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" <gaurav.pa...@gmail.com on behalf of
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 <glass...@wustl.edu> wrote:
>> 
>> So you are saying that the Pipelines work fine on the Mac for you aside
>>from this cp issue?
>> 
>> Matt.
>> 
>> From: <hcp-users-boun...@humanconnectome.org> on behalf of "Sanchez,
>>Juan (NYSPI)" <juan.sanc...@nyspi.columbia.edu>
>> Date: Friday, March 2, 2018 at 1:24 PM
>> To: "hcp-users@humanconnectome.org" <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
>><hcp-users-boun...@humanconnectome.org> on behalf of
>>hcp-users-requ...@humanconnectome.org
>><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
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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 +0000
>> From: "Stevens, Michael" <michael.stev...@hhchealth.org>
>> Subject: Re: [HCP-Users] Best Approach for using old volumetric data
>>         to pick parcels-of-interest
>> To: Timothy Coalson <tsc...@mst.edu>, "Glasser, Matthew"
>>         <glass...@wustl.edu>
>> Cc: "Erin W. E. Dickie" <erin.w.dic...@gmail.com>,
>>         "hcp-users@humanconnectome.org" <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 overlap with at least one subject in
>>the group.  If this isn't enough, you can dilate the volume ROI a few mm
>>first.
>> 
>> Tim
>> 
>> 
>> On Fri, Feb 23, 2018 at 11:18 AM, Glasser, Matthew
>><glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
>> Hi Mike,
>> 
>> We have a preprint out on this exact question and the conclusion is
>>that it is really hard to do this accurately for most brain regions:
>> 
>> https://www.biorxiv.org/content/early/2018/01/29/255620
>> 
>> Really the best idea is probably to go back and reanalyze the old data
>>without volume-based smoothing and aligned across surfaces.  Erin
>>Dickie, CCed is working on tools to make this a little easier, but still
>>there are issues like needing a field map to get accurate fMRI to
>>structural registration.  The good news is that one?s statistical power
>>should be much better if brains are actually lined up, and using
>>parcellated analyses instead of smoothing offers further benefits.
>> 
>> Matt.
>> 
>> From: 
>><hcp-users-boun...@humanconnectome.org<mailto:hcp-users-bounces@humanconn
>>ectome.org>> on behalf of "Stevens, Michael"
>><michael.stev...@hhchealth.org<mailto:michael.stev...@hhchealth.org>>
>> Date: Friday, February 23, 2018 at 8:58 AM
>> To: 
>>"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
>><hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
>> Subject: [HCP-Users] Best Approach for using old volumetric data to
>>pick parcels-of-interest
>> 
>> Hi everyone,
>> 
>> There?s been a lot posted here over the past year or two on the
>>challenges and limitations of going back-and-forth between volumetric
>>space and HCP-defined surface space, with solid arguments for moving to
>>(and sticking with) CIFTI-defined brainordinates.  Here, I?m asking a
>>slightly different question? The field has decades of research using
>>volume-space fMRI timeseries analyses that helps to define where to look
>>in the brain to test new hypotheses.  Has anyone got a well-thought-out
>>approach for mapping such volume-space ROIs to the parcels within the
>>new HCP 180 atlas?  I ask because the specificity of the HCP atlas
>>sometimes offers a half dozen candidate parcels for hypothesis-testing
>>for what we previously thought of as just one or two regions.  Even
>>though our group currently has a half dozen newer NIH-funded studies
>>that use HCP compliant sequences, most of that work is still predicated
>>on a ?region-of-interest? approach because the study groups sizes are
>>less than a h
>>  undred, not in the thousands typical of the HCP grantwork.  So we
>>still have to contend with the statistical power limitations inherent in
>>any ROI approach.  It would be great to be able to use our prior
>>volume-space data to have greater confidence in selecting among the
>>various parcel-of-interest candidates when testing hypotheses.
>> 
>> I?m wondering if anyone?s yet worked out a step-by-step approach for a
>>series of warps/surface-maps/transformations that can take ROIs from MNI
>>space and give a ?best guess? as to which HCP 180 atlas parcel(s) should
>>be queried in such instances.  It would be a nice bridge from older work
>>to newer HCP-guided work, that would allow researchers to circumvent the
>>added burden of having to go back and collect new pilot data using HCP
>>sequences.  A thoughtful list of the analytic or conceptual pros/cons of
>>something like this would be helpful as well.
