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]> a écrit : > Send HCP-Users mailing list submissions to > [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] > > You can reach the person managing the list at > [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]> > Subject: [HCP-Users] Estimation of surface area > To: "[email protected]" <[email protected]> > Message-ID: > < > 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]> > Subject: Re: [HCP-Users] Estimation of surface area > To: "Paul, Subhadip" <[email protected]>, > "[email protected]" <[email protected]> > Message-ID: <[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 > <(314)%20747-6173> > St. Louis, MO 63110 Email: [email protected] > > From: <[email protected]> on behalf of "Paul, > Subhadip" <[email protected]> > Date: Wednesday, April 18, 2018 at 1:07 PM > To: "[email protected]" <[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] > 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]> > Subject: Re: [HCP-Users] Estimation of surface area > To: "Paul, Subhadip" <[email protected]> > Cc: "[email protected]" <[email protected]> > Message-ID: > <CAK_=tazZa_YyHhDy=3BGMRvcHuF7KMEbY= > [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]> > 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] > > 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]> > Subject: Re: [HCP-Users] Estimation of surface area > To: NEUROSCIENCE tim <[email protected]>, "Paul, Subhadip" > <[email protected]> > Cc: "[email protected]" <[email protected]> > Message-ID: <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]>> on behalf of Timothy Coalson < > [email protected]<mailto:[email protected]>> > Date: Wednesday, April 18, 2018 at 1:25 PM > To: "Paul, Subhadip" <[email protected]<mailto: > [email protected]>> > Cc: "[email protected]<mailto:[email protected]>" > <[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]>> 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 > > > _______________________________________________ > 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/fd35fdc3/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Wed, 18 Apr 2018 17:37:02 -0700 > From: Jacob Miller <[email protected]> > Subject: [HCP-Users] Native space surface curvature available? > To: [email protected] > Message-ID: > <CAHN-knx= > [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]> > Subject: Re: [HCP-Users] Native space surface curvature available? > To: Jacob Miller <[email protected]>, > "[email protected]" <[email protected]> > Message-ID: <[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 > <(314)%20747-6173> > St. Louis, MO 63110 Email: [email protected] > > From: <[email protected]> on behalf of Jacob Miller < > [email protected]> > Date: Wednesday, April 18, 2018 at 9:04 PM > To: "[email protected]" <[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] > 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] > 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] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
