Re: [HCP-Users] Myelin Mapping

[Seán Froudist Walsh]

after the talk?

On 20 February 2015 at 13:42, Glasser, Matthew glass...@wusm.wustl.edu
wrote:

  If I recall correctly, they withdrew their SFN 2014 presentation.  I
 don’t know the reason for that.

  Peace,

  Matt.

   From: Seán Froudist Walsh froud...@tcd.ie
 Date: Friday, February 20, 2015 at 7:27 AM
 To: Matt Glasser glass...@wusm.wustl.edu
 Cc: Barbara Kreilkamp bakk@googlemail.com, 
 hcp-users@humanconnectome.org hcp-users@humanconnectome.org
 Subject: Re: [HCP-Users] Myelin Mapping

   I wonder if you have an opinion on the talk by Stefano Sandrone from
 Marco Catani's group at OHBM 2014 that showed that this measure doesn't
 correlate with expected myelin patterns in white matter?

 On 20 February 2015 at 13:08, Glasser, Matthew glass...@wusm.wustl.edu
 wrote:

  Please use the HCP Minimal Preprocessing Pipelines to create T1w/T2w
 myelin maps with the latest code/methods (including bias correction and
 normalization):

  https://github.com/Washington-University/Pipelines

  You will need a T1w and a T2w images acquired in the same scanning
 session with the same image intensity filters (e.g. pre scan normalize or
 not) applied to both.  For myelin mapping only, a field map is optional
 (but recommended).

  Peace,

  Matt.

   From: Barbara Kreilkamp bakk@googlemail.com
 Date: Friday, February 20, 2015 at 7:04 AM
 To: hcp-users@humanconnectome.org hcp-users@humanconnectome.org
 Subject: [HCP-Users] Myelin Mapping

   Dear HCP- users,

 Could you please point me to a tutorial for myelin mapping with Human
 Connectome Workbench software?
 Also, is there a way to implement bias-correction for this technique?
 Thank you very much,
 Best wishes,
 Barbara

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[HCP-Users] Custom visualisation help

[Seán Froudist Walsh]

Hey all,

I'm trying to get a colour display on a surface to match a colormap I have
set up in matlab, and have run into a whole world of pain. I would greatly
appreciate your help.

I have created a label text file of the following format:

TCpol_R
12552082081
TCs_R
22551581581
Amyg_R
325581811
PFCoi_R
42552312311

I additionally have a nifti file, and a func.gii surface file (created with
wb_command -volume-to-surface-mapping )

Ideally I would like to display those colours on the surface, in the
correct clusters.

I thought I would try to display them on a volume as a first step, but that
hasn't gone smoothly either.
I used a command of the following format:
wb_command -cifti-label-import my_atlas.nii.gz my_label_table.txt
my_label_volume.nii.gz

Then I tried to display the label file over the volume in wb_view to no
avail (I only see the underlying anatomical volume). Despite this, if I go
to
Overlay Tools --> Settings --> Edit Map's Labels
I can see all of the labels I wanted listed, next to the correct colours.

I would greatly appreciate if you could help fill in the gaps in my
knowledge so that I can display my custom coloured labels on the surface.

Many thanks,

Sean

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Re: [HCP-Users] Custom visualisation help

[Seán Froudist Walsh]

Sorry, made a mistake in my e-mail. I tried wb_command -volume-label-import
and got the results explained previously. Any ideas?