>> 
>> Thanks,
>> Mike
>> 
>> 
>> This e-mail message, including any attachments, is for the sole use of
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>> _______________________________________________
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>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
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>> _______________________________________________
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>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
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>> 
>> 
>> Reminder: This e-mail and any attachments are subject to the current
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>> ------------------------------
>> 
>> Message: 2
>> Date: Thu, 1 Mar 2018 20:02:08 +0000
>> From: "Linnman, Clas,Ph.D." <clinn...@partners.org>
>> Subject: [HCP-Users] Movement regressor missing
>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> Message-ID: <14e25807-db1b-4132-ad77-1ff863216...@contoso.com>
>> Content-Type: text/plain; charset="utf-8"
>> 
>> Hi,
>> I downloaded the ?resting state fMRI FIX 1 Denoised (Extended)?
>>datasets, but there are no Movement_Regressors.txt included in the
>>unzipped folder.
>> Are these not there for a reason? I can grab them from the other
>>preprocessed datasets, but I was curious as to why they are missing, and
>>if they would be identical to those in the ?Resting State fMRI 1
>>Preprocessed? package
>> 
>> Best
>> Clas
>> 
>> 
>> The information in this e-mail is intended only for the person to whom
>>it is
>> addressed. If you believe this e-mail was sent to you in error and the
>>e-mail
>> contains patient information, please contact the Partners Compliance
>>HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>in error
>> but does not contain patient information, please contact the sender and
>>properly
>> dispose of the e-mail.
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>>/c9c590f9/attachment-0001.html
>> 
>> ------------------------------
>> 
>> Message: 3
>> Date: Thu, 1 Mar 2018 20:05:01 +0000
>> From: "Glasser, Matthew" <glass...@wustl.edu>
>> Subject: Re: [HCP-Users] Movement regressor missing
>> To: "Linnman, Clas,Ph.D." <clinn...@partners.org>,
>>         "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> Message-ID: <d6bdb8ec.1637d7%glass...@wustl.edu>
>> Content-Type: text/plain; charset="windows-1252"
>> 
>> That?s right. To keep the packages smaller we tried not to repeat files.
>> 
>> Peace,
>> 
>> Matt.
>> 
>> From: 
>><hcp-users-boun...@humanconnectome.org<mailto:hcp-users-bounces@humanconn
>>ectome.org>> on behalf of "Linnman, Clas,Ph.D."
>><clinn...@partners.org<mailto:clinn...@partners.org>>
>> Date: Thursday, March 1, 2018 at 2:02 PM
>> To: 
>>"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
>><hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
>> Subject: [HCP-Users] Movement regressor missing
>> 
>> Hi,
>> I downloaded the ?resting state fMRI FIX 1 Denoised (Extended)?
>>datasets, but there are no Movement_Regressors.txt included in the
>>unzipped folder.
>> Are these not there for a reason? I can grab them from the other
>>preprocessed datasets, but I was curious as to why they are missing, and
>>if they would be identical to those in the ?Resting State fMRI 1
>>Preprocessed? package
>> 
>> Best
>> Clas
>> 
>> The information in this e-mail is intended only for the person to whom
>>it is
>> addressed. If you believe this e-mail was sent to you in error and the
>>e-mail
>> contains patient information, please contact the Partners Compliance
>>HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>in error
>> but does not contain patient information, please contact the sender and
>>properly
>> dispose of the e-mail.
>> 
>> _______________________________________________
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
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>> 
>> ------------------------------
>> 
>> Message: 4
>> Date: Thu, 1 Mar 2018 20:09:05 +0000
>> From: Pubuditha Abeyasinghe <pabey...@uwo.ca>
>> Subject: [HCP-Users] Error in FreeSurfer processing
>>         "recon-all.v6.hires: command not found"
>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> Message-ID:
>>         
>><ytxpr0101mb1711242b943ee17bf6d1c719af...@ytxpr0101mb1711.canprd01.prod.O
>>UTLOOK.COM>
>> 
>> Content-Type: text/plain; charset="iso-8859-1"
>> 
>> Hi all,
>> 
>> I am very new to the HCP pipeline for preprocessing the data and I am
>>trying to adopt to the pipeline.
>> As the first step I am trying the execution of the pipeline with the
>>example data that is given in the tutorial. The first part which is the
>>PreFreeSurfer processing was completed successfully.
>> 
>> But I am having a problem with the second part, the FreeSurfer
>>processing. When I start it, the process instantly comes to an end
>>giving me the following error;
>> 
>> ~/Pipelines/FreeSurfer/FreeSurferPipeline.sh: line 41:
>>recon-all.v6.hires: command not found
>> 
>> I double check the freesurfer installation and I source it as explained
>>as well. Does this error has something to do with the installation? How
>>can I fix it?
