Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space?
Yes. Sent from my Verizon, Samsung Galaxy smartphone Original message From: Yael Shavit Date: 2/12/19 8:18 AM (GMT-06:00) To: "Glasser, Matthew" Cc: hcp-users , NEUROSCIENCE tim Subject: Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space? I'll be more specific - if I use the T1w/fsaverage_LR32k folder to project to surface, will the surfaces be comparable to one another? בתאריך יום ג׳, 12 בפבר׳ 2019, 15:42, מאת Glasser, Matthew mailto:glass...@wustl.edu>>: Standard meshes are (32k, 164k), native meshes are not. What volume space the meshes are in doesn’t matter. Matt. From: Yael Shavit mailto:yael.sh...@gmail.com>> Date: Tuesday, February 12, 2019 at 7:38 AM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: hcp-users mailto:hcp-users@humanconnectome.org>>, Timothy Coalson mailto:tsc...@mst.edu>> Subject: Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space? Thanks. Another question -are individual mesh surfaces comparable across subjects? בתאריך יום ד׳, 30 בינו׳ 2019, 1:34, מאת Glasser, Matthew mailto:glass...@wustl.edu>>: For the cortex you can do as Tim suggests and map either to the native mesh and then resample on the surface to the standard mesh or directly to the standard mesh. It is important that you use the meshes that are in the subject’s real physical space, as that is where the diffusion data is. For subcortical you would first resample the maps to MNI space and then could use a similar mapping to how we map the data into CIFTI space. Examples of how to do this are found the fMRISurface Pipeline: https://github.com/Washington-University/HCPpipelines/tree/master/fMRISurface Which is explained in this paper: https://www.sciencedirect.com/science/article/pii/S1053811913005053 Matt. From: Yael Shavit mailto:yael.sh...@gmail.com>> Date: Tuesday, January 29, 2019 at 1:42 AM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: hcp-users mailto:hcp-users@humanconnectome.org>>, Timothy Coalson mailto:tsc...@mst.edu>> Subject: Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space? Only cortex for now, but we're still looking into the option of working on the sub-cortex as well in the future. So I would be happy to hear your opinion on both. בתאריך יום ב׳, 28 בינו׳ 2019 ב-14:11 מאת Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>>: Of the cortex only or subcortical also? Matt. From: Yael Shavit mailto:yael.sh...@gmail.com>> Date: Monday, January 28, 2019 at 1:55 AM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: hcp-users mailto:hcp-users@humanconnectome.org>>, Timothy Coalson mailto:tsc...@mst.edu>> Subject: Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space? I would like to compare diffusion properties of grey matter areas across subjects. I was wondering whether projecting them to individual native surfaces as they are would allowing comparing them to one another, or would it be better to project them all to MNI, and if so, how can I do so. Thanks again. בתאריך יום א׳, 27 בינו׳ 2019 ב-17:43 מאת Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>>: I guess you are going to have to be a lot more specific as to what kind of analysis you are trying to do. I guess that is the only way we will be able to give you good advice. Matt. From: Yael Shavit mailto:yael.sh...@gmail.com>> Date: Sunday, January 27, 2019 at 2:39 AM To: hcp-users mailto:hcp-users@humanconnectome.org>> Cc: Timothy Coalson mailto:tsc...@mst.edu>>, Matt Glasser mailto:glass...@wustl.edu>> Subject: Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space? Hi, thank you for your answers. My issue is not specifically with projection to surface, but with the fact that the diffusion data is in native space and not in common space (I am interested in working on cortical and subcortical the gray matter). Should I apply transformations to MNI and then project to the individual's surface in MNI for group comparison? Thanks again. בתאריך יום ו׳, 18 בינו׳ 2019 ב-0:32 מאת Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>>: If this is about tractography, the advice will be different however. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Coalson mailto:tsc...@mst.edu>> Date: Thursday, January 17, 2019 at 12:57 PM To: Yael Shavit mailto:yael.sh...@gmail.com>> Cc: hcp-users mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space? The strongest directional information in the diffusion data is in the white matter, so I assume you are computing some measure from the scans and specific
Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space?