Thanks,

Sean

On 20 June 2017 at 20:08, Glasser, Matthew <glass...@wustl.edu> wrote:

> I think you want wb_command -volume-label-import.
>
> Peace,
>
> Matt.
>
> From: <hcp-users-boun...@humanconnectome.org> on behalf of Seán Froudist
> Walsh <froud...@tcd.ie>
> Date: Tuesday, June 20, 2017 at 7:04 PM
> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
> Subject: [HCP-Users] Custom visualisation help
>
> Hey all,
>
> I'm trying to get a colour display on a surface to match a colormap I have
> set up in matlab, and have run into a whole world of pain. I would greatly
> appreciate your help.
>
> I have created a label text file of the following format:
>
> TCpol_R
> 12552082081
> TCs_R
> 22551581581
> Amyg_R
> 325581811
> PFCoi_R
> 42552312311
>
> I additionally have a nifti file, and a func.gii surface file (created
> with wb_command -volume-to-surface-mapping )
>
> Ideally I would like to display those colours on the surface, in the
> correct clusters.
>
> I thought I would try to display them on a volume as a first step, but
> that hasn't gone smoothly either.
> I used a command of the following format:
> wb_command -cifti-label-import my_atlas.nii.gz my_label_table.txt
> my_label_volume.nii.gz
>
> Then I tried to display the label file over the volume in wb_view to no
> avail (I only see the underlying anatomical volume). Despite this, if I go
> to
> Overlay Tools --> Settings --> Edit Map's Labels
> I can see all of the labels I wanted listed, next to the correct colours.
>
> I would greatly appreciate if you could help fill in the gaps in my
> knowledge so that I can display my custom coloured labels on the surface.
>
> Many thanks,
>
> Sean
>
> ___
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> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>

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Re: [HCP-Users] Custom visualisation help

[Seán Froudist Walsh]

Thanks a lot for the suggestion Timothy. Unfortunately I'm still getting a
colourless map. I did get the result I wanted using the matlab gifti
toolbox ( http://www.artefact.tk/software/matlab/gifti/ ), so no rush.

Perhaps I'm saving under the wrong name, or doing something wrong when
trying to visualise? Here's the actual command I'm using.

wb_command -volume-label-import sequential_region_map_no_hipp.nii.gz
hipp_pre_color_palette_table.txt sequential_region_map_no_hipp_
hcp_label.nii.gz

Then when I'm trying to visualise it, I'm just loading it in and trying to
display over the atlas I'm using.

Not sure if there's more info I can give.

Thanks again for the help.

Best wishes,

Sean


On 21 June 2017 at 11:42, Timothy Coalson <tsc...@mst.edu> wrote:

> The fourth "color" specifier in your text file should be 255, not 1.
>
> Tim
>
>
> On Wed, Jun 21, 2017 at 8:34 AM, Seán Froudist Walsh <froud...@tcd.ie>
> wrote:
>
>> Sorry, made a mistake in my e-mail. I tried wb_command
>> -volume-label-import and got the results explained previously. Any ideas?
>>
>> Thanks,
>>
>> Sean
>>
>> On 20 June 2017 at 20:08, Glasser, Matthew <glass...@wustl.edu> wrote:
>>
>>> I think you want wb_command -volume-label-import.
>>>
>>> Peace,
>>>
>>> Matt.
>>>
>>> From: <hcp-users-boun...@humanconnectome.org> on behalf of Seán
>>> Froudist Walsh <froud...@tcd.ie>
>>> Date: Tuesday, June 20, 2017 at 7:04 PM
>>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>>> Subject: [HCP-Users] Custom visualisation help
>>>
>>> Hey all,
>>>
>>> I'm trying to get a colour display on a surface to match a colormap I
>>> have set up in matlab, and have run into a whole world of pain. I would
>>> greatly appreciate your help.
>>>
>>> I have created a label text file of the following format:
>>>
>>> TCpol_R
>>> 12552082081
>>> TCs_R
>>> 22551581581
>>> Amyg_R
>>> 325581811
>>> PFCoi_R
>>> 42552312311
>>>
>>> I additionally have a nifti file, and a func.gii surface file (created
>>> with wb_command -volume-to-surface-mapping )
>>>
>>> Ideally I would like to display those colours on the surface, in the
>>> correct clusters.
>>>
>>> I thought I would try to display them on a volume as a first step, but
>>> that hasn't gone smoothly either.
>>> I used a command of the following format:
>>> wb_command -cifti-label-import my_atlas.nii.gz my_label_table.txt
>>> my_label_volume.nii.gz
>>>
>>> Then I tried to display the label file over the volume in wb_view to no
>>> avail (I only see the underlying anatomical volume). Despite this, if I go
>>> to
>>> Overlay Tools --> Settings --> Edit Map's Labels
>>> I can see all of the labels I wanted listed, next to the correct
>>> colours.
>>>
>>> I would greatly appreciate if you could help fill in the gaps in my
>>> knowledge so that I can display my custom coloured labels on the surface.
>>>
>>> Many thanks,
>>>
>>> Sean
>>>
>>> ___
>>> HCP-Users mailing list
>>> HCP-Users@humanconnectome.org
>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>
>>
>> ___
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>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>
>
>

