Xiaozhen You, My understanding is that the images have already had field map correction applied to them as part of the minimal preprocessing pipeline. As I mentioned previously, I recall HCP recommending not to perform temporal concatenations. However if you going to do so mean-centering prior to concatenation is vital, otherwise you create a step function between the high SNR scan and low SNR scan which inflates correlation. I would not think variance normalization would be crucial. Alternatively, perhaps you could calculate intrahemispheric connectivity for each of the LR/RL runs separately and then average the results across runs instead of concatenating.
Thomas Campbell Arnold On Sat, Nov 12, 2016 at 7:16 AM, <[email protected]> wrote: > 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. Re: L-R or R-L phase encoding? (Horn,Andreas (BIDMC - Neurology)) > 2. Re: L-R or R-L phase encoding? (Horn,Andreas (BIDMC - Neurology)) > 3. Re: L-R or R-L phase encoding? (Glasser, Matthew) > 4. Re: L-R or R-L phase encoding? (Horn,Andreas (BIDMC - Neurology)) > 5. Re: L-R or R-L phase encoding? (Glasser, Matthew) > 6. Re: Phase Encoding left-to-right and right-to-left > systematically affect intra hemisphere connections (Xiaozhen You) > 7. Re: L-R or R-L phase encoding? (Horn,Andreas (BIDMC - Neurology)) > 8. Re: Phase Encoding left-to-right and right-to-left > systematically affect intra hemisphere connections (Stephen Smith) > 9. Re: Phase Encoding left-to-right and right-to-left > systematically affect intra hemisphere connections (Glasser, Matthew) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 11 Nov 2016 23:30:48 +0000 > From: "Horn,Andreas (BIDMC - Neurology)" <[email protected]> > Subject: Re: [HCP-Users] L-R or R-L phase encoding? > To: "[email protected]" <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset="us-ascii" > > Dear HCP users, > > I am looking for preprocessed rs-fMRI runs in MNI space (if available). > Would the file > > HCP/hcp-openaccess/HCP_900/100307/MNINonLinear/Results/ > rfMRI_REST1_LR/rfMRI_REST1_LR_hp2000_clean.nii.gz > > be such a file? > I know about the four runs and how to concatenate them. > > But I am not > > -- > Andreas Horn, MD > Laboratory for Brain Network Imaging and Modulation > Berenson-Allen Center for Noninvasive Brain Stimulation > Department for Neurology, Beth Israel Deaconess Center > Harvard Medical School > 330 Brooklin Avenue, Kirstein Building KS 423 > 02215 Boston > > t: +1 6174077649 > w: http://www.brainnetworkstim.com > > > ________________________________ > > This message is intended for the use of the person(s) to whom it may be > addressed. It may contain information that is privileged, confidential, or > otherwise protected from disclosure under applicable law. If you are not > the intended recipient, any dissemination, distribution, copying, or use of > this information is prohibited. If you have received this message in error, > please permanently delete it and immediately notify the sender. Thank you. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://lists.humanconnectome.org/pipermail/hcp-users/ > attachments/20161111/56314cbb/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Fri, 11 Nov 2016 23:41:05 +0000 > From: "Horn,Andreas (BIDMC - Neurology)" <[email protected]> > Subject: Re: [HCP-Users] L-R or R-L phase encoding? > To: "[email protected]" <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset="us-ascii" > > Dear HCP-Users, > > I am looking for preprocessed rs-fMRI data of all 900 HCP subjects (if > available). > > Would the file: > HCP/hcp-openaccess/HCP_900/100307/MNINonLinear/Results/ > rfMRI_REST1_LR/rfMRI_REST1_LR_hp2000_clean.nii.gz > be such a file? I.e. is it already preprocessed in a standard way? I > learned it is cleaned by ICA but what else has been done with it? > > I know about the four runs and how to concatenate them after subtracting > the mean signal as described here<https://www.mail-archive. > com/[email protected]/msg01558.html>. > > Thanks so much for your help, > > Andreas > > > ________________________________ > > This message is intended for the use of the person(s) to whom it may be > addressed. It may contain information that is privileged, confidential, or > otherwise protected from disclosure under applicable law. If you are not > the intended recipient, any dissemination, distribution, copying, or use of > this information is prohibited. If you have received this message in error, > please permanently delete it and immediately notify the sender. Thank you. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://lists.humanconnectome.org/pipermail/hcp-users/ > attachments/20161111/83367407/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Sat, 12 Nov 2016 01:30:08 +0000 > From: "Glasser, Matthew" <[email protected]> > Subject: Re: [HCP-Users] L-R or R-L phase encoding? > To: "Horn,Andreas (BIDMC - Neurology)" <[email protected]>, > "[email protected]" <[email protected]> > Message-ID: <d44bcbc8.12cca8%[email protected]> > Content-Type: text/plain; charset="iso-8859-1" > > That file has had linear trends removed (sigma=2000s highpass filtering), > 24 movement parameters removed, and noise ICA components removed. It has > not had global physiological noise removed as we have not yet released a > good way of doing this. No spatial smoothing has been applied. In > general, we don't recommend using this data for cross-subject analysis > because of poor alignment across subjects from non-linear volume > registration. The recommended data to use is the CIFTI data aligned on the > surface with areal feature-based registration: ${StudyFolder}/${Subject}/ > MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas_ > MSMAll_hp2000_clean.dtseries.nii > > Peace, > > Matt. > > From: <[email protected]<mailto:hcp-users-bounces@ > humanconnectome.org>> on behalf of "Horn,Andreas (BIDMC - Neurology)" < > [email protected]<mailto:[email protected]>> > Date: Friday, November 11, 2016 at 5:41 PM > To: "[email protected]<mailto:[email protected]>" > <[email protected]<mailto:[email protected]>> > Subject: Re: [HCP-Users] L-R or R-L phase encoding? > > Dear HCP-Users, > > I am looking for preprocessed rs-fMRI data of all 900 HCP subjects (if > available). > > Would the file: > HCP/hcp-openaccess/HCP_900/100307/MNINonLinear/Results/ > rfMRI_REST1_LR/rfMRI_REST1_LR_hp2000_clean.nii.gz > be such a file? I.e. is it already preprocessed in a standard way? I > learned it is cleaned by ICA but what else has been done with it? > > I know about the four runs and how to concatenate them after subtracting > the mean signal as described here<https://www.mail-archive. > com/[email protected]/msg01558.html>. > > Thanks so much for your help, > > Andreas > > > ________________________________ > > This message is intended for the use of the person(s) to whom it may be > addressed. It may contain information that is privileged, confidential, or > otherwise protected from disclosure under applicable law. If you are not > the intended recipient, any dissemination, distribution, copying, or use of > this information is prohibited. If you have received this message in error, > please permanently delete it and immediately notify the sender. Thank you. > > _______________________________________________ > 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/20161112/a58ce7a0/attachment-0001.html > > ------------------------------ > > Message: 4 > Date: Sat, 12 Nov 2016 02:04:10 +0000 > From: "Horn,Andreas (BIDMC - Neurology)" <[email protected]> > Subject: Re: [HCP-Users] L-R or R-L phase encoding? > To: "Glasser, Matthew" <[email protected]> > Cc: "[email protected]" <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset="utf-8" > > Dear Matt, > > thanks so much for your quick response! > Unfortunately, the cifti data doesn?t apply to our question since we need > whole-brain coverage. > Could you by any chance specify how nonlinear volumetric normalization was > done in case of the file I mentioned? > > Thanks so much! > > Best, Andy > > -- > Andreas Horn, MD > Laboratory for Brain Network Imaging and Modulation > Berenson-Allen Center for Noninvasive Brain Stimulation > Department for Neurology, Beth Israel Deaconess Center > Harvard Medical School > 330 Brooklin Avenue, Kirstein Building KS 423 > 02215 Boston > > t: +1 6174077649 > w: http://www.brainnetworkstim.com > > On Nov 11, 2016, at 5:30 PM, Glasser, Matthew <[email protected]<mailto: > [email protected]>> wrote: > > That file has had linear trends removed (sigma=2000s highpass filtering), > 24 movement parameters removed, and noise ICA components removed. It has > not had global physiological noise