What is meant by that is the spatial effects of motion. Temporal (i.e. intensity fluctuation) effects of motion are not removed, though we hope to make such data available in the future.
Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of Yassine Benhajali <[email protected]<mailto:[email protected]>> Date: Thursday, April 19, 2018 at 12:08 PM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] Motion in second level task activation analysis Hi, any one knows how head motion is handled in the second level task activation activation analysis for the 1200 Subjects Release. when I read the documentation it says :" First, the minimal preprocessing pipeline handled motion correction, distortion correction,...." Is it an ICA-fix ? did they regress out movement? and how? Thanks Yassine Le jeu. 19 avr. 2018 à 13:00, <[email protected]<mailto:[email protected]>> a écrit : Send HCP-Users mailing list submissions to [email protected]<mailto:[email protected]> 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 [email protected]<mailto:[email protected]> You can reach the person managing the list at [email protected]<mailto:[email protected]> When replying, please edit your Subject line so it is more specific than "Re: Contents of HCP-Users digest..." Today's Topics: 1. Estimation of surface area (Paul, Subhadip) 2. Re: Estimation of surface area (Harms, Michael) 3. Re: Estimation of surface area (Timothy Coalson) 4. Re: Estimation of surface area (Glasser, Matthew) 5. Native space surface curvature available? (Jacob Miller) 6. Re: Native space surface curvature available? (Harms, Michael) ---------------------------------------------------------------------- Message: 1 Date: Wed, 18 Apr 2018 18:07:28 +0000 From: "Paul, Subhadip" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] Estimation of surface area To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Message-ID: <am6pr03mb3526a795a205c25daa39fcfdb4...@am6pr03mb3526.eurprd03.prod.outlook.com<mailto:am6pr03mb3526a795a205c25daa39fcfdb4...@am6pr03mb3526.eurprd03.prod.outlook.com>> Content-Type: text/plain; charset="iso-8859-1" Dear HCP users, HCP has released thickness, surface area values based on DK (Desikan-Killiany) atlas in a csv file. I would like to extract those values using Destrieux atlas. To verify, whether am I following the correct procedure, I have extracted regional cortical thickness data using MATLAB from the HCP directory (/HCP_1200/100206/MNINonLinear/Native/) using DK atlas and compared with HCP released values. The values are same. Now, I am using connectome-workbench to estimate regional surface area using DK atlas. However, the extracted value does not match with HCP provided value. To extract the area of left bankssts area (key 1) from /HCP_1200/100206/MNINonLinear/Native/, I am using the following connectome workbench commands: wb_command -gifti-label-to-roi 100206.L.aparc.native.label.gii roi.func.gii -key 1 wb_command -metric-weighted-stats roi.func.gii -sum -area-surface 100206.L.midthickness.native.surf.gii -show-map-name Could you please tell me whether am I using the correct commands? When I used *pial*.surf.gii or *white*.surf.gii instead of *midthickness*.surf.gii file in the second command, still the extracted value does not match with the HCP released value. Once I figure out the correct approach, I would replace the *aparc.*.label.gii file in the first command, with *aparc.a2009s*.label.gii to extract surface area using Destrieux atlas. Thanking you, Subhadip Subhadip Paul King's College London 16 De Crespigny Park, London SE5 8AF<https://maps.google.com/?q=16+De+Crespigny+Park,+London+SE5+8AF&entry=gmail&source=g> -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20180418/904ebcef/attachment-0001.html ------------------------------ Message: 2 Date: Wed, 18 Apr 2018 18:25:06 +0000 From: "Harms, Michael" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] Estimation of surface area To: "Paul, Subhadip" <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Message-ID: <[email protected]<mailto:[email protected]>> Content-Type: text/plain; charset="utf-8" Hi, The FS values that we report in the spreadsheets on ConnectomeDB are taken directly from FS?s own output ? i.e., from FS?s stats/{lh,rh}.aparc.stats files. They are not derived through any wb_command options. If you have Connectome-in-a-Box, have downloaded the ?Structural Extended? packages, or access to the data on S3, the easiest thing for you to do would probably be to pull the values directly from FS?s relevant .stats files. In the HCP file organization, the original FS stats output can be found at ${subject}/T1w/${subject}/stats You can create a FS-style ?