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Re: [HCP-Users] surf2surf

[Seán Froudist Walsh]

Hi Tim,

Was there a response to the question about sumsDB requesting login
information? I also ran into that problem a couple of days ago.

Best wishes,

Sean

Sean Froudist-Walsh
Postdoc
New York University

On 16 October 2017 at 16:49, Timothy Coalson  wrote:

> The s...@brainvis.wustl.edu address is still active, but it is a manual
> process.  As David gave you the information, I don't plan on redundantly
> responding to the email to sums@brainvis.
>
> Tim
>
>
> On Mon, Oct 16, 2017 at 11:40 AM, Mars, R.B. (Rogier) <
> r.m...@donders.ru.nl> wrote:
>
>> Hi David,
>>
>> Thank you very much. Could it be that the public  SumsDB also asks for
>> user name and password when you try to download? I’ve written an email to
>> s...@brainvis.wustl.edu for a login, but I’m not sure that’s still
>> active?
>>
>> Thanks, sorry for the bother,
>>
>> Rogier
>> __
>> Rogier B. Mars, PhD
>>
>> Principal Investigator
>> Donders Institute for Brain, Cognition and Behaviour
>> Radboud University Nijmegen
>>
>> Associate Professor
>> Wellcome Centre for Integrative Neuroimaging
>> Centre for Functional MRI of the Brain (FMRIB)
>> Nuffield Department of Clinical Neurosciences
>> John Radcliffe Hospital
>> University of Oxford
>>
>> www.neuroecologylab.org
>> @NeuroecologyLab
>>
>> On 15 Oct 2017, at 18:00, hcp-users-requ...@humanconnectome.org wrote:
>>
>> Send HCP-Users mailing list submissions to
>> hcp-users@humanconnectome.org
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>> or, via email, send a message with subject or body 'help' to
>> hcp-users-requ...@humanconnectome.org
>>
>> You can reach the person managing the list at
>> hcp-users-ow...@humanconnectome.org
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of HCP-Users digest..."
>>
>>
>> Today's Topics:
>>
>>   1. Re: surf2surf (David Van Essen)
>>
>>
>> --
>>
>> Message: 1
>> Date: Sun, 15 Oct 2017 10:24:40 -0500
>> From: David Van Essen 
>> Subject: Re: [HCP-Users] surf2surf
>> To: "Mars, R.B. (Rogier)" 
>> Cc: "hcp-users@humanconnectome.org" 
>> Message-ID: 
>> Content-Type: text/plain; charset="utf-8"
>>
>> Hi Rogier,
>>
>> The files you need are in the SumsDB database, which remains in
>> life-support mode but is still accessible.  Go to
>> http://brainvis.wustl.edu/sumsdb/public_archive_index.html, scroll down
>> to the bottom, and download archive 8293223:
>>
>> 8293223 download > sdb/public/8293223_inter-atlas_deformation_maps.zip> info <
>> http://brainvis.wustl.edu/sumsdb/public/ROOT/public/ATLAS_
>> DATA_SETS/HUMAN/CONTE69/Inter-atlas_deformation_mapsinter-
>> atlas_deformation_maps.zip/8293223_info.html>
>> /ROOT/public/ATLAS_DATA_SETS/HUMAN/CONTE69/Inter-atlas_defor
>> mation_maps/inter-atlas_deformation_maps.zip
>>
>> It includes a readme file that gives instructions on How to convert
>> (register) data between 164k_fs_LR and 74k_pals meshes
>>
>> Good luck! If you encounter difficulties, you know where to ask!
>>
>> David
>>
>> On Oct 12, 2017, at 10:27 AM, Mars, R.B. (Rogier) 
>> wrote:
>>
>> Hello,
>>
>> I?m trying to place the data from a results.func.gii associated with a
>> particular surface (say, OLD.surf.gii, created from OLD_T1w.nii.gz) into
>> the space of another surface (say, NEW.surf.gii, created from
>> NEW_T1w.nii.gz). The surfaces do not necessarily have the number of
>> vertices. Is there an easy way to do this? I seem to be stuck on the
>> surf2surf options.
>>
>> Thanks very much,
>>
>> Rogier
>> __
>> Rogier B. Mars, PhD
>>
>> Principal Investigator
>> Donders Institute for Brain, Cognition and Behaviour
>> Radboud University Nijmegen
>>
>> Associate Professor
>> Wellcome Centre for Integrative Neuroimaging
>> Centre for Functional MRI of the Brain (FMRIB)
>> Nuffield Department of Clinical Neurosciences
>> John Radcliffe Hospital
>> University of Oxford
>>
>> www.neuroecologylab.org 
>> @NeuroecologyLab
>>
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>>
>> -- next part --
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>> URL: http://lists.humanconnectome.org/pipermail/hcp-users/attachm
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>>
>> End of HCP-Users Digest, Vol 59, Issue 23
>> 