Standard meshes are (32k, 164k), native meshes are not. What volume space the meshes are in doesn’t matter. Matt. From: Yael Shavit mailto:yael.sh...@gmail.com>> Date: Tuesday, February 12, 2019 at 7:38 AM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: hcp-users mailto:hcp-users@humanconnectome.org>>, Timothy Coalson mailto:tsc...@mst.edu>> Subject: Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space? Thanks. Another question -are individual mesh surfaces comparable across subjects? בתאריך יום ד׳, 30 בינו׳ 2019, 1:34, מאת Glasser, Matthew mailto:glass...@wustl.edu>>: For the cortex you can do as Tim suggests and map either to the native mesh and then resample on the surface to the standard mesh or directly to the standard mesh. It is important that you use the meshes that are in the subject’s real physical space, as that is where the diffusion data is. For subcortical you would first resample the maps to MNI space and then could use a similar mapping to how we map the data into CIFTI space. Examples of how to do this are found the fMRISurface Pipeline: https://github.com/Washington-University/HCPpipelines/tree/master/fMRISurface Which is explained in this paper: https://www.sciencedirect.com/science/article/pii/S1053811913005053 Matt. From: Yael Shavit mailto:yael.sh...@gmail.com>> Date: Tuesday, January 29, 2019 at 1:42 AM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: hcp-users mailto:hcp-users@humanconnectome.org>>, Timothy Coalson mailto:tsc...@mst.edu>> Subject: Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space? Only cortex for now, but we're still looking into the option of working on the sub-cortex as well in the future. So I would be happy to hear your opinion on both. בתאריך יום ב׳, 28 בינו׳ 2019 ב-14:11 מאת Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>>: Of the cortex only or subcortical also? Matt. From: Yael Shavit mailto:yael.sh...@gmail.com>> Date: Monday, January 28, 2019 at 1:55 AM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: hcp-users mailto:hcp-users@humanconnectome.org>>, Timothy Coalson mailto:tsc...@mst.edu>> Subject: Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space? I would like to compare diffusion properties of grey matter areas across subjects. I was wondering whether projecting them to individual native surfaces as they are would allowing comparing them to one another, or would it be better to project them all to MNI, and if so, how can I do so. Thanks again. בתאריך יום א׳, 27 בינו׳ 2019 ב-17:43 מאת Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>>: I guess you are going to have to be a lot more specific as to what kind of analysis you are trying to do. I guess that is the only way we will be able to give you good advice. Matt. From: Yael Shavit mailto:yael.sh...@gmail.com>> Date: Sunday, January 27, 2019 at 2:39 AM To: hcp-users mailto:hcp-users@humanconnectome.org>> Cc: Timothy Coalson mailto:tsc...@mst.edu>>, Matt Glasser mailto:glass...@wustl.edu>> Subject: Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space? Hi, thank you for your answers. My issue is not specifically with projection to surface, but with the fact that the diffusion data is in native space and not in common space (I am interested in working on cortical and subcortical the gray matter). Should I apply transformations to MNI and then project to the individual's surface in MNI for group comparison? Thanks again. בתאריך יום ו׳, 18 בינו׳ 2019 ב-0:32 מאת Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>>: If this is about tractography, the advice will be different however. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Coalson mailto:tsc...@mst.edu>> Date: Thursday, January 17, 2019 at 12:57 PM To: Yael Shavit mailto:yael.sh...@gmail.com>> Cc: hcp-users mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space? The strongest directional information in the diffusion data is in the white matter, so I assume you are computing some measure from the scans and specifically want to study its value only in gray matter? The main command for this purpose is wb_command -volume-to-surface-mapping, and we recommend the ribbon mapping method (to capture the entire signal between white and pial surfaces, and downweight partial volumed voxels). We do not recommend downsampling the voxel data before this step, it would be better to use the 1.25mm^3 data directly. If you want the subcortical gray matter in our standard cifti space, then you should make a downsampled version for only that purpose (and st
Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space?
