Either of those options is fine. Certain kinds of analyses may benefit from one or the other approach.
Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of Thomas Arnold <[email protected]<mailto:[email protected]>> Date: Saturday, November 12, 2016 at 9:51 AM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] HCP-Users Digest, Vol 48, Issue 22 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]<mailto:[email protected]>> wrote: 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. 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]<mailto:[email protected]>> Subject: Re: [HCP-Users] L-R or R-L phase encoding? To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Message-ID: <[email protected]<mailto:[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<tel:%2B1%206174077649> 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]<mailto:[email protected]>> Subject: Re: [HCP-Users] L-R or R-L phase encoding? To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Message-ID: <[email protected]<mailto:[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]<mailto:[email protected]>> Subject: Re: [HCP-Users] L-R or R-L phase encoding? To: "Horn,Andreas (BIDMC - Neurology)" <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Message-ID: <d44bcbc8.12cca8%[email protected]<mailto: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:[email protected]><mailto:[email protected]<mailto:[email protected]>>> on behalf of "Horn,Andreas (BIDMC - Neurology)" <[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>> Date: Friday, November 11, 2016 at 5:41 PM To: "[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] 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]><mailto:[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]<mailto:[email protected]>> Subject: Re: [HCP-Users] L-R or R-L phase encoding? To: "Glasser, Matthew" <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Message-ID: <[email protected]<mailto:[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<tel:%2B1%206174077649> w: http://www.brainnetworkstim.com On Nov 11, 2016, at 5:30 PM, Glasser, Matthew <[email protected]<mailto:[email protected]><mailto:[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:[email protected]><mailto:[email protected]<mailto:[email protected]>>> on behalf of "Horn,Andreas (BIDMC - Neurology)" <[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>> Date: Friday, November 11, 2016 at 5:41 PM To: "[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] 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]><mailto:[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]<mailto:[email protected]>> Subject: Re: [HCP-Users] L-R or R-L phase encoding? To: "Horn,Andreas (BIDMC - Neurology)" <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Message-ID: <d44bd4ec.12ccf8%[email protected]<mailto: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]><mailto:[email protected]<mailto:[email protected]>>> Date: Friday, November 11, 2016 at 8:04 PM To: Matt Glasser <[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] 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<tel:%2B1%206174077649> w: http://www.brainnetworkstim.com On Nov 11, 2016, at 5:30 PM, Glasser, Matthew <[email protected]<mailto:[email protected]><mailto:[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:[email protected]><mailto:[email protected]<mailto:[email protected]>>> on behalf of "Horn,Andreas (BIDMC - Neurology)" <[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>> Date: Friday, November 11, 2016 at 5:41 PM To: "[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] 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]><mailto:[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]<mailto:[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]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Message-ID: <[email protected]<mailto:[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<tel:2024764294> Email: [email protected]<mailto:[email protected]> Developmental Cognitive Neuroscience Lab Georgetown University Phone: 202-687-9133<tel: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:[email protected]>> > 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<tel:2024764294> > Email: [email protected]<mailto:[email protected]> > > Developmental Cognitive Neuroscience Lab > Georgetown University > Phone: 202-687-9133<tel: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> -------------- 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]<mailto:[email protected]>> Subject: Re: [HCP-Users] L-R or R-L phase encoding? To: "Glasser, Matthew" <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Message-ID: <[email protected]<mailto:[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]><mailto:[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]><mailto:[email protected]<mailto:[email protected]>>> Date: Friday, November 11, 2016 at 8:04 PM To: Matt Glasser <[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] 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<tel:%2B1%206174077649> 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]><mailto:[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:[email protected]><mailto:[email protected]<mailto:[email protected]>>> on behalf of "Horn,Andreas (BIDMC - Neurology)" <[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>> Date: Friday, November 11, 2016 at 5:41 PM To: "[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] 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]><mailto:[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]<mailto:[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]<mailto:[email protected]>> Cc: "[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 - 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]<mailto:[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]<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<tel:2024764294> > Email: [email protected]<mailto:[email protected]> > <mailto:[email protected]<mailto:[email protected]>> > > Developmental Cognitive Neuroscience Lab > Georgetown University > Phone: 202-687-9133<tel:202-687-9133> > Email: [email protected]<mailto:[email protected]> > <mailto:[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<tel:%2B44%20%280%29%201865%20222726> (fax 222717) [email protected]<mailto:[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]<mailto:[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]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Message-ID: <d44c63a5.12cd54%[email protected]<mailto: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]><mailto:[email protected]<mailto:[email protected]>>> Date: Friday, November 11, 2016 at 10:31 PM To: Matt Glasser <[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] 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<tel:2024764294> Email: [email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>> Developmental Cognitive Neuroscience Lab Georgetown University Phone: 202-687-9133 Email: [email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>> On Nov 11, 2016, at 3:47 PM, Glasser, Matthew <[email protected]<mailto:[email protected]><mailto:[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:[email protected]><mailto:[email protected]<mailto:[email protected]>>> on behalf of Xiaozhen You <[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>> Date: Friday, November 11, 2016 at 1:29 PM To: "[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] 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]><mailto:[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]><mailto:[email protected]<mailto:[email protected]>> Developmental Cognitive Neuroscience Lab Georgetown University Phone: 202-687-9133 Email: [email protected]<mailto:[email protected]><mailto:[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... 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