Re: [HCP-Users] Dear HCP users,

[Seán Froudist Walsh]

Hi Yassine,

If you're interested in surface visualisation,  Guillaume Flandin's gifti
toolbox for Matlab ( http://www.artefact.tk/software/matlab/gifti/ ) is an
alternative. That way you can create any colour palette you like (or choose
one of Matlab's ready-made options).

Cheers,

Sean


On 18 January 2018 at 15:27, Glasser, Matthew  wrote:

> This is a relatively frequently requested feature that we do intend to add
> at some point, perhaps after the upcoming release.
>
>
> Peace,
>
>
> Matt.
> --
> *From:* hcp-users-boun...@humanconnectome.org  humanconnectome.org> on behalf of Yassine Benhajali 
> *Sent:* Thursday, January 18, 2018 2:24:05 PM
> *To:* hcp-users@humanconnectome.org
> *Subject:* [HCP-Users] Dear HCP users,
>
> Does any one knows how to add a custom colour palette in the connectome
> workbench viewer?
>
> Best,
> Yassine
>
>
> --
> Yassine Benhajali
> Doctorant en Neuroanthropologie
> au Laboratoire SIMEXP - http://www.simexp-lab.org/members/
> Université de Montréal, Québec, Canada
> 514 839 0501
>
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Re: [HCP-Users] volume to average surface with Nearest Neighbour interpolation

[Seán Froudist Walsh]

or, more accurately, I would like to ask if my understanding of the surface
registration, conversions and wb_command steps is correct.

Thanks,

Sean

On 15 January 2018 at 13:43, Seán Froudist Walsh <froud...@tcd.ie> wrote:

