Re: [HCP-Users] MNI atlas registration in volume space for task fMRI grayordinates datasets?
To summarize the thread and some off-list conversations for future readers, it is the case that the HCP pipelines normalize the task fMRI images to the MNI atlas in volume space. This part of the preprocessing pipeline is different from the procedure used in Anticevic et al. 2008 (doi:10.1016/j.neuroimage.2008.02.052), and was chosen for computational efficiency (since the subcortical data needs to be mapped to MNI volume space), and since the resolution costs were judged to be small. These threads refer to similar issues: http://www.mail-archive.com/hcp-users@humanconnectome.org/msg01323.html http://www.mail-archive.com/hcp-users@humanconnectome.org/msg01234.html http://www.mail-archive.com/hcp-users@humanconnectome.org/msg00356.html thanks again Matt and Tim, Jo On 4/24/2015 11:56 AM, Glasser, Matthew wrote: I don’t really want to recapitulate my more detailed responses to this question previously on the list (why atlas register the fMRI data to MNI space in the volume vs to native subject space or even vs bringing the surfaces into the original EPI space). The basics are that motion correction, distortion correction, volume registration, etc are all done in the volume. The data are then mapped onto the cortical surface and alignment across subjects in CIFTI space for cortical data is based on surface registration. Surface and volume registration are independent things (you are right that the surface alignment occurs using spheres), and the volume registration does not contribute to the cross-subject surface alignment. Volume registrations can be applied to surface mesh coordinates exactly, so the volume to surface mapping can occur in MNI space (though using individual subject surfaces and individual subject timeseries―a very different thing than group average data to group average surfaces). Peace, Matt. On 4/24/15, 11:48 AM, J.A. Etzel jet...@artsci.wustl.edu wrote: Sorry, but now I'm confused: I thought you confirmed that the HCP task fMRI pipelines perform motion correction and spatial normalization (MNI atlas registration) on the task fMRI images in volume space, before mapping the data to the surface. Doesn't that mean that the surface version of the task fMRI data relies upon the volumetric atlas registration, and is so a different procedure than the spherical registration to atlas space described in Anticevic et al., 2008? thanks, Jo On 4/24/2015 11:24 AM, Glasser, Matthew wrote: There were a few threads on this in the past. The volume and surface registration are pretty much independent. The cortical data are aligned with surface registration. Peace, Matt. From: Timothy Coalson tsc...@mst.edu mailto:tsc...@mst.edu Date: Friday, April 24, 2015 at 10:55 AM To: J.A. Etzel jet...@artsci.wustl.edu mailto:jet...@artsci.wustl.edu Cc: Matt Glasser glass...@wusm.wustl.edu mailto:glass...@wusm.wustl.edu, hcp-users@humanconnectome.org mailto:hcp-users@humanconnectome.org hcp-users@humanconnectome.org mailto:hcp-users@humanconnectome.org Subject: Re: [HCP-Users] MNI atlas registration in volume space for task fMRI grayordinates datasets? You can't do surface registration before you have data on the surface to register with, which is what the volume to surface mapping does. We do use surface registration, and we highly recommend its use to everyone, but volume registration is still an important preceding step - they are not mutually exclusive. Tim On Fri, Apr 24, 2015 at 10:48 AM, J.A. Etzel jet...@artsci.wustl.edu mailto:jet...@artsci.wustl.edu wrote: Thanks for the quick reply. Why was this chosen, as opposed to surface-based registration, such as described in Anticevic et al. 2008 (doi:10.1016/j.neuroimage.2008.02.052)? Have you done comparisons suggesting that volume-based registration is preferable? thanks again, Jo On 4/24/2015 9:59 AM, Glasser, Matthew wrote: Yes that¹s how it works. Peace, Matt. On 4/24/15, 9:56 AM, J.A. Etzel jet...@artsci.wustl.edu mailto:jet...@artsci.wustl.edu wrote: I have a question about the preprocessing for the task-fMRI grayordinates datasets, specifically the images from the Level 2 fixed-effects analysis. For clarity, the images I'm asking about are those like /104820/MNINonLinear/Results/tfMRI_WM/tfMRI_WM_hp200_s4_level2.feat/Grayo r dinatesStats/cope2.feat/pe1.dtseries.nii From Barch et al. (2013) and the HCP_S500 Reference Manual, these participant-level analyses were performed with a grayordinates-adapted version of the FSL Level 1 and Level 2 analysis routines, using as input the output of the fMRISurface pipeline. Which brings me to the question: Is it correct that the pipelines producing these images perform (amongst other preprocessing steps) motion correction
Re: [HCP-Users] MNI atlas registration in volume space for task fMRI grayordinates datasets?
