Re: [HCP-Users] A few specific questions about the HCP data | MNI space dedrifting & file structure
Do not multiply any warpfield by anything, that is not a meaningful operation. Concatenation of warpfields is a special operation, use convertwarp to do this (this is why it has --warp1 and --warp2 options). Be aware that if you have any changes in volume dimension or origin, you will have to be very careful about which volume you use as the reference space for each step (including inversion), because FSL's spatial transform code doesn't use the full nifti header correctly. Yes, concatenating the group drift removal warp onto each subject's acpc to MNI warp will give you the acpc to dedrifted warp for each subject. You can also apply it to any MNI space data to get the version in dedrifted space. The "carefully" in my comment about measuring brain volume is about the fact that you are resampling a binary mask, where if you did trilinear interpolation (the default in some tools) and then fed it into a tool that treats the now-nonbinary volume as if it is supposed to be a binary mask, that could result in something similar to a dilation of the original mask. Personally, I would probably use trilinear interpolation (not cubic, we don't have continuous features to preserve) and then making sure that the result was treated as a weighting volume, not a binary mask. wb_command -volume-weighted-stats will use the voxel volume as the weights by default, and the input is never specially treated as a binary mask, so it would be a good way to calculate the brain volume. What you would be looking for is, if you take the average of the brain volumes across subjects as measured in acpc space, and compared it to the average across subjects of those same "masks" after resampling them to the dedrifted space, the dedrifted space should have only slightly less average volume (~1%? purely guessing here). If it is a large change in average volume, either the acpc alignments weren't as good as you thought, or something else has gone wrong. Back to your original question: your tractography data is already in subject acpc space, yes? If you want to measure something about the tractography data in an anatomically-correct manner, the most obvious thing to me is to measure it in each subject's acpc space, and then average or look at the distributions of these numbers afterwards. Of course, if you plan on doing patients vs controls or some other condition-related test, you may need to control for overall brain size, in which case a dedrifted registered space could be a good idea (or maybe you could use the acpc space measures with a nuisance regressor based on brain size instead, paying attention to the nonlinear relationship between volume, area, and length). Tim On Wed, Jul 11, 2018 at 12:50 PM, Bajada, Claude Julien < c.baj...@fz-juelich.de> wrote: > Hi Tim, > > I am trying to follow the drifting procedure below. Can I clarify a few > points? > > You state: > "Once you have this average, you can invert it (like any other warpfield), > and then concatenate it after the acpc to MNI warp for each subject, giving > you a new dedrifted (for the chosen population) template space." > > From this I understand that the multiplication and inversion gives us a > warp field that warps the MNI registered subject to the new "drifted" > space, correct? > > By "concatenate it after the acpc to MNI warp" do you mean multiply the > acpc2mni warp by the new mni2dedrift? Thus generating an acpc2dedrift? > > Second, you state: "By carefully finding the volume of brain masks in acpc > space and after resampling to this new dedrifted space, you can check for > this effect" > > What exactly am I meant to be checking? I should compare the volume of the > mask in acpc (native) space and in the drifted space. Should they be > roughly the same volume? Also you say that I should "carefully find the > volume" what exactly do you mean by "carefully" > > Thanks in advance, > > Claude > > ____ > From: Timothy Coalson [tsc...@mst.edu] > Sent: 02 July 2018 19:28 > To: Glasser, Matthew > Cc: Harms, Michael; Bajada, Claude Julien; hcp-users@humanconnectome.org > Subject: Re: [HCP-Users] A few specific questions about the HCP data | MNI > space dedrifting & file structure > > We previously looked at the MNI drift, and found that it is almost > entirely an affine, even for the nonlinear template. We have a suspicion > that this means that it was originally caused by the early MNI linear > template, and that the issue was known by the time MNI nonlinear templates > were released, as it implies that the nonlinear template was dedrifted, but > then an affine was deliberately added in order to match the previous MNI > linear template. However, we have not investigated whether this was the > ca
Re: [HCP-Users] A few specific questions about the HCP data | MNI space dedrifting & file structure
Hi Tim,
I am trying to follow the drifting procedure below. Can I clarify a few points?