>> 
>> 
>> Your help is much appreciated!
>> 
>> 
>> Regards,
>> Pubuditha
>> 
>> 
>> [Western University]
>> Pubuditha Abeyasinghe
>> PhD Candidate
>> Department of Physics and Astronomy
>> Brain and Mind Institute
>> Western University
>> London, ON, Canada
>> email: pabey...@uwo.ca
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
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>>/4c2b4aff/attachment-0001.html
>> 
>> ------------------------------
>> 
>> Message: 5
>> Date: Thu, 1 Mar 2018 20:12:21 +0000
>> From: "Glasser, Matthew" <glass...@wustl.edu>
>> Subject: Re: [HCP-Users] Error in FreeSurfer processing
>>         "recon-all.v6.hires: command not found"
>> To: Pubuditha Abeyasinghe <pabey...@uwo.ca>,
>>         "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> Message-ID: <d6bdbab8.1637e5%glass...@wustl.edu>
>> Content-Type: text/plain; charset="us-ascii"
>> 
>> We are working on a response to your question.
>> 
>> Peace,
>> 
>> Matt.
>> 
>> From: 
>><hcp-users-boun...@humanconnectome.org<mailto:hcp-users-bounces@humanconn
>>ectome.org>> on behalf of Pubuditha Abeyasinghe
>><pabey...@uwo.ca<mailto:pabey...@uwo.ca>>
>> Date: Thursday, March 1, 2018 at 2:09 PM
>> To: 
>>"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
>><hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
>> Subject: [HCP-Users] Error in FreeSurfer processing
>>"recon-all.v6.hires: command not found"
>> 
>> 
>> Hi all,
>> 
>> I am very new to the HCP pipeline for preprocessing the data and I am
>>trying to adopt to the pipeline.
>> As the first step I am trying the execution of the pipeline with the
>>example data that is given in the tutorial. The first part which is the
>>PreFreeSurfer processing was completed successfully.
>> 
>> But I am having a problem with the second part, the FreeSurfer
>>processing. When I start it, the process instantly comes to an end
>>giving me the following error;
>> 
>> ~/Pipelines/FreeSurfer/FreeSurferPipeline.sh: line 41:
>>recon-all.v6.hires: command not found
>> 
>> I double check the freesurfer installation and I source it as explained
>>as well. Does this error has something to do with the installation? How
>>can I fix it?
>> 
>> 
>> Your help is much appreciated!
>> 
>> 
>> Regards,
>> Pubuditha
>> 
>> 
>> [Western University]
>> Pubuditha Abeyasinghe
>> PhD Candidate
>> Department of Physics and Astronomy
>> Brain and Mind Institute
>> Western University
>> London, ON, Canada
>> email: pabey...@uwo.ca<mailto:pabey...@uwo.ca>
>> 
>> _______________________________________________
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL: 
>>http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20180301
>>/4fad907d/attachment-0001.html
>> 
>> ------------------------------
>> 
>> Message: 6
>> Date: Thu, 1 Mar 2018 14:30:18 -0600
>> From: "Timothy B. Brown" <tbbr...@wustl.edu>
>> Subject: Re: [HCP-Users] Error in FreeSurfer processing
>>         "recon-all.v6.hires: command not found"
>> To: hcp-users@humanconnectome.org, pabey...@uwo.ca
>> Message-ID: <c2e47123-5ab6-a82c-7d3e-4f9f187ec...@wustl.edu>
>> Content-Type: text/plain; charset="windows-1252"
>> 
>> Hi Pubuditha,
>> 
>> 
>> I'm assuming that you are using the latest release of the HCP Pipelines
>> (v3.25.0). The changes that are causing you a problem are part of those
>> being made as part of conversion to using FreeSurfer version 6. Those
>> changes should not have made it in to a release as of yet. I apologize
>> for that mistake.
>> 
>> 
>> Please try using version v3.24.0. I have briefly reviewed that version,
>> and I believe that those FreeSurfer 6 related changes were not included
>> in that release.
>> 
>> 
>> In the meantime, I will back those changes out of version v3.25.0 and
>> create a new "bug-fix" release (v3.25.1).
>> 
>> 
>> Thank you for pointing this problem out so that others (hopefully) do
>> not have to encounter it also.