For the cortex you can do as Tim suggests and map either to the native mesh and then resample on the surface to the standard mesh or directly to the standard mesh. It is important that you use the meshes that are in the subject’s real physical space, as that is where the diffusion data is. For subcortical you would first resample the maps to MNI space and then could use a similar mapping to how we map the data into CIFTI space. Examples of how to do this are found the fMRISurface Pipeline: https://github.com/Washington-University/HCPpipelines/tree/master/fMRISurface Which is explained in this paper: https://www.sciencedirect.com/science/article/pii/S1053811913005053 Matt. From: Yael Shavit mailto:yael.sh...@gmail.com>> Date: Tuesday, January 29, 2019 at 1:42 AM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: hcp-users mailto:hcp-users@humanconnectome.org>>, Timothy Coalson mailto:tsc...@mst.edu>> Subject: Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space? Only cortex for now, but we're still looking into the option of working on the sub-cortex as well in the future. So I would be happy to hear your opinion on both. בתאריך יום ב׳, 28 בינו׳ 2019 ב-14:11 מאת Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>>: Of the cortex only or subcortical also? Matt. From: Yael Shavit mailto:yael.sh...@gmail.com>> Date: Monday, January 28, 2019 at 1:55 AM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: hcp-users mailto:hcp-users@humanconnectome.org>>, Timothy Coalson mailto:tsc...@mst.edu>> Subject: Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space? I would like to compare diffusion properties of grey matter areas across subjects. I was wondering whether projecting them to individual native surfaces as they are would allowing comparing them to one another, or would it be better to project them all to MNI, and if so, how can I do so. Thanks again. בתאריך יום א׳, 27 בינו׳ 2019 ב-17:43 מאת Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>>: I guess you are going to have to be a lot more specific as to what kind of analysis you are trying to do. I guess that is the only way we will be able to give you good advice. Matt. From: Yael Shavit mailto:yael.sh...@gmail.com>> Date: Sunday, January 27, 2019 at 2:39 AM To: hcp-users mailto:hcp-users@humanconnectome.org>> Cc: Timothy Coalson mailto:tsc...@mst.edu>>, Matt Glasser mailto:glass...@wustl.edu>> Subject: Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space? Hi, thank you for your answers. My issue is not specifically with projection to surface, but with the fact that the diffusion data is in native space and not in common space (I am interested in working on cortical and subcortical the gray matter). Should I apply transformations to MNI and then project to the individual's surface in MNI for group comparison? Thanks again. בתאריך יום ו׳, 18 בינו׳ 2019 ב-0:32 מאת Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>>: If this is about tractography, the advice will be different however. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Coalson mailto:tsc...@mst.edu>> Date: Thursday, January 17, 2019 at 12:57 PM To: Yael Shavit mailto:yael.sh...@gmail.com>> Cc: hcp-users mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space? The strongest directional information in the diffusion data is in the white matter, so I assume you are computing some measure from the scans and specifically want to study its value only in gray matter? The main command for this purpose is wb_command -volume-to-surface-mapping, and we recommend the ribbon mapping method (to capture the entire signal between white and pial surfaces, and downweight partial volumed voxels). We do not recommend downsampling the voxel data before this step, it would be better to use the 1.25mm^3 data directly. If you want the subcortical gray matter in our standard cifti space, then you should make a downsampled version for only that purpose (and still using the original 1.25mm^3 volume in the -volume-to-surface-mapping part). Note that you should generally do a small amount of smoothing (on the order of the larger voxel size) before downsampling volume files, in order to not effectively waste SNR, because the volume resampling methods are point estimates. You can look through the fMRISurface pipeline for how we go about doing this for fMRI data. Tim On Thu, Jan 17, 2019 at 10:42 AM Yael Shavit mailto:yael.sh...@gmail.com>> wrote: It seems that the diffusion HCP data is in native space in a resolution of 1.25mm^3. I am interested in projecting it to
Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space?