You state:
"Once you have this average, you can invert it (like any other warpfield), and
then concatenate it after the acpc to MNI warp for each subject, giving you a
new dedrifted (for the chosen population) template space."
>From this I understand that the multiplication and inversion gives us a warp
>field that warps the MNI registered subject to the new "drifted" space,
>correct?
By "concatenate it after the acpc to MNI warp" do you mean multiply the
acpc2mni warp by the new mni2dedrift? Thus generating an acpc2dedrift?
Second, you state: "By carefully finding the volume of brain masks in acpc
space and after resampling to this new dedrifted space, you can check for this
effect"
What exactly am I meant to be checking? I should compare the volume of the mask
in acpc (native) space and in the drifted space. Should they be roughly the
same volume? Also you say that I should "carefully find the volume" what
exactly do you mean by "carefully"
Thanks in advance,
Claude
From: Timothy Coalson [tsc...@mst.edu]
Sent: 02 July 2018 19:28
To: Glasser, Matthew
Cc: Harms, Michael; Bajada, Claude Julien; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] A few specific questions about the HCP data | MNI
space dedrifting & file structure
We previously looked at the MNI drift, and found that it is almost entirely an
affine, even for the nonlinear template. We have a suspicion that this means
that it was originally caused by the early MNI linear template, and that the
issue was known by the time MNI nonlinear templates were released, as it
implies that the nonlinear template was dedrifted, but then an affine was
deliberately added in order to match the previous MNI linear template.
However, we have not investigated whether this was the case.
Since all of our anatomical size and shape measurements are computed using a
rigid acpc space (after gradient distortion correction), this drift in MNI
space is largely unimportant to many steps of analysis of things like fMRI. Be
aware that even with proper dedrifting, any non-rigid volume registration will
hide differences in brain size (and shape if nonlinear) across subjects, by
design, so non-rigid volume-registered data won't ever tell you the whole story
of the anatomical features. If you want to make some anatomical measurement
(distance, area, volume), then you should generally measure it in each
individual's own rigid/acpc space, not in any kind of template space.
Now, on to the explanation: the registration warpfields from each subject's
rigid acpc ("T1w") space to MNI nonlinear space provide the information needed
to compute a dedrifted template that matches the population represented by the
subjects. Warpfields are displacement vector fields from the output coordinate
system to the input coordinate system (because of how volume resampling works -
the output needs to be a regular grid, so you actually need to transform output
coordinates backwards to the original location). So, we can take the vector
fields for each subjects that specify where the MNI-aligned features originally
were in acpc space, and average those locations for each voxel. This is simply
averaging the warpfields that are used to resample volume data from T1w/acpc
space to MNI space. Once you have this average, you can invert it (like any
other warpfield), and then concatenate it after the acpc to MNI warp for each
subject, giving you a new dedrifted (for the ch
osen population) template space.
Note, however, that this requires the acpc alignment to have worked well (in
the HCP pipelines, it is really a rigid registration to an MNI template, not
specifically using the ac and pc) - if there are any non-matching rotations
among the rigidly aligned volumes, they can result in causing a shrinkage from
the true average brain volume. By carefully finding the volume of brain masks
in acpc space and after resampling to this new dedrifted space, you can check
for this effect (it will never be an expansion). However, the effect may not
be isotropic, so actually fixing the effect properly requires more thought.
However, if the acpc alignments are generally close to being the correct
orientation, this effect should be small.
Note, in particular, that coordinates in this new space will not match MNI
coordinates, probably not even at (0, 0, 0), you would need to put any
coordinates through that same average warpfield in order to go between MNI and
this new space. You could also tweak the new space by adding a rigid affine to
the end, so you could line up (0, 0, 0) with MNI space, or similar.