>> 
>> 
>> Best Regards,
>> 
>> 
>>  ? Tim
>> 
>> 
>> On 03/01/2018 02:12 PM, Glasser, Matthew wrote:
>> > We are working on a response to your question.
>> >
>> > Peace,
>> >
>> > Matt.
>> >
>> > From: <hcp-users-boun...@humanconnectome.org
>> > <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Pubuditha
>> > Abeyasinghe <pabey...@uwo.ca <mailto:pabey...@uwo.ca>>
>> > Date: Thursday, March 1, 2018 at 2:09 PM
>> > To: "hcp-users@humanconnectome.org
>> > <mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org
>> > <mailto:hcp-users@humanconnectome.org>>
>> > Subject: [HCP-Users] Error in FreeSurfer processing
>> > "recon-all.v6.hires: command not found"
>> >
>> > Hi all,
>> >
>> > I am very new to the HCP pipeline for preprocessing the data and I am
>> > trying to adopt to the pipeline.
>> > As the first step I am trying the execution of the pipeline with the
>> > example data that is given in the tutorial. The first part which is
>> > the PreFreeSurfer processing was completed successfully.
>> >
>> > But I am having a problem with the second part, the FreeSurfer
>> > processing. When I start it, the process instantly comes to an end
>> > giving me the following error;
>> >
>> > ~/Pipelines/FreeSurfer/FreeSurferPipeline.sh: line 41:
>> > recon-all.v6.hires: command not found
>> >
>> > I double check the freesurfer installation and I source it as
>> > explained as well. Does this error has something to do with the
>> > installation? How can I fix it?
>> >
>> >
>> > Your help is much appreciated!
>> >
>> >
>> > Regards,
>> > Pubuditha
>> >
>> >
>> > Western University
>> > *Pubuditha Abeyasinghe*
>> > PhD Candidate
>> > Department of Physics and Astronomy
>> > Brain and Mind Institute
>> > Western University
>> > London, ON, Canada
>> > email: pabey...@uwo.ca <mailto:pabey...@uwo.ca>
>> >
>> > _______________________________________________
>> > HCP-Users mailing list
>> > HCP-Users@humanconnectome.org <mailto: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
>> >
>> 
>> --
>> /Timothy B. Brown
>> Business & Technology Application Analyst III
>> Pipeline Developer (Connectome Coordination Facility)
>> tbbrown(at)wustl.edu
>> /
>> ------------------------------------------------------------------------
>> The material in this message is private and may contain Protected
>> Healthcare Information (PHI). If you are not the intended recipient, be
>> advised that any unauthorized use, disclosure, copying or the taking of
>> any action in reliance on the contents of this information is strictly
>> prohibited. If you have received this email in error, please immediately
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>> ------------------------------
>> 
>> Message: 7
>> Date: Thu, 1 Mar 2018 16:40:54 -0600
>> From: Timothy Coalson <tsc...@mst.edu>
>> Subject: Re: [HCP-Users] Best Approach for using old volumetric data
>>         to pick parcels-of-interest
>> To: "Stevens, Michael" <michael.stev...@hhchealth.org>
>> Cc: "Erin W. E. Dickie" <erin.w.dic...@gmail.com>,
>>         "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> Message-ID:
>>         
>><CAK_=tayd6uzegzd1qgpf6l238tsg4rqazqnh4t9qomt8yfx...@mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>> 
>> The command to use is wb_command -volume-to-surface-mapping, the main
>> surface should generally be the midthickness.  Using the
>> -ribbon-constrained method will give you small positive values on the
>> surface when the cortical ribbon just grazes your ROI, so it may be the
>> thing to use (use pial and white surfaces as outer and inner).  You
>>could
>> use -trilinear which is simpler, but it has more risk of false
>>negatives.
>> You may need to experiment, I don't think the effectiveness of this
>>kind of
>> salvage effort has been explored much.
>> 
>> Tim
>> 
>> 
>> On Thu, Mar 1, 2018 at 1:22 PM, Stevens, Michael <
>> michael.stev...@hhchealth.org> wrote:
>> 
>> > 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
>> > overlap with at least one subject in the group.  If this isn't
>>enough, you
>> > can dilate the volume ROI a few mm first.
