratories
UMASS Amherst
Office: 413-577-0538
Website: http://www.umass.edu/ials/hmrc



-Original Message-
From: Glasser, Matthew [mailto:glass...@wustl.edu] 
Sent: Friday, March 02, 2018 11:16 AM
To: Kwan-Jin Jung ; hcp-users@humanconnectome.org
Cc: Hae-Min Jung 
Subject: Re: [HCP-Users] Change of FreeSurferHiresPial.sh for MacBook IOS

I¹m not sure we support the HCP Pipelines on Mac OS X.  You definitely need to 
be using a bash interpreter.

What issues were you having on Ubuntu?

Peace,

Matt.

On 3/2/18, 10:13 AM, "hcp-users-boun...@humanconnectome.org on behalf of 
Kwan-Jin Jung"  wrote:

>Hi,
>
>After I failed to run FreeSurfer pipeline on both Ubuntu and Centos, I 
>tried it on MacBook.
>
>It runs without library issues, but it seems to have differences in 
>shell scripting commands.
>
>The first example is Œcp¹ which needs to be replaced into Œrsync¹ in 
>both FreeSurferHiresWhite.sh and FreeSurferHiresPial.sh.
>
>Then there was another issue in FreeSurferHiresPial.sh at the line #92 of:
>"${CARET7DIR}/wb_command -set-structure "$surfdir"/lh.white.surf.gii 
>CORTEX_LEFT"
>
>I converted this into:
>"open -a ${CARET7DIR}/wb_command -set-structure 
>"$surfdir"/lh.white.surf.gii CORTEX_LEFT"
>
>However, I am getting an error of:
>"The file /Users/kjjung/MRI/HCP/Practice/CORTEX_LEFT does not exist."
>
>Does any one know how to fix this issue?
>
>My MacBook is macOS High Sierra, v10.13.3.
>
>Kwan-Jin Jung
>UMASS Amherst
>
>___
>HCP-Users mailing list
>HCP-Users@humanconnectome.org
>http://lists.humanconnectome.org/mailman/listinfo/hcp-users


___
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Re: [HCP-Users] Change of FreeSurferHiresPial.sh for MacBook IOS

[Glasser, Matthew]

I¹m not sure we support the HCP Pipelines on Mac OS X.  You definitely
need to be using a bash interpreter.

What issues were you having on Ubuntu?

Peace,

Matt.

On 3/2/18, 10:13 AM, "hcp-users-boun...@humanconnectome.org on behalf of
Kwan-Jin Jung"  wrote:

>Hi,
>
>After I failed to run FreeSurfer pipeline on both Ubuntu and Centos, I
>tried it on MacBook.
>
>It runs without library issues, but it seems to have differences in shell
>scripting commands.
>
>The first example is Œcp¹ which needs to be replaced into Œrsync¹ in both
>FreeSurferHiresWhite.sh and FreeSurferHiresPial.sh.
>
>Then there was another issue in FreeSurferHiresPial.sh at the line #92 of:
>"${CARET7DIR}/wb_command -set-structure "$surfdir"/lh.white.surf.gii
>CORTEX_LEFT"
>
>I converted this into:
>"open -a ${CARET7DIR}/wb_command -set-structure
>"$surfdir"/lh.white.surf.gii CORTEX_LEFT"
>
>However, I am getting an error of:
>"The file /Users/kjjung/MRI/HCP/Practice/CORTEX_LEFT does not exist."
>
>Does any one know how to fix this issue?
>
>My MacBook is macOS High Sierra, v10.13.3.
>
>Kwan-Jin Jung
>UMASS Amherst
>
>___
>HCP-Users mailing list
>HCP-Users@humanconnectome.org
>http://lists.humanconnectome.org/mailman/listinfo/hcp-users


___
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HCP-Users@humanconnectome.org
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[HCP-Users] Change of FreeSurferHiresPial.sh for MacBook IOS

[Kwan-Jin Jung]

Hi,

After I failed to run FreeSurfer pipeline on both Ubuntu and Centos, I tried it 
on MacBook.

It runs without library issues, but it seems to have differences in shell 
scripting commands.

The first example is ‘cp’ which needs to be replaced into ‘rsync’ in both 
FreeSurferHiresWhite.sh and FreeSurferHiresPial.sh.

Then there was another issue in FreeSurferHiresPial.sh at the line #92 of:
"${CARET7DIR}/wb_command -set-structure "$surfdir"/lh.white.surf.gii 
CORTEX_LEFT"

I converted this into:
"open -a ${CARET7DIR}/wb_command -set-structure "$surfdir"/lh.white.surf.gii 
CORTEX_LEFT"

However, I am getting an error of:
"The file /Users/kjjung/MRI/HCP/Practice/CORTEX_LEFT does not exist."

Does any one know how to fix this issue?

My MacBook is macOS High Sierra, v10.13.3.

Kwan-Jin Jung
UMASS Amherst

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Re: [HCP-Users] Split dtseries

[Glasser, Matthew]

wb_command -cifti-merge contains this functionality, rather than a
separate command.