Only cortex for now, but we're still looking into the option of working on the sub-cortex as well in the future. So I would be happy to hear your opinion on both. בתאריך יום ב׳, 28 בינו׳ 2019 ב-14:11 מאת Glasser, Matthew < glass...@wustl.edu>: > Of the cortex only or subcortical also? > > Matt. > > From: Yael Shavit > Date: Monday, January 28, 2019 at 1:55 AM > To: Matt Glasser > Cc: hcp-users , Timothy Coalson < > tsc...@mst.edu> > Subject: Re: [HCP-Users] How can the diffusion HCP data be registered to > the MNI space? > > I would like to compare diffusion properties of grey matter areas across > subjects. I was wondering whether projecting them to individual native > surfaces as they are would allowing comparing them to one another, or would > it be better to project them all to MNI, and if so, how can I do so. > > Thanks again. > > בתאריך יום א׳, 27 בינו׳ 2019 ב-17:43 מאת Glasser, Matthew < > glass...@wustl.edu>: > >> I guess you are going to have to be a lot more specific as to what kind >> of analysis you are trying to do. I guess that is the only way we will be >> able to give you good advice. >> >> Matt. >> >> From: Yael Shavit >> Date: Sunday, January 27, 2019 at 2:39 AM >> To: hcp-users >> Cc: Timothy Coalson , Matt Glasser >> Subject: Re: [HCP-Users] How can the diffusion HCP data be registered to >> the MNI space? >> >> Hi, thank you for your answers. My issue is not specifically with >> projection to surface, but with the fact that the diffusion data is in >> native space and not in common space (I am interested in working on >> cortical and subcortical the gray matter). Should I apply transformations >> to MNI and then project to the individual's surface in MNI for group >> comparison? >> >> Thanks again. >> >> בתאריך יום ו׳, 18 בינו׳ 2019 ב-0:32 מאת Glasser, Matthew < >> glass...@wustl.edu>: >> >>> If this is about tractography, the advice will be different however. >>> >>> Matt. >>> >>> From: on behalf of Timothy >>> Coalson >>> Date: Thursday, January 17, 2019 at 12:57 PM >>> To: Yael Shavit >>> Cc: hcp-users >>> Subject: Re: [HCP-Users] How can the diffusion HCP data be registered >>> to the MNI space? >>> >>> The strongest directional information in the diffusion data is in the >>> white matter, so I assume you are computing some measure from the scans and >>> specifically want to study its value only in gray matter? >>> >>> The main command for this purpose is wb_command >>> -volume-to-surface-mapping, and we recommend the ribbon mapping method (to >>> capture the entire signal between white and pial surfaces, and downweight >>> partial volumed voxels). We do not recommend downsampling the voxel data >>> before this step, it would be better to use the 1.25mm^3 data directly. If >>> you want the subcortical gray matter in our standard cifti space, then you >>> should make a downsampled version for only that purpose (and still using >>> the original 1.25mm^3 volume in the -volume-to-surface-mapping part). Note >>> that you should generally do a small amount of smoothing (on the order of >>> the larger voxel size) before downsampling volume files, in order to not >>> effectively waste SNR, because the volume resampling methods are point >>> estimates. >>> >>> You can look through the fMRISurface pipeline for how we go about doing >>> this for fMRI data. >>> >>> Tim >>> >>> >>> On Thu, Jan 17, 2019 at 10:42 AM Yael Shavit >>> wrote: >>> >>>> It seems that the diffusion HCP data is in native space in a resolution >>>> of 1.25mm^3. I am interested in projecting it to surface, in 2mm^3. >>>> What would be the best way to do so, preferably using the HCP Pipelines? >>>> Thank you in advance. >>>> >>>> Yael Shavit >>>> Tel Aviv University >>>> >>>> ___ >>>> 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 >>> >>> >>> -- >>>
Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space?