>> >
>> >
>> >
>> > Tim
>> >
>> >
>> >
>> >
>> >
>> > On Fri, Feb 23, 2018 at 11:18 AM, Glasser, Matthew
>><glass...@wustl.edu>
>> > wrote:
>> >
>> > Hi Mike,
>> >
>> >
>> >
>> > We have a preprint out on this exact question and the conclusion is
>>that
>> > it is really hard to do this accurately for most brain regions:
>> >
>> >
>> >
>> > https://www.biorxiv.org/content/early/2018/01/29/255620
>> >
>> >
>> >
>> > Really the best idea is probably to go back and reanalyze the old data
>> > without volume-based smoothing and aligned across surfaces.  Erin
>>Dickie,
>> > CCed is working on tools to make this a little easier, but still
>>there are
>> > issues like needing a field map to get accurate fMRI to structural
>> > registration.  The good news is that one?s statistical power should
>>be much
>> > better if brains are actually lined up, and using parcellated analyses
>> > instead of smoothing offers further benefits.
>> >
>> >
>> >
>> > Matt.
>> >
>> >
>> >
>> > *From: *<hcp-users-boun...@humanconnectome.org> on behalf of "Stevens,
>> > Michael" <michael.stev...@hhchealth.org>
>> > *Date: *Friday, February 23, 2018 at 8:58 AM
>> > *To: *"hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> > *Subject: *[HCP-Users] Best Approach for using old volumetric data to
>> > pick parcels-of-interest
>> >
>> >
>> >
>> > Hi everyone,
>> >
>> >
>> >
>> > There?s been a lot posted here over the past year or two on the
>>challenges
>> > and limitations of going back-and-forth between volumetric space and
>> > HCP-defined surface space, with solid arguments for moving to (and
>>sticking
>> > with) CIFTI-defined brainordinates.  Here, I?m asking a slightly
>>different
>> > question? The field has decades of research using volume-space fMRI
>> > timeseries analyses that helps to define where to look in the brain
>>to test
>> > new hypotheses.  Has anyone got a well-thought-out approach for
>>mapping
>> > such volume-space ROIs to the parcels within the new HCP 180 atlas?
>>I ask
>> > because the specificity of the HCP atlas sometimes offers a half dozen
>> > candidate parcels for hypothesis-testing for what we previously
>>thought of
>> > as just one or two regions.  Even though our group currently has a
>>half
>> > dozen newer NIH-funded studies that use HCP compliant sequences, most
>>of
>> > that work is still predicated on a ?region-of-interest? approach
>>because
>> > the study groups sizes are less than a hundred, not in the thousands
>> > typical of the HCP grantwork.  So we still have to contend with the
>> > statistical power limitations inherent in any ROI approach.  It would
>>be
>> > great to be able to use our prior volume-space data to have greater
>> > confidence in selecting among the various parcel-of-interest
>>candidates
>> > when testing hypotheses.
>> >
>> >
>> >
>> > I?m wondering if anyone?s yet worked out a step-by-step approach for a
>> > series of warps/surface-maps/transformations that can take ROIs from
>>MNI
>> > space and give a ?best guess? as to which HCP 180 atlas parcel(s)
>>should be
>> > queried in such instances.  It would be a nice bridge from older work
>>to
>> > newer HCP-guided work, that would allow researchers to circumvent the
>>added
>> > burden of having to go back and collect new pilot data using HCP
>> > sequences.  A thoughtful list of the analytic or conceptual pros/cons
>>of
>> > something like this would be helpful as well.
>> >
>> >
>> >
>> > Thanks,
>> >
>> > Mike
>> >
>> >
>> >
>> >
>> > *This e-mail message, including any attachments, is for the sole use
>>of
>> > the intended recipient(s) and may contain confidential and privileged
>> > information. Any unauthorized review, use, disclosure, or
>>distribution is
>> > prohibited. If you are not the intended recipient, or an employee or
>>agent
>> > responsible for delivering the message to the intended recipient,
>>please
>> > contact the sender by reply e-mail and destroy all copies of the
>>original
>> > message, including any attachments. *
>> >
>> > _______________________________________________
>> > 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
>> >
>> >
>> >
>> >
>> >
>> > *Reminder: This e-mail and any attachments are subject to the current
>>HHC
>> > email retention policies. Please save or store appropriately in
>>accordance
>> > with policy. *
>> >
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>> 
>> ------------------------------
>> 
>> Message: 8
>> Date: Thu, 1 Mar 2018 17:08:39 -0600
>> From: Timothy Coalson <tsc...@mst.edu>
>> Subject: Re: [HCP-Users] ROI cluster centers to surface grayordinates
>> To: Manasij Venkatesh <mana...@umd.edu>
>> Cc: hcp-users@humanconnectome.org
>> Message-ID:
>>         
>><CAK_=tawZFTcB-L2KUw1A--=ouz-+pbuq5zd4wdbwl-3d5hg...@mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>> 
>> Unfortunately, it is worse than that - even ignoring the individual
>> variability issue (which should not be ignored), a small change in MNI
>> coordinate can jump from one bank of a sulcus to the other, so having
>>only
>> the center coordinate of a cluster makes this a badly posed problem (and
>> thus explains why peak or center of gravity MNI coordinate reporting is
>>not
>> nearly as useful as actual data files).