$SUBJECTS_DIR? directory that contains symlinks to ${subject}/T1w/${subject} for each subject. Then you can run FS?s own handy ?aparcstats2table? to aggregate everything together in one swoop. All that said, it should be possible match the FS reported results for surface area if you are using the native, white surfaces. But you need to be using the surfaces in ${subject}/T1w/Native (not MNINonLinear). Cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173<tel:(314)%20747-6173> St. Louis, MO 63110 Email: [email protected]<mailto:[email protected]> From: <[email protected]<mailto:[email protected]>> on behalf of "Paul, Subhadip" <[email protected]<mailto:[email protected]>> Date: Wednesday, April 18, 2018 at 1:07 PM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] Estimation of surface area Dear HCP users, HCP has released thickness, surface area values based on DK (Desikan-Killiany) atlas in a csv file. I would like to extract those values using Destrieux atlas. To verify, whether am I following the correct procedure, I have extracted regional cortical thickness data using MATLAB from the HCP directory (/HCP_1200/100206/MNINonLinear/Native/) using DK atlas and compared with HCP released values. The values are same. Now, I am using connectome-workbench to estimate regional surface area using DK atlas. However, the extracted value does not match with HCP provided value. To extract the area of left bankssts area (key 1) from /HCP_1200/100206/MNINonLinear/Native/, I am using the following connectome workbench commands: wb_command -gifti-label-to-roi 100206.L.aparc.native.label.gii roi.func.gii -key 1 wb_command -metric-weighted-stats roi.func.gii -sum -area-surface 100206.L.midthickness.native.surf.gii -show-map-name Could you please tell me whether am I using the correct commands? When I used *pial*.surf.gii or *white*.surf.gii instead of *midthickness*.surf.gii file in the second command, still the extracted value does not match with the HCP released value. Once I figure out the correct approach, I would replace the *aparc.*.label.gii file in the first command, with *aparc.a2009s*.label.gii to extract surface area using Destrieux atlas. Thanking you, Subhadip Subhadip Paul King's College London 16 De Crespigny Park, London SE5 8AF<https://maps.google.com/?q=16+De+Crespigny+Park,+London+SE5+8AF&entry=gmail&source=g> _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. 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/20180418/e46f7872/attachment-0001.html ------------------------------ Message: 3 Date: Wed, 18 Apr 2018 13:25:55 -0500 From: Timothy Coalson <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] Estimation of surface area To: "Paul, Subhadip" <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Message-ID: <CAK_=tazZa_YyHhDy=3BGMRvcHuF7KMEbY=ib1ndgirae7au...@mail.gmail.com<mailto:[email protected]>> Content-Type: text/plain; charset="utf-8" Those commands look correct, however MNI space may not be the correct place to make these measurements, as the registration distorts the subject anatomy to match a template (and the template happens to be significantly larger than the average subject). I suspect we do not actually recompute thickness in MNI space, so a thickness file in the MNINonLinear folder may simply be a copy from the T1w folder. Similarly, I would expect that our released values for surface area are measured in T1w space, which is a rigidly aligned, distortion corrected scanner space, matching the true shape of the subject's brain. Note that with cifti files, you can use -cifti-parcellate to do these per-area summaries for all areas at once, rather than one at a time. You can use -cifti-convert -to-text to dump the data values after that (and -file-information will tell you the order of areas in the parcellated file). Tim On Wed, Apr 18, 2018 at 1:07 PM, Paul, Subhadip <[email protected]<mailto:[email protected]>> wrote: > Dear HCP users, > > HCP has released thickness, surface area values based on DK > (Desikan-Killiany) atlas in a csv file. I would like to extract those > values using Destrieux atlas. To verify, whether am I following the correct > procedure, I have extracted regional cortical thickness data using MATLAB > from the HCP directory (/HCP_1200/100206/MNINonLinear/Native/) using DK > atlas and compared with HCP released values. The values are same. Now, I am > using connectome-workbench to estimate regional surface area using DK > atlas. However, the extracted value does not match with HCP provided value. > > To extract the area of left bankssts area (key 1) from > /HCP_1200/100206/MNINonLinear/Native/, I am using the following > connectome workbench commands: > > wb_command -gifti-label-to-roi 100206.L.aparc.native.label.gii > roi.func.gii -key 1 > > wb_command -metric-weighted-stats roi.func.gii -sum -area-surface > 100206.L.midthickness.native.surf.gii -show-map-name > > Could you please tell me whether am I using the correct commands? When I > used *pial*.surf.gii or *white*.surf.gii instead of *midthickness*.surf.gii > file in the second command, still the extracted value does not match with > the HCP released value. > > Once I figure out the correct approach, I would replace the > *aparc.