Thanks Jo for the summary. The important registration for cortical data is still on the surface like Anticevic et al and other surface-based studies. Currently it is folding-based, but will be based on areal features in the future. Peace, Matt. On 4/29/15, 2:50 PM, J.A. Etzel jet...@artsci.wustl.edu wrote: To summarize the thread and some off-list conversations for future readers, it is the case that the HCP pipelines normalize the task fMRI images to the MNI atlas in volume space. This part of the preprocessing pipeline is different from the procedure used in Anticevic et al. 2008 (doi:10.1016/j.neuroimage.2008.02.052), and was chosen for computational efficiency (since the subcortical data needs to be mapped to MNI volume space), and since the resolution costs were judged to be small. These threads refer to similar issues: http://www.mail-archive.com/hcp-users@humanconnectome.org/msg01323.html http://www.mail-archive.com/hcp-users@humanconnectome.org/msg01234.html http://www.mail-archive.com/hcp-users@humanconnectome.org/msg00356.html thanks again Matt and Tim, Jo On 4/24/2015 11:56 AM, Glasser, Matthew wrote: I don’t really want to recapitulate my more detailed responses to this question previously on the list (why atlas register the fMRI data to MNI space in the volume vs to native subject space or even vs bringing the surfaces into the original EPI space). The basics are that motion correction, distortion correction, volume registration, etc are all done in the volume. The data are then mapped onto the cortical surface and alignment across subjects in CIFTI space for cortical data is based on surface registration. Surface and volume registration are independent things (you are right that the surface alignment occurs using spheres), and the volume registration does not contribute to the cross-subject surface alignment. Volume registrations can be applied to surface mesh coordinates exactly, so the volume to surface mapping can occur in MNI space (though using individual subject surfaces and individual subject timeseries―a very different thing than group average data to group average surfaces). Peace, Matt. On 4/24/15, 11:48 AM, J.A. Etzel jet...@artsci.wustl.edu wrote: Sorry, but now I'm confused: I thought you confirmed that the HCP task fMRI pipelines perform motion correction and spatial normalization (MNI atlas registration) on the task fMRI images in volume space, before mapping the data to the surface. Doesn't that mean that the surface version of the task fMRI data relies upon the volumetric atlas registration, and is so a different procedure than the spherical registration to atlas space described in Anticevic et al., 2008? thanks, Jo On 4/24/2015 11:24 AM, Glasser, Matthew wrote: There were a few threads on this in the past. The volume and surface registration are pretty much independent. The cortical data are aligned with surface registration. Peace, Matt. From: Timothy Coalson tsc...@mst.edu mailto:tsc...@mst.edu Date: Friday, April 24, 2015 at 10:55 AM To: J.A. Etzel jet...@artsci.wustl.edu mailto:jet...@artsci.wustl.edu Cc: Matt Glasser glass...@wusm.wustl.edu mailto:glass...@wusm.wustl.edu, hcp-users@humanconnectome.org mailto:hcp-users@humanconnectome.org hcp-users@humanconnectome.org mailto:hcp-users@humanconnectome.org Subject: Re: [HCP-Users] MNI atlas registration in volume space for task fMRI grayordinates datasets? You can't do surface registration before you have data on the surface to register with, which is what the volume to surface mapping does. We do use surface registration, and we highly recommend its use to everyone, but volume registration is still an important preceding step - they are not mutually exclusive. Tim On Fri, Apr 24, 2015 at 10:48 AM, J.A. Etzel jet...@artsci.wustl.edu mailto:jet...@artsci.wustl.edu wrote: Thanks for the quick reply. Why was this chosen, as opposed to surface-based registration, such as described in Anticevic et al. 2008 (doi:10.1016/j.neuroimage.2008.02.052)? Have you done comparisons suggesting that volume-based registration is preferable? thanks again, Jo On 4/24/2015 9:59 AM, Glasser, Matthew wrote: Yes that¹s how it works. Peace, Matt. On 4/24/15, 9:56 AM, J.A. Etzel jet...@artsci.wustl.edu mailto:jet...@artsci.wustl.edu wrote: I have a question about the preprocessing for the task-fMRI grayordinates datasets, specifically the images from the Level 2 fixed-effects analysis. For clarity, the images I'm asking about are those like /104820/MNINonLinear/Results/tfMRI_WM/tfMRI_WM_hp200_s4_level2.feat/Gra yo r dinatesStats/cope2.feat/pe1.dtseries.nii From Barch et al. (2013) and the HCP_S500 Reference Manual, these participant-level analyses were performed with a grayordinates-adapted
Re: [HCP-Users] MNI atlas registration in volume space for task fMRI grayordinates datasets?
