Re: [HCP-Users] HCP-Users Digest, Vol 64, Issue 2
I believe you need to use the "bin_macosx64" folder as the path to
wb_command on mac, so try this as CARET7DIR:
/Applications/workbench/bin_macosx64
Tim
On Mon, Mar 5, 2018 at 3:03 PM, Kwan-Jin Jung wrote:
> Hi Gaurav,
>
> Thank you.
> I updated the workbench, but I got the same error as before: "CORTEX_LEFT
> does not exist."
>
> Without changing “${CARET7DIR}/wb_command” to “open -a
> ${CARET7DIR}/wb_command” in FreeSurferHiresPial.sh, the wb_command cannot
> start:
> "/Users/kjjung/bin/HCP/FreeSurfer/scripts/FreeSurferHiresPial.sh: line
> 92: /Applications/workbench/macosx64_apps/wb_command: No such file or
> directory"
>
> Can you guide me once again?
>
> Kwan-Jin Jung
> HMRC, IALS, UMASS Amherst
> Phone: 413-577-0538 <(413)%20577-0538>
>
>
>
> On Mar 2, 2018, at 2:45 PM, Gaurav Patel wrote:
>
> Well, I guess that would be us every time we update our local
> installation. We’ll let you know how it goes
>
> gaurav patel
> gauravpa...@gmail.com
> pateldsclab.net
>
> On Mar 2, 2018, at 2:30 PM, Glasser, Matthew wrote:
>
> Hi Gaurav,
>
> I guess they are supported on mac for now, but I don¹t know that anyone is
> actively testing them for macŠ
>
> Matt.
>
> On 3/2/18, 1:28 PM, "Gaurav Patel" gauravpa...@gmail.com> wrote:
>
> YesŠwe¹ve been 3.4 for many years without problems, and 3.22 only
> required those minor changes. We recently verified that it was easy to
> install and run on macs when we expanded the network of mac pros we use
> to run the HCP pipelines
>
> gaurav patel
> gauravpa...@gmail.com
> pateldsclab.net
>
> On Mar 2, 2018, at 2:25 PM, Glasser, Matthew wrote:
>
> So you are saying that the Pipelines work fine on the Mac for you aside
> from this cp issue?
>
> Matt.
>
> From: on behalf of "Sanchez,
> Juan (NYSPI)"
> Date: Friday, March 2, 2018 at 1:24 PM
> To: "hcp-users@humanconnectome.org"
> Subject: Re: [HCP-Users] HCP-Users Digest, Vol 64, Issue 2
>
> Dear
> Kwan-Jin Jung
>
> I had rthe same problems when I installed the 3_22 HCP Pipleines
> Here is what we did:
>
>
> €
> syntax in
> scripts:
> Just remove the "--preserve=timestamps" from all of the Pipeline
> scripts
> 2. workbench:
>
> Get the "dev_latest" zip file that says "mac64" from here:
>
> http://brainvis.wustl.edu/workbench/
>
> From: hcp-users-boun...@humanconnectome.org
> on behalf of
> hcp-users-requ...@humanconnectome.org
>
> Sent: Friday, March 2, 2018 1:00:01 PM
> To: hcp-users@humanconnectome.org
> Subject: HCP-Users Digest, Vol 64, Issue 2
>
> ATTENTION: This email came from an external source. Do not open
> attachments or click on links from unknown senders or unexpected emails.
>
>
> Send HCP-Users mailing list submissions to
> hcp-users@humanconnectome.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> or, via email, send a message with subject or body 'help' to
> hcp-users-requ...@humanconnectome.org
>
> You can reach the person managing the list at
> hcp-users-ow...@humanconnectome.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of HCP-Users digest..."
>
>
> Today's Topics:
>
> 1. Re: Best Approach for using old volumetric data to pick
> parcels-of-interest (Stevens, Michael)
> 2. Movement regressor missing (Linnman, Clas,Ph.D.)