*.label.gii file in the first command, with *aparc.a2009s*.label.gii > to extract surface area using Destrieux atlas. > > Thanking you, > > Subhadip > > > *Subhadip Paul* > > King's College London > > 16 De Crespigny Park, London > <https://maps.google.com/?q=16+De+Crespigny+Park,+London++SE5+8AF&entry=gmail&source=g>SE5 > 8AF > <https://maps.google.com/?q=16+De+Crespigny+Park,+London++SE5+8AF&entry=gmail&source=g> > > > _______________________________________________ > HCP-Users mailing list > [email protected]<mailto:[email protected]> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20180418/c56919d6/attachment-0001.html ------------------------------ Message: 4 Date: Wed, 18 Apr 2018 19:11:25 +0000 From: "Glasser, Matthew" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] Estimation of surface area To: NEUROSCIENCE tim <[email protected]<mailto:[email protected]>>, "Paul, Subhadip" <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Message-ID: <d6fd0263.16a149%[email protected]<mailto:d6fd0263.16a149%[email protected]>> Content-Type: text/plain; charset="us-ascii" That is correct. MNI space IS NOT the correct place to measure areas, volumes, thicknesses. Peace, Matt. From: <[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>> on behalf of Timothy Coalson <[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>> Date: Wednesday, April 18, 2018 at 1:25 PM To: "Paul, Subhadip" <[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>> Cc: "[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>" <[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>> Subject: Re: [HCP-Users] Estimation of surface area Those commands look correct, however MNI space may not be the correct place to make these measurements, as the registration distorts the subject anatomy to match a template (and the template happens to be significantly larger than the average subject). I suspect we do not actually recompute thickness in MNI space, so a thickness file in the MNINonLinear folder may simply be a copy from the T1w folder. Similarly, I would expect that our released values for surface area are measured in T1w space, which is a rigidly aligned, distortion corrected scanner space, matching the true shape of the subject's brain. Note that with cifti files, you can use -cifti-parcellate to do these per-area summaries for all areas at once, rather than one at a time. You can use -cifti-convert -to-text to dump the data values after that (and -file-information will tell you the order of areas in the parcellated file). Tim On Wed, Apr 18, 2018 at 1:07 PM, Paul, Subhadip <[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>> wrote: Dear HCP users, HCP has released thickness, surface area values based on DK (Desikan-Killiany) atlas in a csv file. I would like to extract those values using Destrieux atlas. To verify, whether am I following the correct procedure, I have extracted regional cortical thickness data using MATLAB from the HCP directory (/HCP_1200/100206/MNINonLinear/Native/) using DK atlas and compared with HCP released values. The values are same. Now, I am using connectome-workbench to estimate regional surface area using DK atlas. However, the extracted value does not match with HCP provided value. To extract the area of left bankssts area (key 1) from /HCP_1200/100206/MNINonLinear/Native/, I am using the following connectome workbench commands: wb_command -gifti-label-to-roi 100206.L.aparc.native.label.gii roi.func.gii -key 1 wb_command -metric-weighted-stats roi.func.gii -sum -area-surface 100206.L.midthickness.native.surf.gii -show-map-name Could you please tell me whether am I using the correct commands? When I used *pial*.surf.gii or *white*.surf.gii instead of *midthickness*.surf.gii file in the second command, still the extracted value does not match with the HCP released value. Once I figure out the correct approach, I would replace the *aparc.