Yes that¹s how it works. Peace, Matt. On 4/24/15, 9:56 AM, J.A. Etzel jet...@artsci.wustl.edu wrote: I have a question about the preprocessing for the task-fMRI grayordinates datasets, specifically the images from the Level 2 fixed-effects analysis. For clarity, the images I'm asking about are those like /104820/MNINonLinear/Results/tfMRI_WM/tfMRI_WM_hp200_s4_level2.feat/Grayor dinatesStats/cope2.feat/pe1.dtseries.nii From Barch et al. (2013) and the HCP_S500 Reference Manual, these participant-level analyses were performed with a grayordinates-adapted version of the FSL Level 1 and Level 2 analysis routines, using as input the output of the fMRISurface pipeline. Which brings me to the question: Is it correct that the pipelines producing these images perform (amongst other preprocessing steps) motion correction and spatial normalization (MNI atlas registration) on the fMRI images in volume space, before the surface mapping? Figures 19 and 20 in Glasser et al. (2013) suggest that this is the case, but it is a bit unclear. thanks, Jo -- Joset A. Etzel, Ph.D. Research Analyst Cognitive Control Psychopathology Lab Washington University in St. Louis http://mvpa.blogspot.com/ ___ 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
[HCP-Users] MNI atlas registration in volume space for task fMRI grayordinates datasets?
I have a question about the preprocessing for the task-fMRI grayordinates datasets, specifically the images from the Level 2 fixed-effects analysis. For clarity, the images I'm asking about are those like /104820/MNINonLinear/Results/tfMRI_WM/tfMRI_WM_hp200_s4_level2.feat/GrayordinatesStats/cope2.feat/pe1.dtseries.nii From Barch et al. (2013) and the HCP_S500 Reference Manual, these participant-level analyses were performed with a grayordinates-adapted version of the FSL Level 1 and Level 2 analysis routines, using as input the output of the fMRISurface pipeline. Which brings me to the question: Is it correct that the pipelines producing these images perform (amongst other preprocessing steps) motion correction and spatial normalization (MNI atlas registration) on the fMRI images in volume space, before the surface mapping? Figures 19 and 20 in Glasser et al. (2013) suggest that this is the case, but it is a bit unclear. thanks, Jo -- Joset A. Etzel, Ph.D. Research Analyst Cognitive Control Psychopathology Lab Washington University in St. Louis http://mvpa.blogspot.com/ ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] MNI atlas registration in volume space for task fMRI grayordinates datasets?
There were a few threads on this in the past. The volume and surface registration are pretty much independent. The cortical data are aligned with surface registration. Peace, Matt. From: Timothy Coalson tsc...@mst.edu Date: Friday, April 24, 2015 at 10:55 AM To: J.A. Etzel jet...@artsci.wustl.edu Cc: Matt Glasser glass...@wusm.wustl.edu, hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] MNI atlas registration in volume space for task fMRI grayordinates datasets? You can't do surface registration before you have data on the surface to register with, which is what the volume to surface mapping does. We do use surface registration, and we highly recommend its use to everyone, but volume registration is still an important preceding step - they are not mutually exclusive. Tim On Fri, Apr 24, 2015 at 10:48 AM, J.A. Etzel jet...@artsci.wustl.edu wrote: Thanks for the quick reply. Why was this chosen, as opposed to surface-based registration, such as described in Anticevic et al. 2008 (doi:10.1016/j.neuroimage.2008.02.052)? Have you done comparisons suggesting that volume-based registration is preferable? thanks again, Jo On 4/24/2015 9:59 AM, Glasser, Matthew wrote: Yes that¹s how it works. Peace, Matt. On 4/24/15, 9:56 AM, J.A. Etzel jet...@artsci.wustl.edu wrote: I have a question about the preprocessing for the task-fMRI grayordinates datasets, specifically the images from the Level 2 fixed-effects analysis. For clarity, the images I'm asking about are those like /104820/MNINonLinear/Results/tfMRI_WM/tfMRI_WM_hp200_s4_level2.feat/Grayor dinatesStats/cope2.feat/pe1.dtseries.nii From Barch et al. (2013) and the HCP_S500 Reference Manual, these participant-level analyses were performed with a grayordinates-adapted version of the FSL Level 1 and Level 2 analysis routines, using as input the output of the fMRISurface pipeline. Which brings me to the question: Is it correct that the pipelines producing these images perform (amongst other preprocessing steps) motion correction and spatial normalization (MNI atlas registration) on the fMRI images in volume space, before the surface mapping? Figures 19 and 20 in Glasser et al. (2013) suggest that this is the case, but it is a bit unclear. thanks, Jo -- Joset A. Etzel, Ph.D. Research Analyst Cognitive Control Psychopathology Lab Washington University in St. Louis http://mvpa.blogspot.com/ ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users ___ 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] MNI atlas registration in volume space for task fMRI grayordinates datasets?