> 3. Re: Movement regressor missing (Glasser, Matthew)
> 4. Error in FreeSurfer processing "recon-all.v6.hires: command
> not found" (Pubuditha Abeyasinghe)
> 5. Re: Error in FreeSurfer processing "recon-all.v6.hires:
> command not found" (Glasser, Matthew)
> 6. Re: Error in FreeSurfer processing "recon-all.v6.hires:
> command not found" (Timothy B. Brown)
> 7. Re: Best Approach for using old volumetric data to pick
> parcels-of-interest (Timothy Coalson)
> 8. Re: ROI cluster centers to surface grayordinates (Timothy Coalson)
> 9. Re: Best Approach for using old volumetric data to pick
> parcels-of-interest (Erin W. E. Dickie)
> 10. Re: Correct interpretation of NIH battery test
> 'Words-in-Noise' in HCP subjects (Robert Becker)
> 11. Split dtseries (A R)
> 12. Re: Split dtseries (Glasser, Matthew)
> 13. Change of FreeSurferHiresPial.sh for MacBook IOS (Kwan-Jin Jung)
> 14. Re: Change of FreeSurferHiresPial.sh for MacBook IOS
> (Glasser, Matthew)
>
>
> -
Re: [HCP-Users] HCP-Users Digest, Vol 64, Issue 2
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,
Re: [HCP-Users] HCP-Users Digest, Vol 64, Issue 2
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
Re: [HCP-Users] HCP-Users Digest, Vol 64, Issue 2
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 open
Re: [HCP-Users] HCP-Users Digest, Vol 64, Issue 2
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: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Sanchez, Juan (NYSPI)" mailto:juan.sanc...@nyspi.columbia.edu>> Date: Friday, March 2, 2018 at 1:24 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto: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<mailto:hcp-users-boun...@humanconnectome.org> mailto:hcp-users-boun...@humanconnectome.org>> on behalf of hcp-users-requ...@humanconnectome.org<mailto:hcp-users-requ...@humanconnectome.org> mailto:hcp-users-requ...@humanconnectome.org>> Sent: Friday, March 2, 2018 1:00:01 PM To: hcp-users@humanconnectome.org<mailto: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<mailto: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<mailto:hcp-users-requ...@humanconnectome.org> You can reach the person managing the list at hcp-users-ow...@humanconnectome.org<mailto: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" mailto:michael.stev...@hhchealth.org>> Subject: Re: [HCP-Users] Best Approach for using old volumetric data to pick parcels-of-interest To: Timothy Coalson mailto:tsc...@mst.edu>>, "Glasser, Matthew" mailto:glass...@wustl.edu>> Cc: "Erin W. E. Dickie" mailto:erin.w.dic...@gmail.com>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Message-ID: <1cf06fac1128cf49ab6143a2d6a10f859345e...@hhcexchmb04.hhcsystem.org<mailto: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 wel
Re: [HCP-Users] HCP-Users Digest, Vol 64, Issue 2
So you are saying that the Pipelines work fine on the Mac for you aside from this cp issue? Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Sanchez, Juan (NYSPI)" mailto:juan.sanc...@nyspi.columbia.edu>> Date: Friday, March 2, 2018 at 1:24 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto: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<mailto:hcp-users-boun...@humanconnectome.org> mailto:hcp-users-boun...@humanconnectome.org>> on behalf of hcp-users-requ...@humanconnectome.org<mailto:hcp-users-requ...@humanconnectome.org> mailto:hcp-users-requ...@humanconnectome.org>> Sent: Friday, March 2, 2018 1:00:01 PM To: hcp-users@humanconnectome.org<mailto: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<mailto: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<mailto:hcp-users-requ...@humanconnectome.org> You can reach the person managing the list at hcp-users-ow...@humanconnectome.org<mailto: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" mailto:michael.stev...@hhchealth.org>> Subject: Re: [HCP-Users] Best Approach for using old volumetric data to pick parcels-of-interest To: Timothy Coalson mailto:tsc...@mst.edu>>, "Glasser, Matthew" mailto:glass...@wustl.edu>> Cc: "Erin W. E. Dickie" mailto:erin.w.dic...@gmail.com>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Message-ID: <1cf06fac1128cf49ab6143a2d6a10f859345e...@hhcexchmb04.hhcsystem.org<mailto: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<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Best Approach for using old volumetric data to pick parcels-of-interest This is an email fro
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 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 mailto:glass...@wustl.edu>> wr