Hi, thank you for your answers. My issue is not specifically with projection to surface, but with the fact that the diffusion data is in native space and not in common space (I am interested in working on cortical and subcortical the gray matter). Should I apply transformations to MNI and then project to the individual's surface in MNI for group comparison? Thanks again. בתאריך יום ו׳, 18 בינו׳ 2019 ב-0:32 מאת Glasser, Matthew < glass...@wustl.edu>: > If this is about tractography, the advice will be different however. > > Matt. > > From: on behalf of Timothy > Coalson > Date: Thursday, January 17, 2019 at 12:57 PM > To: Yael Shavit > Cc: hcp-users > Subject: Re: [HCP-Users] How can the diffusion HCP data be registered to > the MNI space? > > The strongest directional information in the diffusion data is in the > white matter, so I assume you are computing some measure from the scans and > specifically want to study its value only in gray matter? > > The main command for this purpose is wb_command > -volume-to-surface-mapping, and we recommend the ribbon mapping method (to > capture the entire signal between white and pial surfaces, and downweight > partial volumed voxels). We do not recommend downsampling the voxel data > before this step, it would be better to use the 1.25mm^3 data directly. If > you want the subcortical gray matter in our standard cifti space, then you > should make a downsampled version for only that purpose (and still using > the original 1.25mm^3 volume in the -volume-to-surface-mapping part). Note > that you should generally do a small amount of smoothing (on the order of > the larger voxel size) before downsampling volume files, in order to not > effectively waste SNR, because the volume resampling methods are point > estimates. > > You can look through the fMRISurface pipeline for how we go about doing > this for fMRI data. > > Tim > > > On Thu, Jan 17, 2019 at 10:42 AM Yael Shavit wrote: > >> It seems that the diffusion HCP data is in native space in a resolution >> of 1.25mm^3. I am interested in projecting it to surface, in 2mm^3. What >> would be the best way to do so, preferably using the HCP Pipelines? >> Thank you in advance. >> >> Yael Shavit >> Tel Aviv University >> >> ___ >> 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 list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space?
I would like to compare diffusion properties of grey matter areas across subjects. I was wondering whether projecting them to individual native surfaces as they are would allowing comparing them to one another, or would it be better to project them all to MNI, and if so, how can I do so. Thanks again. בתאריך יום א׳, 27 בינו׳ 2019 ב-17:43 מאת Glasser, Matthew < glass...@wustl.edu>: > I guess you are going to have to be a lot more specific as to what kind of > analysis you are trying to do. I guess that is the only way we will be > able to give you good advice. > > Matt. > > From: Yael Shavit > Date: Sunday, January 27, 2019 at 2:39 AM > To: hcp-users > Cc: Timothy Coalson , Matt Glasser > Subject: Re: [HCP-Users] How can the diffusion HCP data be registered to > the MNI space? > > Hi, thank you for your answers. My issue is not specifically with > projection to surface, but with the fact that the diffusion data is in > native space and not in common space (I am interested in working on > cortical and subcortical the gray matter). Should I apply transformations > to MNI and then project to the individual's surface in MNI for group > comparison? > > Thanks again. > > בתאריך יום ו׳, 18 בינו׳ 2019 ב-0:32 מאת Glasser, Matthew < > glass...@wustl.edu>: > >> If this is about tractography, the advice will be different however. >> >> Matt. >> >> From: on behalf of Timothy >> Coalson >> Date: Thursday, January 17, 2019 at 12:57 PM >> To: Yael Shavit >> Cc: hcp-users >> Subject: Re: [HCP-Users] How can the diffusion HCP data be registered to >> the MNI space? >> >> The strongest directional information in the diffusion data is in the >> white matter, so I assume you are computing some measure from the scans and >> specifically want to study its value only in gray matter? >> >> The main command for this purpose is wb_command >> -volume-to-surface-mapping, and we recommend the ribbon mapping method (to >> capture the entire signal between white and pial surfaces, and downweight >> partial volumed voxels). We do not recommend downsampling the voxel data >> before this step, it would be better to use the 1.25mm^3 data directly. If >> you want the subcortical gray matter in our standard cifti space, then you >> should make a downsampled version for only that purpose (and still using >> the original 1.25mm^3 volume in the -volume-to-surface-mapping part). Note >> that you should generally do a small amount of smoothing (on the order of >> the larger voxel size) before downsampling volume files, in order to not >> effectively waste SNR, because the volume resampling methods are point >> estimates. >> >> You can look through the fMRISurface pipeline for how we go about doing >> this for fMRI data. >> >> Tim >> >> >> On Thu, Jan 17, 2019 at 10:42 AM Yael Shavit >> wrote: >> >>> It seems that the diffusion HCP data is in native space in a resolution >>> of 1.25mm^3. I am interested in projecting it to surface, in 2mm^3. >>> What would be the best way to do so, preferably using the HCP Pipelines? >>> Thank you in advance. >>> >>> Yael Shavit >>> Tel Aviv University >>> >>> ___ >>> 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. >> > > -- > > 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
Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space?