removed as we have not yet released a > good way of doing this. No spatial smoothing has been applied. In > general, we don?t recommend using this data for cross-subject analysis > because of poor alignment across subjects from non-linear volume > registration. The recommended data to use is the CIFTI data aligned on the > surface with areal feature-based registration: ${StudyFolder}/${Subject}/ > MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas_ > MSMAll_hp2000_clean.dtseries.nii > > Peace, > > Matt. > > From: <[email protected]<mailto:hcp-users-bounces@ > humanconnectome.org>> on behalf of "Horn,Andreas (BIDMC - Neurology)" < > [email protected]<mailto:[email protected]>> > Date: Friday, November 11, 2016 at 5:41 PM > To: "[email protected]<mailto:[email protected]>" > <[email protected]<mailto:[email protected]>> > Subject: Re: [HCP-Users] L-R or R-L phase encoding? > > Dear HCP-Users, > > I am looking for preprocessed rs-fMRI data of all 900 HCP subjects (if > available). > > Would the file: > HCP/hcp-openaccess/HCP_900/100307/MNINonLinear/Results/ > rfMRI_REST1_LR/rfMRI_REST1_LR_hp2000_clean.nii.gz > be such a file? I.e. is it already preprocessed in a standard way? I > learned it is cleaned by ICA but what else has been done with it? > > I know about the four runs and how to concatenate them after subtracting > the mean signal as described here<https://urldefense. > proofpoint.com/v2/url?u=https-3A__www.mail-2Darchive.com_ > hcp-2Dusers-40humanconnectome.org_msg01558.html&d=CwMFAw&c= > WknmpdNpvrlj2B5K1aWVqL1SOiF30547pqSuOmtwXTQ&r=BTWOP47EynCdRIxIQsxjKLHVp- > ucrpC9iMHv26t1NFM&m=1uKLS6QNG06r1RjFu5MJqSZoFifmP81eLwFPvW_ni7E&s= > 0PVzMmhRd1GgCw286vaEL4XFnJy9T3ijHyaGOd474aU&e=>. > > Thanks so much for your help, > > Andreas > > > ________________________________ > > This message is intended for the use of the person(s) to whom it may be > addressed. It may contain information that is privileged, confidential, or > otherwise protected from disclosure under applicable law. If you are not > the intended recipient, any dissemination, distribution, copying, or use of > this information is prohibited. If you have received this message in error, > please permanently delete it and immediately notify the sender. Thank you. > _______________________________________________ > HCP-Users mailing list > [email protected]<mailto:[email protected]> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users< > https://urldefense.proofpoint.com/v2/url?u=http- > 3A__lists.humanconnectome.org_mailman_listinfo_hcp-2Dusers&d=CwMFAw&c= > WknmpdNpvrlj2B5K1aWVqL1SOiF30547pqSuOmtwXTQ&r=BTWOP47EynCdRIxIQsxjKLHVp- > ucrpC9iMHv26t1NFM&m=1uKLS6QNG06r1RjFu5MJqSZoFifmP81eLwFPvW_ni7E&s= > bbh3Vr485ZkhY3SbEvxDLTjUlrbcwC9b9UhlrC7tYAM&e=> > > > ________________________________ > 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/20161112/ae500186/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Sat, 12 Nov 2016 02:06:44 +0000 > From: "Glasser, Matthew" <[email protected]> > Subject: Re: [HCP-Users] L-R or R-L phase encoding? > To: "Horn,Andreas (BIDMC - Neurology)" <[email protected]> > Cc: "[email protected]" <[email protected]> > Message-ID: <d44bd4ec.12ccf8%[email protected]> > Content-Type: text/plain; charset="iso-8859-1" > > It was done with FNIRT nonlinear volume registration of the T1w image. > > CIFTI doesn't include white matter or CSF, but it does include the > cortical and subcortical grey matter, which is what is required for most > fMRI questions. > > Peace, > > Matt. > > From: "Horn,Andreas (BIDMC - Neurology)" <[email protected]<mailto: > [email protected]>> > Date: Friday, November 11, 2016 at 8:04 PM > To: Matt Glasser <[email protected]<mailto:[email protected]>> > Cc: "[email protected]<mailto:[email protected]>" > <[email protected]<mailto:[email protected]>> > Subject: Re: [HCP-Users] L-R or R-L phase encoding? > > Dear Matt, > > thanks so much for your quick response! > Unfortunately, the cifti data doesn't apply to our question since we need > whole-brain coverage. > Could you by any chance specify how nonlinear volumetric normalization was > done in case of the file I mentioned? > > Thanks so much! > > Best, Andy > > -- > Andreas Horn, MD > Laboratory for Brain Network Imaging and Modulation > Berenson-Allen Center for Noninvasive Brain Stimulation > Department