Re: [HCP-Users] Incorporating physiological monitoring data
Also to Steve: if these are used after ICAFIX, don’t they need to have the 24 motion parameters and noise ICA component timeseries confounds regressed out as well, before being used on the cleaned data? Peace, Matt. From: Harms, Michael mha...@wustl.edu Date: Monday, February 16, 2015 at 10:42 AM To: Matt Glasser glass...@wusm.wustl.edu, Stephen Smith st...@fmrib.ox.ac.uk, Miriam Klein-Flügge miriam.klein-flu...@psy.ox.ac.uk Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Incorporating physiological monitoring data Not only that, but just because a given physiological trace exists, doesn't necessarily mean that it is a *good* trace. There is going to be considerable variability in the quality of the physiological measurements, which presents a challenge in using them in a large scale study. I'm sure that Greg will comment more when he has a chance. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Glasser, Matt Glasser glass...@wusm.wustl.edu Date: Monday, February 16, 2015 10:10 AM To: Stephen Smith st...@fmrib.ox.ac.uk, Miriam Klein-Flügge miriam.klein-flu...@psy.ox.ac.uk Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Incorporating physiological monitoring data Note that a major reason we didn’t use these physiological confound regressors was they don’t exist for every subject, so be sure to select a subset of subjects that have them. We’d also be interested to know if you found they were helpful. Peace, Matt. From: Stephen Smith st...@fmrib.ox.ac.uk Date: Monday, February 16, 2015 at 8:05 AM To: Miriam Klein-Flügge miriam.klein-flu...@psy.ox.ac.uk Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Incorporating physiological monitoring data Hi - I think you would probably be best off taking the FIX-cleaned version of the data, and then apply additional confound regressors if they will help. Don't forget to apply the same highpass filter (to those regressors) that was applied already in the data preproc, before you use them. Cheers. On 16 Feb 2015, at 13:35, Miriam Klein-Flügge miriam.klein-flu...@psy.ox.ac.uk wrote: Dear all, Is it correct that until now the physiological monitoring data is not made use of in the preprocessing of the rfMRI data? I would like to correct for cardiac and respiratory signals and wondered how to best do that. I can see that FIX-denoising probably takes care of this type of noise but I am particularly interested in looking at the brain stem and in my experience, including physiological regressors in the preprocessing makes a big difference there. Would you recommend using the spatially (minimally) pre-processed rfMRI data, performing the high-pass filtering on it myself and then incorporating the physiological regressors at that stage, or is there a better stage at which to do it? Also, is there a standard procedure for regressing out the physiological regressors that you can recommend? Many thanks in advance! Kind regards, Miriam -- Miriam Klein-Flügge Sir Henry Wellcome Postdoctoral Fellow Department of Experimental Psychology University of Oxford ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users --- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK 44 (0) 1865 222726 (fax 222717) st...@fmrib.ox.ac.uk http://www.fmrib.ox.ac.uk/~steve --- Stop the culturaldestructionof Tibet ___ HCP-Users mailing list HCP-Users@humanconnectome.org 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. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users The materials in this message are private and may contain Protected Healthcare
Re: [HCP-Users] Incorporating physiological monitoring data
Note that a major reason we didn’t use these physiological confound regressors was they don’t exist for every subject, so be sure to select a subset of subjects that have them. We’d also be interested to know if you found they were helpful. Peace, Matt. From: Stephen Smith st...@fmrib.ox.ac.uk Date: Monday, February 16, 2015 at 8:05 AM To: Miriam Klein-Flügge miriam.klein-flu...@psy.ox.ac.uk Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Incorporating physiological monitoring data Hi - I think you would probably be best off taking the FIX-cleaned version of the data, and then apply additional confound regressors if they will help. Don't forget to apply the same highpass filter (to those regressors) that was applied already in the data preproc, before you use them. Cheers. On 16 Feb 2015, at 13:35, Miriam Klein-Flügge miriam.klein-flu...