Of the cortex only or subcortical also? Matt. From: Yael Shavit mailto:yael.sh...@gmail.com>> Date: Monday, January 28, 2019 at 1:55 AM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: hcp-users mailto:hcp-users@humanconnectome.org>>, Timothy Coalson mailto:tsc...@mst.edu>> Subject: Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space? I would like to compare diffusion properties of grey matter areas across subjects. I was wondering whether projecting them to individual native surfaces as they are would allowing comparing them to one another, or would it be better to project them all to MNI, and if so, how can I do so. Thanks again. בתאריך יום א׳, 27 בינו׳ 2019 ב-17:43 מאת Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>>: I guess you are going to have to be a lot more specific as to what kind of analysis you are trying to do. I guess that is the only way we will be able to give you good advice. Matt. From: Yael Shavit mailto:yael.sh...@gmail.com>> Date: Sunday, January 27, 2019 at 2:39 AM To: hcp-users mailto:hcp-users@humanconnectome.org>> Cc: Timothy Coalson mailto:tsc...@mst.edu>>, Matt Glasser mailto:glass...@wustl.edu>> Subject: Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space? Hi, thank you for your answers. My issue is not specifically with projection to surface, but with the fact that the diffusion data is in native space and not in common space (I am interested in working on cortical and subcortical the gray matter). Should I apply transformations to MNI and then project to the individual's surface in MNI for group comparison? Thanks again. בתאריך יום ו׳, 18 בינו׳ 2019 ב-0:32 מאת Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>>: If this is about tractography, the advice will be different however. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Coalson mailto:tsc...@mst.edu>> Date: Thursday, January 17, 2019 at 12:57 PM To: Yael Shavit mailto:yael.sh...@gmail.com>> Cc: hcp-users mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space? The strongest directional information in the diffusion data is in the white matter, so I assume you are computing some measure from the scans and specifically want to study its value only in gray matter? The main command for this purpose is wb_command -volume-to-surface-mapping, and we recommend the ribbon mapping method (to capture the entire signal between white and pial surfaces, and downweight partial volumed voxels). We do not recommend downsampling the voxel data before this step, it would be better to use the 1.25mm^3 data directly. If you want the subcortical gray matter in our standard cifti space, then you should make a downsampled version for only that purpose (and still using the original 1.25mm^3 volume in the -volume-to-surface-mapping part). Note that you should generally do a small amount of smoothing (on the order of the larger voxel size) before downsampling volume files, in order to not effectively waste SNR, because the volume resampling methods are point estimates. You can look through the fMRISurface pipeline for how we go about doing this for fMRI data. Tim On Thu, Jan 17, 2019 at 10:42 AM Yael Shavit mailto:yael.sh...@gmail.com>> wrote: It seems that the diffusion HCP data is in native space in a resolution of 1.25mm^3. I am interested in projecting it to surface, in 2mm^3. What would be the best way to do so, preferably using the HCP Pipelines? Thank you in advance. Yael Shavit Tel Aviv University ___ 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<mailto: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. 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
Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space?
I guess you are going to have to be a lot more specific as to what kind of analysis you are trying to do. I guess that is the only way we will be able to give you good advice. Matt. From: Yael Shavit mailto:yael.sh...@gmail.com>> Date: Sunday, January 27, 2019 at 2:39 AM To: hcp-users mailto:hcp-users@humanconnectome.org>> Cc: Timothy Coalson mailto:tsc...@mst.edu>>, Matt Glasser mailto:glass...@wustl.edu>> Subject: Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space? Hi, thank you for your answers. My issue is not specifically with projection to surface, but with the fact that the diffusion data is in native space and not in common space (I am interested in working on cortical and subcortical the gray matter). Should I apply transformations to MNI and then project to the individual's surface in MNI for group comparison? Thanks again. בתאריך יום ו׳, 18 בינו׳ 2019 ב-0:32 מאת Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>>: If this is about tractography, the advice will be different however. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Coalson mailto:tsc...@mst.edu>> Date: Thursday, January 17, 2019 at 12:57 PM To: Yael Shavit mailto:yael.sh...@gmail.com>> Cc: hcp-users mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space? The strongest directional information in the diffusion data is in the white matter, so I assume you are computing some measure from the scans and specifically want to study its value only in gray matter? The main command for this purpose is wb_command -volume-to-surface-mapping, and we recommend the ribbon mapping method (to capture the entire signal between white and pial surfaces, and downweight partial volumed voxels). We do not recommend downsampling the voxel data before this step, it would be better to use the 1.25mm^3 data directly. If you want the subcortical gray matter in our standard cifti space, then you should make a downsampled version for only that purpose (and still using the original 1.25mm^3 volume in the -volume-to-surface-mapping part). Note that you should generally do a small amount of smoothing (on the order of the larger voxel size) before downsampling volume files, in order to not effectively waste SNR, because the volume resampling methods are point estimates. You can look through the fMRISurface pipeline for how we go about doing this for fMRI data. Tim On Thu, Jan 17, 2019 at 10:42 AM Yael Shavit mailto:yael.sh...@gmail.com>> wrote: It seems that the diffusion HCP data is in native space in a resolution of 1.25mm^3. I am interested in projecting it to surface, in 2mm^3. What would be the best way to do so, preferably using the HCP Pipelines? Thank you in advance. Yael Shavit Tel Aviv University ___ 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<mailto: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. 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
Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space?