I don’t really want to recapitulate my more detailed responses to this question previously on the list (why atlas register the fMRI data to MNI space in the volume vs to native subject space or even vs bringing the surfaces into the original EPI space). The basics are that motion correction, distortion correction, volume registration, etc are all done in the volume. The data are then mapped onto the cortical surface and alignment across subjects in CIFTI space for cortical data is based on surface registration. Surface and volume registration are independent things (you are right that the surface alignment occurs using spheres), and the volume registration does not contribute to the cross-subject surface alignment. Volume registrations can be applied to surface mesh coordinates exactly, so the volume to surface mapping can occur in MNI space (though using individual subject surfaces and individual subject timeseries―a very different thing than group average data to group average surfaces). Peace, Matt. On 4/24/15, 11:48 AM, J.A. Etzel jet...@artsci.wustl.edu wrote: Sorry, but now I'm confused: I thought you confirmed that the HCP task fMRI pipelines perform motion correction and spatial normalization (MNI atlas registration) on the task fMRI images in volume space, before mapping the data to the surface. Doesn't that mean that the surface version of the task fMRI data relies upon the volumetric atlas registration, and is so a different procedure than the spherical registration to atlas space described in Anticevic et al., 2008? thanks, Jo On 4/24/2015 11:24 AM, Glasser, Matthew wrote: There were a few threads on this in the past. The volume and surface registration are pretty much independent. The cortical data are aligned with surface registration. Peace, Matt. From: Timothy Coalson tsc...@mst.edu mailto:tsc...@mst.edu Date: Friday, April 24, 2015 at 10:55 AM To: J.A. Etzel jet...@artsci.wustl.edu mailto:jet...@artsci.wustl.edu Cc: Matt Glasser glass...@wusm.wustl.edu mailto:glass...@wusm.wustl.edu, hcp-users@humanconnectome.org mailto:hcp-users@humanconnectome.org hcp-users@humanconnectome.org mailto:hcp-users@humanconnectome.org Subject: Re: [HCP-Users] MNI atlas registration in volume space for task fMRI grayordinates datasets? You can't do surface registration before you have data on the surface to register with, which is what the volume to surface mapping does. We do use surface registration, and we highly recommend its use to everyone, but volume registration is still an important preceding step - they are not mutually exclusive. Tim On Fri, Apr 24, 2015 at 10:48 AM, J.A. Etzel jet...@artsci.wustl.edu mailto:jet...@artsci.wustl.edu wrote: Thanks for the quick reply. Why was this chosen, as opposed to surface-based registration, such as described in Anticevic et al. 2008 (doi:10.1016/j.neuroimage.2008.02.052)? Have you done comparisons suggesting that volume-based registration is preferable? thanks again, Jo On 4/24/2015 9:59 AM, Glasser, Matthew wrote: Yes that¹s how it works. Peace, Matt. On 4/24/15, 9:56 AM, J.A. Etzel jet...@artsci.wustl.edu mailto:jet...@artsci.wustl.edu wrote: I have a question about the preprocessing for the task-fMRI grayordinates datasets, specifically the images from the Level 2 fixed-effects analysis. For clarity, the images I'm asking about are those like /104820/MNINonLinear/Results/tfMRI_WM/tfMRI_WM_hp200_s4_level2.feat/Grayo r dinatesStats/cope2.feat/pe1.dtseries.nii From Barch et al. (2013) and the HCP_S500 Reference Manual, these participant-level analyses were performed with a grayordinates-adapted version of the FSL Level 1 and Level 2 analysis routines, using as input the output of the fMRISurface pipeline. Which brings me to the question: Is it correct that the pipelines producing these images perform (amongst other preprocessing steps) motion correction and spatial normalization (MNI atlas registration) on the fMRI images in volume space, before the surface mapping? Figures 19 and 20 in Glasser et al. (2013) suggest that this is the case, but it is a bit unclear. thanks, Jo -- Joset A. Etzel, Ph.D. Research Analyst Cognitive Control Psychopathology Lab Washington University in St. Louis http://mvpa.blogspot.com/ ___ HCP-Users mailing list HCP-Users@humanconnectome.org mailto:HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users The materials in this message
Re: [HCP-Users] MNI atlas registration in volume space for task fMRI grayordinates datasets?