Tim
On Mon, Jul 2, 2018 at 10:21 AM, Glasser, Matthew
mailto:glass...@wustl.edu>> wrote:
Tim Coalson can explain how to dedrift
Re: [HCP-Users] A few specific questions about the HCP data | MNI space dedrifting & file structure
Hi Tim,
Thank you very much for your detailed explanation
Regards,
Claude
On it-Tnejn, 02 ta Lul, 2018 07:35 , Timothy Coalson wrote:
On Mon, Jul 2, 2018 at 7:13 AM, Claude Bajada
mailto:c.baj...@fz-juelich.de>> wrote:
2) from what I understand, structural qualities such as cortical
thickness etc are measured in the individual's real space. However then,
what I do not understand is the file structure of the HCP data. The
structural measures such as cortical thickness, curvature and myelin
maps etc live in the MNINonLinear/fsaverage_LR32k rather than in the
'native space' directory. Can anyone shed light on this?
It was perhaps not the best choice to put these measures inside the MNINonLinear folder, but for
compatibility, that is where they will remain for now. They were computed in "T1w" space
("native volume space", not to be confused with "native mesh", which is an unrelated
distinction).
However, the myelin measure is based on a combination of imaging contrasts, and
is not sensitive to changes in brain size, so it doesn't quite fit in the same
class as curvature and thickness, which are measures of the cortical
coordinates themselves.
Tim
Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] A few specific questions about the HCP data | MNI space dedrifting & file structure
On Mon, Jul 2, 2018 at 12:26 PM, Bajada, Claude Julien < c.baj...@fz-juelich.de> wrote: > Thanks Matt and Mike, I'll await to hear from Tim re: his thoughts on > drifting. > > Mike, thanks for confirming that all structural quantities are measured in > real (native) space. Just a quick follow-up question / comment to ensure my > understanding. Am I correct in assuming that the quantities have been > resampled to the MSMALL 32K mesh, it is then just a matter of visualising > them on the same mesh that has been warped to either native space or MNI > space. Is there aren't trip different cortical thickness ciftis one for MNI > space and the other for native. Have I understood correctly? > Correct, the volume space of the surface used is independent of the surface registration used. Surface-based resampling is only required to go between different surface registrations or resolutions, while a change in volume registration merely requires the use of a different surface (where all the vertices have been moved according to the relevant warpfield). The cifti files containing measures based on surface coordinates (sulc, curvature, thickness, etc) do not contain subcortical (voxel-based) data, and cifti files in general do not contain surface coordinates. So, yes, there is only one cifti file containing cortical thickness, and it can be displayed on/used with MNI, T1w, or any other type of surfaces, as long as they have the correct mesh (number of vertices and how they are connected) and surface registration. > Regards, > Claude > > > From: Glasser, Matthew [glass...@wustl.edu] > Sent: 02 July 2018 17:21 > To: Harms, Michael; Bajada, Claude Julien; hcp-users@humanconnectome.org > Subject: Re: [HCP-Users] A few specific questions about the HCP data | MNI > space dedrifting & file structure > > Tim Coalson can explain how to dedrift MNI space (which as Mike says is no > longer true MNI space). > > Peace, > > Matt. > > On 7/2/18, 10:10 AM, "hcp-users-boun...@humanconnectome.org on behalf of > Harms, Michael" mha...@wustl.edu> wrote: > > > > >Hi, > >Re (1): > >If you want to work with streamlines in MNI space then you have to accept > >the "drift" (volume expansion) that is part of MNI space itself. > > > >Re (2): > >Maps may be resampled to surfaces in MNI space. But all the FreeSurfer > >structural quantities that we provide in the database/spreadsheet in > >ConnectomeDB are measured in the subject's real (native) space. > > > >Cheers, > >-MH > > > >-- > >Michael Harms, Ph.D. > > > >--- > > > >Associate Professor of Psychiatry > > > >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 > >On 7/2/18, 7:14 AM, "hcp-users-boun...@humanconnectome.org on behalf of > >Claude Bajada" >c.baj...@fz-juelich.de> wrote: > > > >Dear experts, > > > >I have a few questions: > > > >1) I am currently working on a project using tractography and the HCP > >data. I have used the HCP provided FNIRT based MNI registration in order > >to register individual streamlines from "native" or diffusion space (as > >per post HCP minimal processing pipeline) to MNI space. However, in > >Glasser 2016 supplementary text, it states that the MNI space is drifted > >relative to the mean brain size of individual brains (greatest along the > >x and z axes). I've been told that it is possible to "dedrift" these > >data and I wonder if anyone has experience in doing this and is able to > >point me in the right direction. > > > >2) from what I understand, structural qualities such as cortical > >thickness etc are measured in the individual's real space. However then, > >what I do not understand is the file structure of the HCP data. The > >structural measures such as cortical thickness, curvature and myelin > >maps etc live in the MNINonLinear/fsaverage_LR32k rather than in the > >'native space' directory. Can anyone shed light on this? > > > >Regards, > > > >Claude > > > > > > > >--- > --- > >--
Re: [HCP-Users] A few specific questions about the HCP data | MNI space dedrifting & file structure
On Mon, Jul 2, 2018 at 7:13 AM, Claude Bajada
wrote:
>
> 2) from what I understand, structural qualities such as cortical
> thickness etc are measured in the individual's real space. However then,
> what I do not understand is the file structure of the HCP data. The
> structural measures such as cortical thickness, curvature and myelin
> maps etc live in the MNINonLinear/fsaverage_LR32k rather than in the
> 'native space' directory. Can anyone shed light on this?