for Neurology, Beth Israel Deaconess Center > Harvard Medical School > 330 Brooklin Avenue, Kirstein Building KS 423 > 02215 Boston > > t: +1 6174077649 > w: http://www.brainnetworkstim.com > > On Nov 11, 2016, at 5:30 PM, Glasser, Matthew <[email protected]<mailto: > [email protected]>> wrote: > > That file has had linear trends removed (sigma=2000s highpass filtering), > 24 movement parameters removed, and noise ICA components removed. It has > not had global physiological noise removed as we have not yet released a > good way of doing this. No spatial smoothing has been applied. In > general, we don't recommend using this data for cross-subject analysis > because of poor alignment across subjects from non-linear volume > registration. The recommended data to use is the CIFTI data aligned on the > surface with areal feature-based registration: ${StudyFolder}/${Subject}/ > MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas_ > MSMAll_hp2000_clean.dtseries.nii > > Peace, > > Matt. > > From: <[email protected]<mailto:hcp-users-bounces@ > humanconnectome.org>> on behalf of "Horn,Andreas (BIDMC - Neurology)" < > [email protected]<mailto:[email protected]>> > Date: Friday, November 11, 2016 at 5:41 PM > To: "[email protected]<mailto:[email protected]>" > <[email protected]<mailto:[email protected]>> > Subject: Re: [HCP-Users] L-R or R-L phase encoding? > > Dear HCP-Users, > > I am looking for preprocessed rs-fMRI data of all 900 HCP subjects (if > available). > > Would the file: > HCP/hcp-openaccess/HCP_900/100307/MNINonLinear/Results/ > rfMRI_REST1_LR/rfMRI_REST1_LR_hp2000_clean.nii.gz > be such a file? I.e. is it already preprocessed in a standard way? I > learned it is cleaned by ICA but what else has been done with it? > > I know about the four runs and how to concatenate them after subtracting > the mean signal as described here<https://urldefense. > proofpoint.com/v2/url?u=https-3A__www.mail-2Darchive.com_ > hcp-2Dusers-40humanconnectome.org_msg01558.html&d=CwMFAw&c= > WknmpdNpvrlj2B5K1aWVqL1SOiF30547pqSuOmtwXTQ&r=BTWOP47EynCdRIxIQsxjKLHVp- > ucrpC9iMHv26t1NFM&m=1uKLS6QNG06r1RjFu5MJqSZoFifmP81eLwFPvW_ni7E&s= > 0PVzMmhRd1GgCw286vaEL4XFnJy9T3ijHyaGOd474aU&e=>. > > Thanks so much for your help, > > Andreas > > > ________________________________ > > This message is intended for the use of the person(s) to whom it may be > addressed. It may contain information that is privileged, confidential, or > otherwise protected from disclosure under applicable law. If you are not > the intended recipient, any dissemination, distribution, copying, or use of > this information is prohibited. If you have received this message in error, > please permanently delete it and immediately notify the sender. Thank you. > _______________________________________________ > HCP-Users mailing list > [email protected]<mailto:[email protected]> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users< > https://urldefense.proofpoint.com/v2/url?u=http- > 3A__lists.humanconnectome.org_mailman_listinfo_hcp-2Dusers&d=CwMFAw&c= > WknmpdNpvrlj2B5K1aWVqL1SOiF30547pqSuOmtwXTQ&r=BTWOP47EynCdRIxIQsxjKLHVp- > ucrpC9iMHv26t1NFM&m=1uKLS6QNG06r1RjFu5MJqSZoFifmP81eLwFPvW_ni7E&s= > bbh3Vr485ZkhY3SbEvxDLTjUlrbcwC9b9UhlrC7tYAM&e=> > > > ________________________________ > 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. > > > ________________________________ > 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/20161112/531b9014/attachment-0001.html > > ------------------------------ > > Message: 6 > Date: Fri, 11 Nov 2016 23:31:50 -0500 > From: Xiaozhen You <[email protected]> > Subject: Re: [HCP-Users] Phase Encoding left-to-right and > right-to-left systematically affect intra hemisphere connections > To: "Glasser, Matthew" <[email protected]> > Cc: "[email protected]" <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset="windows-1252" > > Thank you Matthew and Arnold for the speedy reply! > But the AP and PA type of acquisition are not in any of the HCP 900 data > release though, right? > So seems there is no way to correct this intrinsic hemispheric > connectivity differences introduced by the RL vs LR encoding?, even though > demean and variance normalization make the two runs overall comparable and > have better coverage, it automatically make left and right hemisphere more > similar in terms of