If this is about tractography, the advice will be different however. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Coalson mailto:tsc...@mst.edu>> Date: Thursday, January 17, 2019 at 12:57 PM To: Yael Shavit mailto:yael.sh...@gmail.com>> Cc: hcp-users mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space? The strongest directional information in the diffusion data is in the white matter, so I assume you are computing some measure from the scans and specifically want to study its value only in gray matter? The main command for this purpose is wb_command -volume-to-surface-mapping, and we recommend the ribbon mapping method (to capture the entire signal between white and pial surfaces, and downweight partial volumed voxels). We do not recommend downsampling the voxel data before this step, it would be better to use the 1.25mm^3 data directly. If you want the subcortical gray matter in our standard cifti space, then you should make a downsampled version for only that purpose (and still using the original 1.25mm^3 volume in the -volume-to-surface-mapping part). Note that you should generally do a small amount of smoothing (on the order of the larger voxel size) before downsampling volume files, in order to not effectively waste SNR, because the volume resampling methods are point estimates. You can look through the fMRISurface pipeline for how we go about doing this for fMRI data. Tim On Thu, Jan 17, 2019 at 10:42 AM Yael Shavit mailto:yael.sh...@gmail.com>> wrote: It seems that the diffusion HCP data is in native space in a resolution of 1.25mm^3. I am interested in projecting it to surface, in 2mm^3. What would be the best way to do so, preferably using the HCP Pipelines? Thank you in advance. Yael Shavit Tel Aviv University ___ 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<mailto: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
Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space?
The strongest directional information in the diffusion data is in the white matter, so I assume you are computing some measure from the scans and specifically want to study its value only in gray matter? The main command for this purpose is wb_command -volume-to-surface-mapping, and we recommend the ribbon mapping method (to capture the entire signal between white and pial surfaces, and downweight partial volumed voxels). We do not recommend downsampling the voxel data before this step, it would be better to use the 1.25mm^3 data directly. If you want the subcortical gray matter in our standard cifti space, then you should make a downsampled version for only that purpose (and still using the original 1.25mm^3 volume in the -volume-to-surface-mapping part). Note that you should generally do a small amount of smoothing (on the order of the larger voxel size) before downsampling volume files, in order to not effectively waste SNR, because the volume resampling methods are point estimates. You can look through the fMRISurface pipeline for how we go about doing this for fMRI data. Tim On Thu, Jan 17, 2019 at 10:42 AM Yael Shavit wrote: > It seems that the diffusion HCP data is in native space in a resolution of > 1.25mm^3. I am interested in projecting it to surface, in 2mm^3. What > would be the best way to do so, preferably using the HCP Pipelines? > Thank you in advance. > > Yael Shavit > Tel Aviv University > > ___ > 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
[HCP-Users] How can the diffusion HCP data be registered to the MNI space?
It seems that the diffusion HCP data is in native space in a resolution of 1.25mm^3. I am interested in projecting it to surface, in 2mm^3. What would be the best way to do so, preferably using the HCP Pipelines? Thank you in advance. Yael Shavit Tel Aviv University ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