>
> It was perhaps not the best choice to put these measures inside the
MNINonLinear folder, but for compatibility, that is where they will remain
for now. They were computed in "T1w" space ("native volume space", not to
be confused with "native mesh", which is an unrelated distinction).
However, the myelin measure is based on a combination of imaging contrasts,
and is not sensitive to changes in brain size, so it doesn't quite fit in
the same class as curvature and thickness, which are measures of the
cortical coordinates themselves.
Tim
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] A few specific questions about the HCP data | MNI space dedrifting & file structure
We previously looked at the MNI drift, and found that it is almost entirely
an affine, even for the nonlinear template. We have a suspicion that this
means that it was originally caused by the early MNI linear template, and
that the issue was known by the time MNI nonlinear templates were released,
as it implies that the nonlinear template was dedrifted, but then an affine
was deliberately added in order to match the previous MNI linear template.
However, we have not investigated whether this was the case.
Since all of our anatomical size and shape measurements are computed using
a rigid acpc space (after gradient distortion correction), this drift in
MNI space is largely unimportant to many steps of analysis of things like
fMRI. Be aware that even with proper dedrifting, any non-rigid volume
registration will hide differences in brain size (and shape if nonlinear)
across subjects, by design, so non-rigid volume-registered data won't ever
tell you the whole story of the anatomical features. If you want to make
some anatomical measurement (distance, area, volume), then you should
generally measure it in each individual's own rigid/acpc space, not in any
kind of template space.
Now, on to the explanation: the registration warpfields from each subject's
rigid acpc ("T1w") space to MNI nonlinear space provide the information
needed to compute a dedrifted template that matches the population
represented by the subjects. Warpfields are displacement vector fields
from the output coordinate system to the input coordinate system (because
of how volume resampling works - the output needs to be a regular grid, so
you actually need to transform output coordinates backwards to the original
location). So, we can take the vector fields for each subjects that
specify where the MNI-aligned features originally were in acpc space, and
average those locations for each voxel. This is simply averaging the
warpfields that are used to resample volume data from T1w/acpc space to MNI
space. Once you have this average, you can invert it (like any other
warpfield), and then concatenate it after the acpc to MNI warp for each
subject, giving you a new dedrifted (for the chosen population) template
space.
Note, however, that this requires the acpc alignment to have worked well
(in the HCP pipelines, it is really a rigid registration to an MNI
template, not specifically using the ac and pc) - if there are any
non-matching rotations among the rigidly aligned volumes, they can result
in causing a shrinkage from the true average brain volume. By carefully
finding the volume of brain masks in acpc space and after resampling to
this new dedrifted space, you can check for this effect (it will never be
an expansion). However, the effect may not be isotropic, so actually
fixing the effect properly requires more thought. However, if the acpc
alignments are generally close to being the correct orientation, this
effect should be small.