intra hemisphere connections, so more difficult to pull > out connectivity laterality as conventional AP and PA resting state data > reveals for language network.. > > Any field map correction might help this at all? > or do you think it will help if to normalize variance for each hemisphere > separately within each run, and then concatenate across RL and LR, for the > purpose of calculating hemispheric connectivity? > > Thanks again for all your help and thoughtful comments! > > Xiaozhen You, PhD > > Research Faculty > Center for Neuroscience Research > Children's National Medical Center > 111 Michigan Ave. NW > M7634 > Washington D.C. 20010 > Phone: 2024764294 > Email: [email protected] > > Developmental Cognitive Neuroscience Lab > Georgetown University > Phone: 202-687-9133 > Email: [email protected] > > On Nov 11, 2016, at 3:47 PM, Glasser, Matthew <[email protected]> wrote: > > > The recommended approach is to use a balanced amount of RL and LR data > in your analysis. This should not be biased in either direction and should > actually have a somewhat better coverage as far as dropout goes. > > > > The reason LR and RL were used was that they allowed for some more > favorable scanner settings on our customized HCP Skyra. On commercial > Prisma scanners there is no advantage to LR and RL, so we have been using > AP and PA (still balanced so that one gets the benefits of better coverage > regarding dropout. > > > > Peace, > > > > Matt. > > > > From: <[email protected]> on behalf of Xiaozhen You > <[email protected]> > > Date: Friday, November 11, 2016 at 1:29 PM > > To: "[email protected]" <[email protected]> > > Subject: Re: [HCP-Users] Phase Encoding left-to-right and right-to-left > systematically affect intra hemisphere connections > > > > Hi HCP experts, > > I noticed the very different effect from the RL or LR phase encoding on > within subject intrahemisphere connections, is there a way to correct for > this objectively if someone is interested in looking at any metric related > to hemispheric connections? > > Here is a sample subject?s intrahemisphere connection map to language > area for RL at Rest1 and Rest2, and then LR at Rest1 and Rest2. > > > > _______________________________________________ > > HCP-Users mailing list > > [email protected] > > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > <PastedGraphic-16.png> > > <PastedGraphic-18.png> > > then LR > > > > <PastedGraphic-19.png> > > <PastedGraphic-20.png> > > > > I also then tried to concatenated the RL and LR within the same session > by demean and variance normalization but then it artificially make it more > bilateral. Here is what I have for just a single run resting state data > from our lab's regular rsfmri acquisition which does reveal left > hemispheric language dominance for connectivity for adult. > > > > Any help will be highly appreciated. > > Thanks! > > Xiaozhen You, PhD > > > > Research Faculty > > Center for Neuroscience Research > > Children's National Medical Center > > 111 Michigan Ave. NW > > M7634 > > Washington D.C. 20010 > > Phone: 2024764294 > > Email: [email protected] > > > > Developmental Cognitive Neuroscience Lab > > Georgetown University > > Phone: 202-687-9133 > > Email: [email protected] > > > > > > > > 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. > > <PastedGraphic-16.png><PastedGraphic-18.png><PastedGraphic-19.png>< > PastedGraphic-20.png> > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://lists.humanconnectome.org/pipermail/hcp-users/ > attachments/20161111/6ee0c040/attachment-0001.html > > ------------------------------ > > Message: 7 > Date: Sat, 12 Nov 2016 04:41:17 +0000 > From: "Horn,Andreas (BIDMC - Neurology)" <[email protected]> > Subject: Re: [HCP-Users] L-R or R-L phase encoding? > To: "Glasser, Matthew" <[email protected]> > Cc: "[email protected]" <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset="utf-8" > > Thanks, super! > > On Nov 11, 2016, at 6:06 PM, Glasser, Matthew <[email protected]<mailto: > [email protected]>> wrote: > > It was done with FNIRT nonlinear volume registration of the T1w image. > > CIFTI doesn?t include white matter or CSF, but it does include the > cortical and subcortical grey matter, which is what is required for most > fMRI questions. > > Peace, > > Matt. > > From: "Horn,Andreas (BIDMC - Neurology)" <[email