@psy.ox.ac.uk wrote: Dear all, Is it correct that until now the physiological monitoring data is not made use of in the preprocessing of the rfMRI data? I would like to correct for cardiac and respiratory signals and wondered how to best do that. I can see that FIX-denoising probably takes care of this type of noise but I am particularly interested in looking at the brain stem and in my experience, including physiological regressors in the preprocessing makes a big difference there. Would you recommend using the spatially (minimally) pre-processed rfMRI data, performing the high-pass filtering on it myself and then incorporating the physiological regressors at that stage, or is there a better stage at which to do it? Also, is there a standard procedure for regressing out the physiological regressors that you can recommend? Many thanks in advance! Kind regards, Miriam -- Miriam Klein-Flügge Sir Henry Wellcome Postdoctoral Fellow Department of Experimental Psychology University of Oxford ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users --- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK 44 (0) 1865 222726 (fax 222717) st...@fmrib.ox.ac.uk http://www.fmrib.ox.ac.uk/~steve --- Stop the culturaldestructionof Tibet ___ HCP-Users mailing list HCP-Users@humanconnectome.org 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. ___HCP-Users mailing listHCP-Users@humanconnectome.orghttp://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Incorporating physiological monitoring data
urgh - yes you're right. On 16 Feb 2015, at 16:47, Glasser, Matthew glass...@wusm.wustl.edu wrote: Also to Steve: if these are used after ICA+FIX, don’t they need to have the 24 motion parameters and noise ICA component timeseries confounds regressed out as well, before being used on the cleaned data? Peace, Matt. From: Harms, Michael mha...@wustl.edu mailto:mha...@wustl.edu Date: Monday, February 16, 2015 at 10:42 AM To: Matt Glasser glass...@wusm.wustl.edu mailto:glass...@wusm.wustl.edu, Stephen Smith st...@fmrib.ox.ac.uk mailto:st...@fmrib.ox.ac.uk, Miriam Klein-Flügge miriam.klein-flu...@psy.ox.ac.uk mailto:miriam.klein-flu...@psy.ox.ac.uk Cc: hcp-users@humanconnectome.org mailto:hcp-users@humanconnectome.org hcp-users@humanconnectome.org mailto:hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Incorporating physiological monitoring data Not only that, but just because a given physiological trace exists, doesn't necessarily mean that it is a *good* trace. There is going to be considerable variability in the quality of the physiological measurements, which presents a challenge in using them in a large scale study. I'm sure that Greg will comment more when he has a chance. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu mailto:mha...@wustl.edu From: Glasser, Matt Glasser glass...@wusm.wustl.edu mailto:glass...@wusm.wustl.edu Date: Monday, February 16, 2015 10:10 AM To: Stephen Smith st...@fmrib.ox.ac.uk mailto:st...@fmrib.ox.ac.uk, Miriam Klein-Flügge miriam.klein-flu...@psy.ox.ac.uk mailto:miriam.klein-flu...@psy.ox.ac.uk Cc: hcp-users@humanconnectome.org mailto:hcp-users@humanconnectome.org hcp-users@humanconnectome.org mailto:hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Incorporating physiological monitoring data Note that a major reason we didn’t use these physiological confound regressors was they don’t exist for every subject, so be sure to select a subset of subjects that have them. We’d also be interested to know if you found they were helpful. Peace, Matt. From: Stephen Smith st...@fmrib.ox.ac.uk mailto:st...@fmrib.ox.ac.uk Date: Monday, February 16, 2015 at 8:05 AM To: Miriam Klein-Flügge miriam.klein-flu...@psy.ox.ac.uk mailto:miriam.klein-flu...@psy.ox.ac.uk Cc: hcp-users@humanconnectome.org mailto:hcp-users@humanconnectome.org hcp-users@humanconnectome.org mailto:hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Incorporating physiological monitoring data Hi - I think you would probably be best off taking the FIX-cleaned version of the data, and then apply additional confound regressors if they will help. Don't forget to apply the same highpass filter (to those regressors) that was applied already in the data preproc, before you use them. Cheers. On 16 Feb 2015, at 13:35, Miriam Klein-Flügge miriam.klein-flu...@psy.ox.ac.uk mailto:miriam.klein-flu...@psy.ox.ac.uk wrote: Dear all, Is it correct that until now the physiological monitoring data is not made use of in the preprocessing of the rfMRI data? I would like to correct for cardiac and respiratory signals and wondered how to best do that. I can see that FIX-denoising probably takes care of this type of noise but I am particularly interested in looking at the brain stem and in my experience, including physiological regressors in the preprocessing makes a big difference there. Would you recommend using the spatially (minimally) pre-processed rfMRI data, performing the high-pass filtering on it myself and then incorporating the physiological regressors at that stage, or is there a better stage at which to do it? Also, is there a standard procedure for regressing out the physiological regressors that you can recommend? Many thanks in advance! Kind regards, Miriam -- Miriam Klein-Flügge Sir Henry Wellcome Postdoctoral Fellow Department of Experimental Psychology University of Oxford ___ HCP-Users mailing list HCP-Users@humanconnectome.org mailto:HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users http://lists.humanconnectome.org/mailman/listinfo/hcp-users --- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) st...@fmrib.ox.ac.uk mailto:st...@fmrib.ox.ac.uk http://www.fmrib.ox.ac.uk/~steve http://www.fmrib.ox.ac.uk/~steve