>> 
>> Coordinates of each vertex are contained in .surf.gii files, but
>>different
>> files can represent different depths of cortex (gray/white boundary
>> ("white"), csf/gray boundary ("pial"), halfway between ("midthickness),
>> etc), or other things entirely (inflated, sphere).  What you could do to
>> get an idea of the problem, is to take a group of subjects, get the 
>>vertex
>> coordinates of the midthickness surface, and compute the euclidean 
>>distance
>> to each of your cluster centers.  If you average these across subjects, 
>>I
>> suspect you will generally end up with 2 similarly low-distance spots 
>>for
>> each cluster center, on opposite sides of a sulcus (for consistent 
>>sulci,
>> anyway - if it is in or near a high-folding-variability region, one of 
>>the
>> two low spots may get blurred out of existence (or the two may be 
>>blurred
>> into one larger spot) because the folding patterns don't align, but it 
>>is
>> the folding patterns that determine where the MNI coordinate is close to
>> cortex).  To make it easier to see this issue, you could transform these
>> distances into a gaussian kernel (matching the size of the original 
>>cluster
>> if you know it, or the amount of smoothing that was used, or...) and 
>>then
>> average that across subjects.
>> 
>> For a less-rigorous answer, there is a -surface-closest-vertex command 
>>in
>> wb_command that will simply find the closest vertex on the given surface
>> (you will need to separate your right and left coordinates), but as this
>> demonstration should show, MNI coordinate data is generally ambiguous to
>> begin with.  Also note that group-average surfaces are missing a lot of
>> folding detail that individual subjects have, and while that may
>> incidentally make "closest vertex" more stable, it doesn't imply that it
>> makes the answer more correct.
>> 
>> Tim
>> 
>> 
>> On Thu, Mar 1, 2018 at 9:32 AM, Manasij Venkatesh <mana...@umd.edu> 
>>wrote:
>> 
>> > Hi,
>> >
>> > I have a set of ROI cluster center coordinates in MNI space. My goal 
>>is to
>> > create similar ROI clusters to use with HCP data. I understand 
>>there's no
>> > true equivalent in terms of surface grayordinates but what would be 
>>the
>> > best way to find their approximate position on the surface? Is this 
>>the
>> > information contained in the surf.gii files? Please let me know.
>> >
>> > Sincerely,
>> > Manasij
>> >
>> > _______________________________________________
>> > HCP-Users mailing list
>> > HCP-Users@humanconnectome.org
>> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>> >
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>> An HTML attachment was scrubbed...
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>>http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20180301
>>/125e4d25/attachment-0001.html
>> 
>> ------------------------------
>> 
>> Message: 9
>> Date: Thu, 1 Mar 2018 17:02:04 -0500
>> From: "Erin W. E. Dickie" <erin.w.dic...@gmail.com>
>> Subject: Re: [HCP-Users] Best Approach for using old volumetric data
>>         to pick parcels-of-interest
>> To: "Stevens, Michael" <michael.stev...@hhchealth.org>
>> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> Message-ID:
>>         
>><CADig-n81fqn6z1cc_jnE6mizX++ViKHrbmsx=iwtnweywed...@mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>> 
>> Hey Mike,
>> 
>> Here's the link to the tools Matt was referring to in the last email.
>> https://edickie.github.io/ciftify
>> 
>> I think I'm still a little confused about your exact problem. What do 
>>you
>> need to map? Do you already have surfaces for all your participants in
>> GIFTI format?
>> 
>> Thanks,
>> Erin
>> 
>> On Thu, Mar 1, 2018 at 2:22 PM, Stevens, Michael <
>> michael.stev...@hhchealth.org> wrote:
>> 
>> > 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
>> > overlap with at least one subject in the group.  If this isn't 
>>enough, you
>> > can dilate the volume ROI a few mm first.