Note, in particular, that coordinates in this new space will not match MNI
coordinates, probably not even at (0, 0, 0), you would need to put any
coordinates through that same average warpfield in order to go between MNI
and this new space. You could also tweak the new space by adding a rigid
affine to the end, so you could line up (0, 0, 0) with MNI space, or
similar.
Tim
On Mon, Jul 2, 2018 at 10:21 AM, Glasser, Matthew
wrote:
> Tim Coalson can explain how to dedrift MNI space (which as Mike says is no
> longer true MNI space).
>
> Peace,
>
> Matt.
>
> On 7/2/18, 10:10 AM, "hcp-users-boun...@humanconnectome.org on behalf of
> Harms, Michael" mha...@wustl.edu> wrote:
>
> >
> >Hi,
> >Re (1):
> >If you want to work with streamlines in MNI space then you have to accept
> >the "drift" (volume expansion) that is part of MNI space itself.
> >
> >Re (2):
> >Maps may be resampled to surfaces in MNI space. But all the FreeSurfer
> >structural quantities that we provide in the database/spreadsheet in
> >ConnectomeDB are measured in the subject's real (native) space.
> >
> >Cheers,
> >-MH
> >
> >--
> >Michael Harms, Ph.D.
> >
> >---
> >
> >Associate Professor of Psychiatry
> >
> >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
> >On 7/2/18, 7:14 AM, "hcp-users-boun...@humanconnectome.org on behalf of
> >Claude Bajada" >c.baj...@fz-juelich.de> wrote:
> >
> >Dear experts,
> >
> >I have a few questions:
> >
> >1) I am currently working on a project using tractography and the HCP
> >data. I have used the HCP provided FNIRT based MNI registration in order
> >to register individual streamlines from "native" or diffusion space (as
> >per post HCP minimal processing pipeline) to MNI space. However, in
> >Glasser 2016 supplementary text, it states that the MNI space is drifted
>
Re: [HCP-Users] A few specific questions about the HCP data | MNI space dedrifting & file structure
Thanks Matt and Mike, I'll await to hear from Tim re: his thoughts on drifting. Mike, thanks for confirming that all structural quantities are measured in real (native) space. Just a quick follow-up question / comment to ensure my understanding. Am I correct in assuming that the quantities have been resampled to the MSMALL 32K mesh, it is then just a matter of visualising them on the same mesh that has been warped to either native space or MNI space. Is there aren't trip different cortical thickness ciftis one for MNI space and the other for native. Have I understood correctly? Regards, Claude From: Glasser, Matthew [glass...@wustl.edu] Sent: 02 July 2018 17:21 To: Harms, Michael; Bajada, Claude Julien; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] A few specific questions about the HCP data | MNI space dedrifting & file structure Tim Coalson can explain how to dedrift MNI space (which as Mike says is no longer true MNI space). Peace, Matt. On 7/2/18, 10:10 AM, "hcp-users-boun...@humanconnectome.org on behalf of Harms, Michael" wrote: > >Hi, >Re (1): >If you want to work with streamlines in MNI space then you have to accept >the "drift" (volume expansion) that is part of MNI space itself. > >Re (2): >Maps may be resampled to surfaces in MNI space. But all the FreeSurfer >structural quantities that we provide in the database/spreadsheet in >ConnectomeDB are measured in the subject's real (native) space. > >Cheers, >-MH > >-- >Michael Harms, Ph.D. > >--- > >Associate Professor of Psychiatry > >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 >On 7/2/18, 7:14 AM, "hcp-users-boun...@humanconnectome.org on behalf of >Claude Bajada" c.baj...@fz-juelich.de> wrote: > >Dear experts, > >I have a few questions: > >1) I am currently working on a project using tractography and the HCP >data. I have used the HCP provided FNIRT based MNI registration in order >to register individual streamlines from "native" or diffusion space (as >per post HCP minimal processing pipeline) to MNI space. However, in >Glasser 2016 supplementary text, it states that the MNI space is drifted >relative to the mean brain size of individual brains (greatest along the >x and z axes). I've been told that it is possible to "dedrift" these >data and I wonder if anyone has experience in doing this and is able to >point me in the right direction. > >2) from what I understand, structural qualities such as cortical >thickness etc are measured in the individual's real space. However then, >what I do not understand is the file structure of the HCP data. The >structural measures such as cortical thickness, curvature and myelin >maps etc live in the MNINonLinear/fsaverage_LR32k rather than in the >'native space' directory. Can anyone shed light on this? > >Regards, > >Claude > > > >-- >-- >-- >-- >Forschungszentrum Juelich GmbH >52425 Juelich >Sitz der Gesellschaft: Juelich >Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 >Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher >Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), >Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, >Prof. Dr. Sebastian M. Schmidt >-- >-- >-- >-- > > >___ >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 mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] A few specific questions about the HCP data | MNI space dedrifting & file structure