protected]<mailto: > [email protected]>> > Date: Friday, November 11, 2016 at 8:04 PM > To: Matt Glasser <[email protected]<mailto:[email protected]>> > Cc: "[email protected]<mailto:[email protected]>" > <[email protected]<mailto:[email protected]>> > Subject: Re: [HCP-Users] L-R or R-L phase encoding? > > Dear Matt, > > thanks so much for your quick response! > Unfortunately, the cifti data doesn?t apply to our question since we need > whole-brain coverage. > Could you by any chance specify how nonlinear volumetric normalization was > done in case of the file I mentioned? > > Thanks so much! > > Best, Andy > > -- > Andreas Horn, MD > Laboratory for Brain Network Imaging and Modulation > Berenson-Allen Center for Noninvasive Brain Stimulation > Department for Neurology, Beth Israel Deaconess Center > Harvard Medical School > 330 Brooklin Avenue, Kirstein Building KS 423 > 02215 Boston > > t: +1 6174077649 > w: http://www.brainnetworkstim.com<https://urldefense. > proofpoint.com/v2/url?u=http-3A__www.brainnetworkstim.com&d=CwMFAw&c= > WknmpdNpvrlj2B5K1aWVqL1SOiF30547pqSuOmtwXTQ&r=BTWOP47EynCdRIxIQsxjKLHVp- > ucrpC9iMHv26t1NFM&m=2sTqsimt4FSgTyQ3szMU1eeSNM- > rl0pYtOYMx5er7Ec&s=822GDuBVN_n1CdnSmj5QRNuHGLXQKXW3G7a0d2NDaIo&e=> > > On Nov 11, 2016, at 5:30 PM, Glasser, Matthew <[email protected]<mailto: > [email protected]>> wrote: > > That file has had linear trends removed (sigma=2000s highpass filtering), > 24 movement parameters removed, and noise ICA components removed. It has > not had global physiological noise removed as we have not yet released a > good way of doing this. No spatial smoothing has been applied. In > general, we don?t recommend using this data for cross-subject analysis > because of poor alignment across subjects from non-linear volume > registration. The recommended data to use is the CIFTI data aligned on the > surface with areal feature-based registration: ${StudyFolder}/${Subject}/ > MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas_ > MSMAll_hp2000_clean.dtseries.nii > > Peace, > > Matt. > > From: <[email protected]<mailto:hcp-users-bounces@ > humanconnectome.org>> on behalf of "Horn,Andreas (BIDMC - Neurology)" < > [email protected]<mailto:[email protected]>> > Date: Friday, November 11, 2016 at 5:41 PM > To: "[email protected]<mailto:[email protected]>" > <[email protected]<mailto:[email protected]>> > Subject: Re: [HCP-Users] L-R or R-L phase encoding? > > Dear HCP-Users, > > I am looking for preprocessed rs-fMRI data of all 900 HCP subjects (if > available). > > Would the file: > HCP/hcp-openaccess/HCP_900/100307/MNINonLinear/Results/ > rfMRI_REST1_LR/rfMRI_REST1_LR_hp2000_clean.nii.gz > be such a file? I.e. is it already preprocessed in a standard way? I > learned it is cleaned by ICA but what else has been done with it? > > I know about the four runs and how to concatenate them after subtracting > the mean signal as described here<https://urldefense. > proofpoint.com/v2/url?u=https-3A__www.mail-2Darchive.com_ > hcp-2Dusers-40humanconnectome.org_msg01558.html&d=CwMFAw&c= > WknmpdNpvrlj2B5K1aWVqL1SOiF30547pqSuOmtwXTQ&r=BTWOP47EynCdRIxIQsxjKLHVp- > ucrpC9iMHv26t1NFM&m=1uKLS6QNG06r1RjFu5MJqSZoFifmP81eLwFPvW_ni7E&s= > 0PVzMmhRd1GgCw286vaEL4XFnJy9T3ijHyaGOd474aU&e=>. > > Thanks so much for your help, > > Andreas > > > ________________________________ > > This message is intended for the use of the person(s) to whom it may be > addressed. It may contain information that is privileged, confidential, or > otherwise protected from disclosure under applicable law. If you are not > the intended recipient, any dissemination, distribution, copying, or use of > this information is prohibited. If you have received this message in error, > please permanently delete it and immediately notify the sender. Thank you. > _______________________________________________ > HCP-Users mailing list > [email protected]<mailto:[email protected]> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users< > https://urldefense.proofpoint.com/v2/url?u=http- > 3A__lists.humanconnectome.org_mailman_listinfo_hcp-2Dusers&d=CwMFAw&c= > WknmpdNpvrlj2B5K1aWVqL1SOiF30547pqSuOmtwXTQ&r=BTWOP47EynCdRIxIQsxjKLHVp- > ucrpC9iMHv26t1NFM&m=1uKLS6QNG06r1RjFu5MJqSZoFifmP81eLwFPvW_ni7E&s= > bbh3Vr485ZkhY3SbEvxDLTjUlrbcwC9b9UhlrC7tYAM&e=> > > > ________________________________ > 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. > > > > ________________________________ > 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/20161112/b6aa61e0/attachment-0001.html > > ------------------------------ > > Message: 8 > Date: Sat, 12 Nov 2016 07:51:14 +0000 > From: Stephen Smith <[email protected]> > Subject: Re: [HCP-Users] Phase Encoding left-to-right and > right-to-left systematically affect intra hemisphere connections > To: Xiaozhen You <[email protected]> > Cc: "[email protected]" <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset="utf-8" > > Hi - there's several images here, and I'm not sure how you estimated these > connectivity patterns? Are you sure this isn't just run-run variability? > Cheers. > > > > > On 11 Nov 2016, at 19:29, Xiaozhen You <[email protected]> wrote: > > > > Hi HCP experts, > > I noticed the very different effect from the RL or LR phase encoding on > within subject intrahemisphere connections, is there a way to correct for > this objectively if someone is interested in looking at any metric related > to hemispheric connections? > > Here is a sample subject?s intrahemisphere connection map to language > area for RL at Rest1 and Rest2, and then LR at Rest1 and Rest2. > > > > _______________________________________________ > > HCP-Users mailing list > > [email protected] > > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > > <PastedGraphic-16.png> > > <PastedGraphic-18.png> > > then LR > > > > <PastedGraphic-19.png> > > <PastedGraphic-20.png> > > > > I also then tried to concatenated the RL and LR within the same session > by demean and variance normalization but then it artificially make it more > bilateral. Here is what I have for just a single run resting state data > from our lab's regular rsfmri acquisition which does reveal left > hemispheric language dominance for connectivity for adult. > > > > Any help will be highly appreciated. > > Thanks! > > Xiaozhen You, PhD > > > > Research Faculty > > Center for Neuroscience Research > > Children's National Medical Center > > 111 Michigan Ave. NW > > M7634 > > Washington D.C. 20010 > > Phone: 2024764294 > > Email: [email protected] <mailto:[email protected]> > > > > Developmental Cognitive Neuroscience Lab > > Georgetown University > > Phone: 202-687-9133 > > Email: [email protected] <mailto:[email protected]> > > > > <PastedGraphic-21.pdf> > > > ------------------------------------------------------------ > --------------- > Stephen M. Smith, Professor of Biomedical Engineering > Head of Analysis, Oxford University FMRIB Centre > > FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK > +44 (0) 1865 222726 (fax 222717) > [email protected] http://www.fmrib.ox.ac.uk/~steve < > http://www.fmrib.ox.ac.uk/~steve> > ------------------------------------------------------------ > --------------- > > Stop the cultural?destruction?of Tibet <http://smithinks.net/> > > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://lists.humanconnectome.org/pipermail/hcp-users/ > attachments/20161112/a212e742/attachment-0001.html > > ------------------------------ > > Message: 9 > Date: Sat, 12 Nov 2016 12:17:27 +0000 > From: "Glasser, Matthew" <[email protected]> > Subject: Re: [HCP-Users] Phase Encoding left-to-right and > right-to-left systematically affect intra hemisphere connections > To: Xiaozhen You <[email protected]> > Cc: "[email protected]" <[email protected]> > Message-ID: <d44c63a5.12cd54%[email protected]> > Content-Type: text/plain; charset="windows-1252" > > I wouldn?t expect one?s results to be dramatically different from > comparing LR + RL to AP + PA. It is certainly possible to identify > lateralized RSNs in the HCP data. It is correct that you should demean and > if desired variance normalize each run separately. > > Peace, > > Matt. > > From: Xiaozhen You <[email protected]<mailto:[email protected]>> > Date: Friday, November 11, 2016 at 10:31 PM > To: Matt Glasser <[email protected]<mailto:[email protected]>> > Cc: "[email protected]<mailto:[email protected]>" > <[email protected]<mailto:[email protected]>> > Subject: Re: [HCP-Users] Phase Encoding left-to-right and right-to-left > systematically affect intra hemisphere connections > > Thank you Matthew and Arnold for the speedy reply! > But the AP and PA type of acquisition are not in any of the HCP 900 