>> >
>> >
>> >
>> > Tim
>> >
>> >
>> >
>> >
>> >
>> > On Fri, Feb 23, 2018 at 11:18 AM, Glasser, Matthew 
>><glass...@wustl.edu>
>> > wrote:
>> >
>> > Hi Mike,
>> >
>> >
>> >
>> > We have a preprint out on this exact question and the conclusion is 
>>that
>> > it is really hard to do this accurately for most brain regions:
>> >
>> >
>> >
>> > https://www.biorxiv.org/content/early/2018/01/29/255620
>> >
>> >
>> >
>> > Really the best idea is probably to go back and reanalyze the old data
>> > without volume-based smoothing and aligned across surfaces.  Erin 
>>Dickie,
>> > CCed is working on tools to make this a little easier, but still 
>>there are
>> > issues like needing a field map to get accurate fMRI to structural
>> > registration.  The good news is that one?s statistical power should 
>>be much
>> > better if brains are actually lined up, and using parcellated analyses
>> > instead of smoothing offers further benefits.
>> >
>> >
>> >
>> > Matt.
>> >
>> >
>> >
>> > *From: *<hcp-users-boun...@humanconnectome.org> on behalf of "Stevens,
>> > Michael" <michael.stev...@hhchealth.org>
>> > *Date: *Friday, February 23, 2018 at 8:58 AM
>> > *To: *"hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> > *Subject: *[HCP-Users] Best Approach for using old volumetric data to
>> > pick parcels-of-interest
>> >
>> >
>> >
>> > Hi everyone,
>> >
>> >
>> >
>> > There?s been a lot posted here over the past year or two on the 
>>challenges
>> > and limitations of going back-and-forth between volumetric space and
>> > HCP-defined surface space, with solid arguments for moving to (and 
>>sticking
>> > with) CIFTI-defined brainordinates.  Here, I?m asking a slightly 
>>different
>> > question? The field has decades of research using volume-space fMRI
>> > timeseries analyses that helps to define where to look in the brain 
>>to test
>> > new hypotheses.  Has anyone got a well-thought-out approach for 
>>mapping
>> > such volume-space ROIs to the parcels within the new HCP 180 atlas?  
>>I ask
>> > because the specificity of the HCP atlas sometimes offers a half dozen
>> > candidate parcels for hypothesis-testing for what we previously 
>>thought of
>> > as just one or two regions.  Even though our group currently has a 
>>half
>> > dozen newer NIH-funded studies that use HCP compliant sequences, most 
>>of
>> > that work is still predicated on a ?region-of-interest? approach 
>>because
>> > the study groups sizes are less than a hundred, not in the thousands
>> > typical of the HCP grantwork.  So we still have to contend with the
>> > statistical power limitations inherent in any ROI approach.  It would 
>>be
>> > great to be able to use our prior volume-space data to have greater
>> > confidence in selecting among the various parcel-of-interest 
>>candidates
>> > when testing hypotheses.
>> >
>> >
>> >
>> > I?m wondering if anyone?s yet worked out a step-by-step approach for a
>> > series of warps/surface-maps/transformations that can take ROIs from 
>>MNI
>> > space and give a ?best guess? as to which HCP 180 atlas parcel(s) 
>>should be
>> > queried in such instances.  It would be a nice bridge from older work 
>>to
>> > newer HCP-guided work, that would allow researchers to circumvent the 
>>added
>> > burden of having to go back and collect new pilot data using HCP
>> > sequences.  A thoughtful list of the analytic or conceptual pros/cons 
>>of
>> > something like this would be helpful as well.