Sorry, but now I'm confused: I thought you confirmed that the HCP task fMRI pipelines perform motion correction and spatial normalization (MNI atlas registration) on the task fMRI images in volume space, before mapping the data to the surface. Doesn't that mean that the surface version of the task fMRI data relies upon the volumetric atlas registration, and is so a different procedure than the spherical registration to atlas space described in Anticevic et al., 2008? thanks, Jo On 4/24/2015 11:24 AM, Glasser, Matthew wrote: There were a few threads on this in the past. The volume and surface registration are pretty much independent. The cortical data are aligned with surface registration. Peace, Matt. From: Timothy Coalson tsc...@mst.edu mailto:tsc...@mst.edu Date: Friday, April 24, 2015 at 10:55 AM To: J.A. Etzel jet...@artsci.wustl.edu mailto:jet...@artsci.wustl.edu Cc: Matt Glasser glass...@wusm.wustl.edu mailto:glass...@wusm.wustl.edu, hcp-users@humanconnectome.org mailto:hcp-users@humanconnectome.org hcp-users@humanconnectome.org mailto:hcp-users@humanconnectome.org Subject: Re: [HCP-Users] MNI atlas registration in volume space for task fMRI grayordinates datasets? You can't do surface registration before you have data on the surface to register with, which is what the volume to surface mapping does. We do use surface registration, and we highly recommend its use to everyone, but volume registration is still an important preceding step - they are not mutually exclusive. Tim On Fri, Apr 24, 2015 at 10:48 AM, J.A. Etzel jet...@artsci.wustl.edu mailto:jet...@artsci.wustl.edu wrote: Thanks for the quick reply. Why was this chosen, as opposed to surface-based registration, such as described in Anticevic et al. 2008 (doi:10.1016/j.neuroimage.2008.02.052)? Have you done comparisons suggesting that volume-based registration is preferable? thanks again, Jo On 4/24/2015 9:59 AM, Glasser, Matthew wrote: Yes that¹s how it works. Peace, Matt. On 4/24/15, 9:56 AM, J.A. Etzel jet...@artsci.wustl.edu mailto:jet...@artsci.wustl.edu wrote: I have a question about the preprocessing for the task-fMRI grayordinates datasets, specifically the images from the Level 2 fixed-effects analysis. For clarity, the images I'm asking about are those like /104820/MNINonLinear/Results/tfMRI_WM/tfMRI_WM_hp200_s4_level2.feat/Grayor dinatesStats/cope2.feat/pe1.dtseries.nii From Barch et al. (2013) and the HCP_S500 Reference Manual, these participant-level analyses were performed with a grayordinates-adapted version of the FSL Level 1 and Level 2 analysis routines, using as input the output of the fMRISurface pipeline. Which brings me to the question: Is it correct that the pipelines producing these images perform (amongst other preprocessing steps) motion correction and spatial normalization (MNI atlas registration) on the fMRI images in volume space, before the surface mapping? Figures 19 and 20 in Glasser et al. (2013) suggest that this is the case, but it is a bit unclear. thanks, Jo -- Joset A. Etzel, Ph.D. Research Analyst Cognitive Control Psychopathology Lab Washington University in St. Louis http://mvpa.blogspot.com/ ___ HCP-Users mailing list HCP-Users@humanconnectome.org mailto:HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
