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 <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 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 +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-boun...@humanconnectome.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 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<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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/d798ca00/attachment-0001.html ------------------------------ 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20180301/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-boun...@humanconnectome.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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20180301/6c3b8429/attachment-0001.html ------------------------------ 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.outlook.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... URL: http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20180301/4c2b4aff/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-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 -------------- 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 notify the sender via telephone or return mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20180301/abfce907/attachment-0001.html ------------------------------ 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. * > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20180301/b0aca16d/attachment-0001.html ------------------------------ 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: 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/<http://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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20180302/ad320ef0/attachment-0001.html ------------------------------ 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 **************************************** _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