Peace,

Matt.

On 3/2/18, 6:47 AM, "hcp-users-boun...@humanconnectome.org on behalf of A
R" 
wrote:

>Dear HCP users,
>
>How to split/trim a dtseries or ptseries file by number of time points?
>Basically an equivalent of fslroi...
>
>Thanks for any info
>___
>HCP-Users mailing list
>HCP-Users@humanconnectome.org
>http://lists.humanconnectome.org/mailman/listinfo/hcp-users


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[HCP-Users] Split dtseries

[A R]

Dear HCP users,

How to split/trim a dtseries or ptseries file by number of time points? 
Basically an equivalent of fslroi...

Thanks for any info
___
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Re: [HCP-Users] Correct interpretation of NIH battery test 'Words-in-Noise' in HCP subjects

[Robert Becker]

Hi, Jennifer,

That's great, thanks for the clarification!


Best,
Robert

Am 01/03/2018 um 18:26 schrieb Elam, Jennifer:


Hi Robert,

Thank you for pointing us to this problem. The HCP Words in Noise 
score is indeed the NIH Toolbox Words in Noise (WIN) Test computed 
score, rather than the Toolbox Hearing Threshold Test that was 
erroneously used for the description in the Data Dictionary. We will 
fix the data dictionary with the upcoming data release of the 
corrected 7T fMRI data slated to occur within the month.



Here's the full description for the Words in Noise measure from the 
NIH Toolbox Interpretation Guide from the 2012 version we used for HCP:



NIH Toolbox Words-in-Noise Test (WIN)Description:
This test measures a person’s ability to recognize single words 
presented amid varying levels of background noise. It measures how 
much difficulty a person might have hearing in a noisy environment. A 
recorded voice instructs the participant to listen to and then repeat 
words. The task becomes increasingly difficult as the background noise 
gets louder, thus reducing the signal-to-noise ratio. The test is 
recommended for participants ages 6-85 and takes approximately six 
minutes to administer.
Scoring Process: The examiner scores the participant’s responses as 
correct or incorrect, and a total raw score (out of a maximum of 35 
points) is calculated by the software for each ear. A percent correct 
is calculated, which is then translated into a threshold score for 
each ear, in decibels of signal-to-noise ratio (dB S/N), using a 
look-up table (see Appendix C). Alternatively, the following equation 
can be used to calculate the S/N score based on the raw score, in lieu 
of the look-up table. For each ear:WIN_Score = 26-0.8*WIN_NCorrect
Thus, the best score that can be attained (35 correct) for either ear 
is -2.0 dB S/N, and the worst score (0correct) is 26.0 dB S/N. Lower 
scores, therefore, are indicative of better performance on this test. 
In the Toolbox Assessment Scores output file, the score for the better 
ear is provided in the Computed Score column.
Interpretation: Assessment of the ability to understand speech in a 
noisy background yields an ecologically valid measure of hearing 
because a substantial portion of communication in the real world 
occurs in less-than-ideal environments. Moreover, speech perception in 
noise is often difficult to predict from pure-tone thresholds or from 
speech perception in quiet settings. The NIH Toolbox version of the 
Words-in-Noise Test is newly released, so the interpretive guidelines 
provided are preliminary and may need further adjustment as future 
studies are conducted.As noted above, the range of possible scores for 
each ear is -2.0 to 26.0 dB S/N, with lower scores indicative of 
better performance and, conversely, higher scores potentially 
suggestive of hearing difficulties. For score interpretation with ages 
13 and above, a cutoff of 10 dB S/N is recommended for the Toolbox 
version of this measure. Participants with a score higher than this 
cutoff should follow up with a hearing professional, specifically an 
otolaryngologist, who would then refer to an audiologist as needed. 
Users should note that the cutoff suggested here is slightly higher 
than other published versions of this test because other versions were 
conducted in quieter environments.


Again, sorry for the oversight. Let me know if you have further questions.

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 Robert Becker 


*Sent:* Thursday, March 1, 2018 8:41:06 AM
*To:* hcp-users@humanconnectome.org
*Subject:* [HCP-Users] Correct interpretation of NIH battery test 
'Words-in-Noise' in HCP subjects


Dear all,

we have trouble understanding what the above test actually tests in 
the context of HCP data. Despite its suggestive name, this test is 
described (in the updated HCP Data Dictionary and its previous 
version), as a pure-tone thresholding test that seems to have nothing 
to do with understanding words embedded in noise or any similar scenario.


The description in the Data Dictionary is pretty clear and excludes 
any such interpretation, it is just that the naming seems confusing 
and also, there actually is a NIH toolbox test called 
'"Words-in-Noise" that does test how subjects comprehend one-syllable 
words.



Can anyone comment on the exact nature of this test and help us out?

Thanks for your help!

Robert
--
Robert Becker, PhD
Universität Zürich
Psychologisches Institut
Binzmühlestrasse 14
8050