You can make T1w/164K_fs_LR versions of the surfaces by resampling the native
mesh surfaces in T1w space to the 164k mesh:
wb_command -surface-resample
${StudyFolder}/${Subject}/T1w/Native/${Subject}.${Hemisphere}.${Surface}.native.surf.gii
${StudyFolder}/${Subject}/MNINonLinear/Native/${Subject}.${Hemisphere}.sphere.${RegName}.native.surf.gii
${StudyFolder}/${Subject}/MNINonLinear/${Subject}.${Hemisphere}.sphere.164k_fs_LR.surf.gii
BARYCENTRIC
${StudyFolder}/${Subject}/T1w/${Subject}.${Hemisphere}.${Surface}.164k_fs_LR.surf.gii
Peace,
Matt.
From: Jean-François Cabana <[email protected]<mailto:[email protected]>>
Date: Monday, July 25, 2016 at 4:56 PM
To: Matt Glasser <[email protected]<mailto:[email protected]>>,
"[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: Re: [HCP-Users] Mapping volumetric maps on brain surfaces
Dear Matt,
Thank you for your answer. I read the paper, and things are much clearer now. I
have another question though.
In addition to the parametric maps derived from DWI, we also have quantitative
parametric maps (T1, T2*, PD and susceptibility) computed from a
multi-parametric mapping sequence, acquired at the same resolution as our
structural data (1mm isotropic). These maps will also be processed in the
subject native space. As with the DWI maps, I would like to transfert them onto
the subject surfaces, and perform group analysis. I would like to take
advantage of the high-res 164k mesh since our maps have higher resolution than
the 32k mesh (2mm). For what I understand, the 164k mesh exists only in the
MNINonLinear space.
My question is, should I transform the 164k_fs_LR mesh from the MNI space to
the native space? Or do you think I still should use the 32k_fs_LR mesh in the
native space? Or maybe I should rather transform our multi-parametric data in
MNI space and use the 164k mesh?
Many thanks,
JF
From: Glasser, Matthew<mailto:[email protected]>
Sent: Sunday, July 24, 2016 1:38 PM
To: Jean-François Cabana<mailto:[email protected]> ;
[email protected]<mailto:[email protected]>
Subject: Re: [HCP-Users] Mapping volumetric maps on brain surfaces
I would have a look at this paper:
http://www.sciencedirect.com/science/article/pii/S1053811913005053 for a
description of how the data are organized. If you want to compare the maps
across subjects and the diffusion data are in the subject’s physical space, I
would use the surfaces in ${StudyFolder}/${Subject}/T1w/fsaverage_LR32k
Peace,
Matt.
From: Jean-François Cabana <[email protected]<mailto:[email protected]>>
Date: Sunday, July 24, 2016 at 7:03 AM
To: Matt Glasser <[email protected]<mailto:[email protected]>>,
"[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: Re: [HCP-Users] Mapping volumetric maps on brain surfaces
Dear Matt,
I tried the –volume-to-surface-mapping as you suggested and it seems to work
fine. However, I am a bit (a lot) confused by all the different spaces and
surfaces, and I’m not sure which one to use. What I have are parametric maps
computed in the native space of each subjects. What I want to do is map these
parameters on the surfaces (and on subcortical GM structures), perform group
averages and comparison. What surfaces should I map onto? I see surfaces files
in :
- T1w/Native
- T1w/fsaverage_LR32k
- MNINonLinear/Native
- MNINonLinear/fsaverage_LR32k
Thank you for your help,
JF
From: Glasser, Matthew<mailto:[email protected]>
Sent: Friday, July 8, 2016 7:00 PM
To: Harms, Michael<mailto:[email protected]> ; Jean-Francois
Cabana<mailto:[email protected]> ;
[email protected]<mailto:[email protected]>
Subject: Re: [HCP-Users] Mapping volumetric maps on brain surfaces
I wouldn’t do the up sampling. I also would use the -ribbon-constrained
approach rather than the -myelin-style approach unless you want the maps
weighted towards the midthickness. The command to use is wb_command
-volume-to-surface-mapping.
Peace,
Matt.
From:
<[email protected]<mailto:[email protected]>>
on behalf of "Harms, Michael" <[email protected]<mailto:[email protected]>>
Date: Friday, July 8, 2016 at 10:06 AM
To: "Harms, Michael" <[email protected]<mailto:[email protected]>>, Jean-Francois
Cabana <[email protected]<mailto:[email protected]>>, "
[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: Re: [HCP-Users] Mapping volumetric maps on brain surfaces
BTW: You should be able to do the sampling to the surface directly on DWI
parameter maps processed at the native 2 mm acquisition resolution. No need to
upsample the DWI to match the resolution of your structurals.
--
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: [email protected]<mailto:[email protected]>
From:
<[email protected]<mailto:[email protected]>>
on behalf of "Harms, Michael" <[email protected]<mailto:[email protected]>>
Date: Friday, July 8, 2016 at 10:01 AM
To: Jean-Francois Cabana <[email protected]<mailto:[email protected]>>, "
[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: Re: [HCP-Users] Mapping volumetric maps on brain surfaces
Hi,
I’m not sure if such an example script exists. You might have to wrestle with
how the myelin maps are created a little bit — in particular, the parts related
to -volume-to-surface-mapping and the resampling to a smaller mesh. A very
similar sort of thing happens in the fMRISurface pipeline as well (see
RibbonVolumeToSurfaceMapping.sh).
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: [email protected]<mailto:[email protected]>
From:
<[email protected]<mailto:[email protected]>>
on behalf of Jean-Francois Cabana
<[email protected]<mailto:[email protected]>>
Date: Friday, July 8, 2016 at 7:03 AM
To: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: [HCP-Users] Mapping volumetric maps on brain surfaces
Dear HCP community,
I am using the HCP pipelines to process our data, which include a 1mm isotropic
T1w, T2w and multiparametric, and a 2mm isotropic DWI sequences. I have
modified the diffusion pipeline script so that the preprocessed DWI is
upsampled to 1mm as it is registered to the native T1w (afterit’s been
processed using the structural pipeline).
I am using the DWI to compute several parameters maps, from NODDI and DKI. What
I want to do is map these parameters on the brain surfaces (pial,
mid-thickness, inflated, ...), much like what is done with the myelin maps in
the PostFreeSurfer pipeline. The goal is to compute individuals maps and also
group average maps and compare between groups. I have no idea how to do that. I
looked at the CreateMyelinMaps.sh script but it does not provides much
comments/explanation, so I have no idea exactly what it is doing.
I will have several maps to transfer on the brain sufaces like this, as we will
also compute quantitative T1, T2* and susceptibility maps in addition to NODDI
and DKI maps. What I want is build a script that takes as argument a subject
name (assuming file names and directories conventions from the structural
preprocessing pipeline) and a path to a parametric volume map, that will
perform the surface mapping and add the results to a the subject’s spec file.
Surely I am not the first one to do that and a script like that must exists
somewhere.
If anyone could provide me with an example script (with comments so I know what
it is doing) that I could adapt, or direct me to a tutorial that explains how
to do that, that would be of great help!
Many thanks in advance,
JF
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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.
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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
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