data > release though, right? > So seems there is no way to correct this intrinsic hemispheric > connectivity differences introduced by the RL vs LR encoding?, even though > demean and variance normalization make the two runs overall comparable and > have better coverage, it automatically make left and right hemisphere more > similar in terms of intra hemisphere connections, so more difficult to pull > out connectivity laterality as conventional AP and PA resting state data > reveals for language network.. > > Any field map correction might help this at all? > or do you think it will help if to normalize variance for each hemisphere > separately within each run, and then concatenate across RL and LR, for the > purpose of calculating hemispheric connectivity? > > Thanks again for all your help and thoughtful comments! > > Xiaozhen You, PhD > > Research Faculty > Center for Neuroscience Research > Children's National Medical Center > 111 Michigan Ave. NW > M7634 > Washington D.C. 20010 > Phone: 2024764294 > Email: [email protected]<mailto:[email protected]> > > Developmental Cognitive Neuroscience Lab > Georgetown University > Phone: 202-687-9133 > Email: [email protected]<mailto:[email protected]> > > On Nov 11, 2016, at 3:47 PM, Glasser, Matthew <[email protected]<mailto: > [email protected]>> wrote: > > The recommended approach is to use a balanced amount of RL and LR data in > your analysis. This should not be biased in either direction and should > actually have a somewhat better coverage as far as dropout goes. > > The reason LR and RL were used was that they allowed for some more > favorable scanner settings on our customized HCP Skyra. On commercial > Prisma scanners there is no advantage to LR and RL, so we have been using > AP and PA (still balanced so that one gets the benefits of better coverage > regarding dropout. > > Peace, > > Matt. > > From: <[email protected]<mailto:hcp-users-bounces@ > humanconnectome.org>> on behalf of Xiaozhen You <[email protected] > <mailto:[email protected]>> > Date: Friday, November 11, 2016 at 1:29 PM > To: "[email protected]<mailto:[email protected]>" > <[email protected]<mailto:[email protected]>> > Subject: Re: [HCP-Users] Phase Encoding left-to-right and right-to-left > systematically affect intra hemisphere connections > > Hi HCP experts, > I noticed the very different effect from the RL or LR phase encoding on > within subject intrahemisphere connections, is there a way to correct for > this objectively if someone is interested in looking at any metric related > to hemispheric connections? > Here is a sample subject?s intrahemisphere connection map to language area > for RL at Rest1 and Rest2, and then LR at Rest1 and Rest2. > > _______________________________________________ > HCP-Users mailing list > [email protected]<mailto:[email protected]> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > <PastedGraphic-16.png> > <PastedGraphic-18.png> > then LR > > <PastedGraphic-19.png> > <PastedGraphic-20.png> > > I also then tried to concatenated the RL and LR within the same session by > demean and variance normalization but then it artificially make it more > bilateral. Here is what I have for just a single run resting state data > from our lab's regular rsfmri acquisition which does reveal left > hemispheric language dominance for connectivity for adult. > > Any help will be highly appreciated. > Thanks! > Xiaozhen You, PhD > > Research Faculty > Center for Neuroscience Research > Children's National Medical Center > 111 Michigan Ave. NW > M7634 > Washington D.C. 20010 > Phone: 2024764294 > Email: [email protected]<mailto:[email protected]> > > Developmental Cognitive Neuroscience Lab > Georgetown University > Phone: 202-687-9133 > Email: [email protected]<mailto:[email protected]> > > > > ________________________________ > 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. > <PastedGraphic-16.png><PastedGraphic-18.png><PastedGraphic-19.png>< > PastedGraphic-20.png> > > > ________________________________ > 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/20161112/f2301574/attachment.html > > ------------------------------ > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > End of HCP-Users Digest, Vol 48, Issue 22 > ***************************************** > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