Re: [HCP-Users] Incorporating physiological monitoring data
Not only that, but just because a given physiological trace exists, doesn't necessarily mean that it is a *good* trace. There is going to be considerable variability in the quality of the physiological measurements, which presents a challenge in using them in a large scale study. I'm sure that Greg will comment more when he has a chance. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Glasser, Matt Glasser glass...@wusm.wustl.edu Date: Monday, February 16, 2015 10:10 AM To: Stephen Smith st...@fmrib.ox.ac.uk, Miriam Klein-Flügge miriam.klein-flu...@psy.ox.ac.uk Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Incorporating physiological monitoring data Note that a major reason we didn’t use these physiological confound regressors was they don’t exist for every subject, so be sure to select a subset of subjects that have them. We’d also be interested to know if you found they were helpful. Peace, Matt. From: Stephen Smith st...@fmrib.ox.ac.uk Date: Monday, February 16, 2015 at 8:05 AM To: Miriam Klein-Flügge miriam.klein-flu...@psy.ox.ac.uk Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Incorporating physiological monitoring data Hi - I think you would probably be best off taking the FIX-cleaned version of the data, and then apply additional confound regressors if they will help. Don't forget to apply the same highpass filter (to those regressors) that was applied already in the data preproc, before you use them. Cheers. On 16 Feb 2015, at 13:35, Miriam Klein-Flügge miriam.klein-flu...@psy.ox.ac.uk wrote: Dear all, Is it correct that until now the physiological monitoring data is not made use of in the preprocessing of the rfMRI data? I would like to correct for cardiac and respiratory signals and wondered how to best do that. I can see that FIX-denoising probably takes care of this type of noise but I am particularly interested in looking at the brain stem and in my experience, including physiological regressors in the preprocessing makes a big difference there. Would you recommend using the spatially (minimally) pre-processed rfMRI data, performing the high-pass filtering on it myself and then incorporating the physiological regressors at that stage, or is there a better stage at which to do it? Also, is there a standard procedure for regressing out the physiological regressors that you can recommend? Many thanks in advance! Kind regards, Miriam -- Miriam Klein-Flügge Sir Henry Wellcome Postdoctoral Fellow Department of Experimental Psychology University of Oxford ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users --- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK 44 (0) 1865 222726 (fax 222717) st...@fmrib.ox.ac.uk http://www.fmrib.ox.ac.uk/~steve --- Stop the culturaldestructionof Tibet ___ HCP-Users mailing list HCP-Users@humanconnectome.org 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. ___ HCP-Users mailing list HCP-Users@humanconnectome.org 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. ___HCP-Users mailing listHCP-Users@humanconnectome.orghttp://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Incorporating physiological monitoring data
Hi - I think you would probably be best off taking the FIX-cleaned version of the data, and then apply additional confound regressors if they will help. Don't forget to apply the same highpass filter (to those regressors) that was applied already in the data preproc, before you use them. Cheers. On 16 Feb 2015, at 13:35, Miriam Klein-Flügge miriam.klein-flu...@psy.ox.ac.uk wrote: Dear all, Is it correct that until now the physiological monitoring data is not made use of in the preprocessing of the rfMRI data? I would like to correct for cardiac and respiratory signals and wondered how to best do that. I can see that FIX-denoising probably takes care of this type of noise but I am particularly interested in looking at the brain stem and in my experience, including physiological regressors in the preprocessing makes a big difference there. Would you recommend using the spatially (minimally) pre-processed rfMRI data, performing the high-pass filtering on it myself and then incorporating the physiological regressors at that stage, or is there a better stage at which to do it? Also, is there a standard procedure for regressing out the physiological regressors that you can recommend? Many thanks in advance! Kind regards, Miriam -- Miriam Klein-Flügge Sir Henry Wellcome Postdoctoral Fellow Department of Experimental Psychology University of Oxford ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users --- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) st...@fmrib.ox.ac.ukhttp://www.fmrib.ox.ac.uk/~steve http://www.fmrib.ox.ac.uk/~steve --- Stop the cultural destruction of Tibet http://smithinks.net/ ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