Tim Coalson can explain how to dedrift MNI space (which as Mike says is no longer true MNI space). Peace, Matt. On 7/2/18, 10:10 AM, "hcp-users-boun...@humanconnectome.org on behalf of Harms, Michael" wrote: > >Hi, >Re (1): >If you want to work with streamlines in MNI space then you have to accept >the "drift" (volume expansion) that is part of MNI space itself. > >Re (2): >Maps may be resampled to surfaces in MNI space. But all the FreeSurfer >structural quantities that we provide in the database/spreadsheet in >ConnectomeDB are measured in the subject's real (native) space. > >Cheers, >-MH > >-- >Michael Harms, Ph.D. > >--- > >Associate Professor of Psychiatry > >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 >On 7/2/18, 7:14 AM, "hcp-users-boun...@humanconnectome.org on behalf of >Claude Bajada" c.baj...@fz-juelich.de> wrote: > >Dear experts, > >I have a few questions: > >1) I am currently working on a project using tractography and the HCP >data. I have used the HCP provided FNIRT based MNI registration in order >to register individual streamlines from "native" or diffusion space (as >per post HCP minimal processing pipeline) to MNI space. However, in >Glasser 2016 supplementary text, it states that the MNI space is drifted >relative to the mean brain size of individual brains (greatest along the >x and z axes). I've been told that it is possible to "dedrift" these >data and I wonder if anyone has experience in doing this and is able to >point me in the right direction. > >2) from what I understand, structural qualities such as cortical >thickness etc are measured in the individual's real space. However then, >what I do not understand is the file structure of the HCP data. The >structural measures such as cortical thickness, curvature and myelin >maps etc live in the MNINonLinear/fsaverage_LR32k rather than in the >'native space' directory. Can anyone shed light on this? > >Regards, > >Claude > > > >-- >-- >-- >-- >Forschungszentrum Juelich GmbH >52425 Juelich >Sitz der Gesellschaft: Juelich >Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 >Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher >Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), >Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, >Prof. Dr. Sebastian M. Schmidt >-- >-- >-- >-- > > >___ >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 mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] A few specific questions about the HCP data | MNI space dedrifting & file structure
Hi, Re (1): If you want to work with streamlines in MNI space then you have to accept the "drift" (volume expansion) that is part of MNI space itself. Re (2): Maps may be resampled to surfaces in MNI space. But all the FreeSurfer structural quantities that we provide in the database/spreadsheet in ConnectomeDB are measured in the subject's real (native) space. Cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry 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 On 7/2/18, 7:14 AM, "hcp-users-boun...@humanconnectome.org on behalf of Claude Bajada" wrote: Dear experts, I have a few questions: 1) I am currently working on a project using tractography and the HCP data. I have used the HCP provided FNIRT based MNI registration in order to register individual streamlines from "native" or diffusion space (as per post HCP minimal processing pipeline) to MNI space. However, in Glasser 2016 supplementary text, it states that the MNI space is drifted relative to the mean brain size of individual brains (greatest along the x and z axes). I've been told that it is possible to "dedrift" these data and I wonder if anyone has experience in doing this and is able to point me in the right direction. 2) from what I understand, structural qualities such as cortical thickness etc are measured in the individual's real space. However then, what I do not understand is the file structure of the HCP data. The structural measures such as cortical thickness, curvature and myelin maps etc live in the MNINonLinear/fsaverage_LR32k rather than in the 'native space' directory. Can anyone shed light on this? Regards, Claude Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ___ 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