>> >
>> >
>> >
>> > Thanks,
>> >
>> > Mike
>> >
>> >
>> >
>> >
>> > *This e-mail message, including any attachments, is for the sole use 
>>of
>> > the intended recipient(s) and may contain confidential and privileged
>> > information. Any unauthorized review, use, disclosure, or 
>>distribution is
>> > prohibited. If you are not the intended recipient, or an employee or 
>>agent
>> > responsible for delivering the message to the intended recipient, 
>>please
>> > contact the sender by reply e-mail and destroy all copies of the 
>>original
>> > message, including any attachments. *
>> >
>> > _______________________________________________
>> > 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
>> >
>> >
>> >
>> >
>> >
>> > *Reminder: This e-mail and any attachments are subject to the current 
>>HHC
>> > email retention policies. Please save or store appropriately in 
>>accordance
>> > with policy. *
>> >
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL: 
>>http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20180301
>>/386b7e49/attachment-0001.html
>> 
>> ------------------------------
>> 
>> Message: 10
>> Date: Fri, 2 Mar 2018 09:11:39 +0100
>> From: Robert Becker <em...@robertbecker.info>
>> Subject: Re: [HCP-Users] Correct interpretation of NIH battery test
>>         'Words-in-Noise' in HCP subjects
>> To: "Elam, Jennifer" <e...@wustl.edu>,  "hcp-users@humanconnectome.org"
>>         <hcp-users@humanconnectome.org>
>> Message-ID: <1bebeeb6-ff94-2473-d78a-b7860b5a0...@robertbecker.info>
>> Content-Type: text/plain; charset="windows-1252"
>> 
>> 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<tel:314-362-9387>
>> > e...@wustl.edu<mailto:e...@wustl.edu>
>> > www.humanconnectome.org<http://www.humanconnectome.org/>
>> >
>> >
>> > 
>>------------------------------------------------------------------------
>> > *From:* hcp-users-boun...@humanconnectome.org
>> > <hcp-users-boun...@humanconnectome.org> on behalf of Robert Becker
>> > <em...@robertbecker.info>
>> > *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
>> > Universit?t Z?rich
>> > Psychologisches Institut
>> > Binzm?hlestrasse 14
>> > 8050 Z?rich
>> >
>> > Tel: +41 44 63 57234
>> > em...@robertbecker.info <mailto:em...@robertbecker.info>
>> >
>> > _______________________________________________
>> > HCP-Users mailing list
>> > HCP-Users@humanconnectome.org
>> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>> >
>> 
>> --
>> Robert Becker, PhD
>> Universit?t Z?rich
>> Psychologisches Institut
>> Binzm?hlestrasse 14
>> 8050 Z?rich
>> 
>> Tel: +41 44 63 57234
>> em...@robertbecker.info
>> 
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>> ------------------------------
>> 
>> Message: 11
>> Date: Fri, 2 Mar 2018 13:47:12 +0100
>> From: A R <aruls...@gmail.com>
>> Subject: [HCP-Users] Split dtseries
>> To: hcp-users@humanconnectome.org
>> Message-ID: <4e282581-45a1-47b5-a40d-a7cdf679a...@gmail.com>
>> Content-Type: text/plain;       charset=us-ascii
>> 
>> 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
>> 
>> 
>> ------------------------------
>> 
>> Message: 12
>> Date: Fri, 2 Mar 2018 14:39:40 +0000
>> From: "Glasser, Matthew" <glass...@wustl.edu>
>> Subject: Re: [HCP-Users] Split dtseries
>> To: A R <aruls...@gmail.com>, "hcp-users@humanconnectome.org"
>>         <hcp-users@humanconnectome.org>
>> Message-ID: <d6bebe37.163961%glass...@wustl.edu>
>> Content-Type: text/plain; charset="us-ascii"
>> 
>> 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" <hcp-users-boun...@humanconnectome.org on behalf of 
>>aruls...@gmail.com>
>> 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
>> 
>> 
>> 
>> 
>> ------------------------------
>> 
>> Message: 13
>> Date: Fri, 2 Mar 2018 16:13:16 +0000
>> From: Kwan-Jin Jung <kjj...@umass.edu>
>> Subject: [HCP-Users] Change of FreeSurferHiresPial.sh for MacBook IOS
>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> Cc: Hae-Min Jung <hae-min.j...@austenriggs.net>
>> Message-ID: <df573886-ad6b-437e-9499-6a9c8283e...@umass.edu>
>> Content-Type: text/plain; charset="utf-8"
>> 
>> 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
>> 
>> 
>> 
>> ------------------------------
>> 
>> Message: 14
>> Date: Fri, 2 Mar 2018 16:16:02 +0000
>> From: "Glasser, Matthew" <glass...@wustl.edu>
>> Subject: Re: [HCP-Users] Change of FreeSurferHiresPial.sh for MacBook
>>         IOS
>> To: Kwan-Jin Jung <kjj...@umass.edu>, "hcp-users@humanconnectome.org"
>>         <hcp-users@humanconnectome.org>
>> Cc: Hae-Min Jung <hae-min.j...@austenriggs.net>
>> Message-ID: <d6bed4a4.1639e4%glass...@wustl.edu>
>> Content-Type: text/plain; charset="Windows-1252"
>> 
>> I?m 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" <hcp-users-boun...@humanconnectome.org on behalf of
>> 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 ?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
>> >
>> >_______________________________________________
>> >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
>> 
>> 
>> End of HCP-Users Digest, Vol 64, Issue 2
>> ****************************************
>> 
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>


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