*.label.gii file in the first command, with *aparc.a2009s*.label.gii to extract surface area using Destrieux atlas. Thanking you, Subhadip Subhadip Paul King's College London 16 De Crespigny Park, London <https://maps.google.com/?q=16+De+Crespigny+Park,+London++SE5+8AF&entry=gmail&source=g> SE5 8AF<https://maps.google.com/?q=16+De+Crespigny+Park,+London++SE5+8AF&entry=gmail&source=g> _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20180418/fd35fdc3/attachment-0001.html ------------------------------ Message: 5 Date: Wed, 18 Apr 2018 17:37:02 -0700 From: Jacob Miller <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] Native space surface curvature available? To: [email protected]<mailto:[email protected]> Message-ID: <CAHN-knx=rqhhdt4jfiabokyzslrr7harvmd7ahv4vn+y4rs...@mail.gmail.com<mailto:rqhhdt4jfiabokyzslrr7harvmd7ahv4vn%2by4rs%[email protected]>> Content-Type: text/plain; charset="utf-8" Hi all, I am seeking to perform an anatomical analysis on the HCP dataset which requires the surfaces and cortical folding (gyri/sulci curvature) for each individual subject, in native space. This information is available in a typical FreeSurfer recon-all analysis. However, in the HCP data (namely, in $subject/T1w/Native/) the surfaces do not appear to have curvature information. Was this information released in the data from the modified HCP FreeSurfer pipelines, and I'm missing where this may be stored? Or, are the gyru/sulci curvature for each subject not available? If so, is there a way to obtain these curvatures without running an entire recon-all pipeline on each native T1 scan? Please let me know if I may be mistaken! I've only just begun trying to use this great dataset. Best, Jacob -- Jacob Miller Graduate Student, D'Esposito Lab Helen Wills Neuroscience Institute (HWNI) University of California, Berkeley https://despolab.berkeley.edu/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20180418/00ad19a9/attachment-0001.html ------------------------------ Message: 6 Date: Thu, 19 Apr 2018 02:12:56 +0000 From: "Harms, Michael" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] Native space surface curvature available? To: Jacob Miller <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Message-ID: <[email protected]<mailto:[email protected]>> Content-Type: text/plain; charset="utf-8" Hi, The entirety of the original FS output is available at ${subject}/T1w/${subject}, which you can obtain via the ?Structural Extended? packages, or as part of ?Connectome-in-a-Box? (no longer taking new orders, but perhaps you already have one) or available on S3. Cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Associate Professor of Psychiatry Washington University School<https://maps.google.com/?q=shington+University+School&entry=gmail&source=g> of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173<tel:(314)%20747-6173> St. Louis, MO 63110 Email: [email protected]<mailto:[email protected]> From: <[email protected]<mailto:[email protected]>> on behalf of Jacob Miller <[email protected]<mailto:[email protected]>> Date: Wednesday, April 18, 2018 at 9:04 PM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] Native space surface curvature available? Hi all, I am seeking to perform an anatomical analysis on the HCP dataset which requires the surfaces and cortical folding (gyri/sulci curvature) for each individual subject, in native space. This information is available in a typical FreeSurfer recon-all analysis. However, in the HCP data (namely, in $subject/T1w/Native/) the surfaces do not appear to have curvature information. Was this information released in the data from the modified HCP FreeSurfer pipelines, and I'm missing where this may be stored? Or, are the gyru/sulci curvature for each subject not available? If so, is there a way to obtain these curvatures without running an entire recon-all pipeline on each native T1 scan? Please let me know if I may be mistaken! I've only just begun trying to use this great dataset. Best, Jacob -- Jacob Miller Graduate Student, D'Esposito Lab Helen Wills Neuroscience Institute (HWNI) University of California, Berkeley https://despolab.berkeley.edu/ _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. 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/20180419/52741330/attachment-0001.html ------------------------------ _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users End of HCP-Users Digest, Vol 65, Issue 27 ***************************************** -- Yassine Benhajali Doctorant en Neuroanthropologie au Laboratoire SIMEXP - http://www.simexp-lab.org/members/ Université de Montréal, Québec, Canada 514 839 0501 _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