> Dear Matt and Tim,
>
> Thanks for your help.
>
> I moved the midthickness-new-out surface from the wb_shortcuts
> -freesurfer-resample-prep command back into the FreeSurfer volume space,
> by converting from RAS to voxel coordinates. This surface seemed to line up
> perfectly with the orig.nii anatomical in conformed FreeSurfer space. When
> I overlay the group average (s1200) myelin map on the midthickness-new-out
> surface it looks like it lines up great with the gyri/sulci.
>
> From this I understand that the surface mesh is overlaid in such a way as
> to impose anatomical correspondence between the native and HCP average
> brains, but the midthickness-new-out surface is still aligned with the
> native (conformed) brain. Is this correct?
>
> I managed to get the Nearest-Neighbour-like mapping I wanted done in
> Matlab. When I display this on the group average surfaces, it also looks
> pretty good. I just want to check that the workbench steps I have taken are
> correct.
>
> Best wishes,
>
> Sean
>
> On 3 January 2018 at 17:19, Timothy Coalson <tsc...@mst.edu> wrote:
>
>> The fs_LR 32k spheres use a resolution (vertex spacing) that is suitable
>> for 2mm fMRI data, but it sounds like you are using structural-resolution
>> voxels.  As Matt says, I would put the fs_LR surface into your volume
>> space, and do only a single mapping, because nearest neighbor or enclosing
>> voxel mapping is extremely lossy - additionally, I would use the 164k
>> spheres instead.
>>
>> Other forms of resampling, meant for continuous data, are not as lossy
>> because they can approximate the underlying function, but "voxel identity"
>> is not a continuous function.  I don't know exactly what you are doing, but
>> I would suggest mapping the data that *is* continuous onto fs_LR registered
>> surfaces, and then re-posing your "element identity" as vertex indices,
>> rather than T1w voxels.  If this doesn't let you do what you want, then
>> maybe you can do per-subject independent volume analysis, and then map the
>> results of that onto the individual's surface before combining across
>> subjects?
>>
>> If you want to explain your bigger-picture goal, we might have other
>> useful suggestions.
>>
>> Tim
>>
>>
>> On Wed, Jan 3, 2018 at 11:58 AM, Glasser, Matthew <glass...@wustl.edu>
>> wrote:
>>
>>> I think I would probably resample the subject’s own FS_LR registered
>>> surfaces into the FreeSurfer space (an exact transformation) and then do a
>>> single mapping from volume to surface.  You would need to figure out the
>>> affine matrix that describes this transform.
>>>
>>> Peace,
>>>
>>> Matt.
>>>
>>> From: <hcp-users-boun...@humanconnectome.org> on behalf of Seán
>>> Froudist Walsh <froud...@tcd.ie>
>>> Date: Wednesday, January 3, 2018 at 10:29 AM
>>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>>> Subject: [HCP-Users] volume to average surface with Nearest Neighbour
>>> interpolation
>>>
>>> Dear HCP experts,
>>>
>>> I am interested in mapping individual voxels in a subject's FreeSurfer
>>> conformed space (orig.nii) onto the HCP template (fsaverage_LR) while
>>> maintaining the original voxel values.
>>>
>>> All of the voxels lie within the LH cortical ribbon in the (conformed)
>>> volume space. There are 186 voxels with non-zero values that act as unique
>>> identifiers, with all other voxels having a value of zero.
>>>
>>> I have prepared the native FreeSurfer to HCP transformations, then
>>> performed volume-to-surface mapping of the sample data, and finally applied
>>> the FreeSurfer-to-HCP transform to the sample data. I have tried to
>>> identify the options that perform something like Nearest Neighbour
>>> assignment, as I need to maintain the original values as identifiers. The
>>> problem I am facing is that volume-to-surface mapping as done below reduces
>>> the number of non-zero voxels/vertices from 186 to 94, and the
>>> Freesufer-to-HCP resampling reduces the number of non-zero vertices further
>>> from 94 to 13 non-zero points.
>>>
>>> I would greatly appreciate your guidance as to the best way to achieve
>>> my desired goal 

Re: [HCP-Users] volume to average surface with Nearest Neighbour interpolation

[Seán Froudist Walsh]

Perfect, thank you

On 17 January 2018 at 18:52, Timothy Coalson <tsc...@mst.edu> wrote:

> Inline comments.
>
> Tim
>
> On Mon, Jan 15, 2018 at 12:43 PM, Seán Froudist Walsh <froud...@tcd.ie>
> wrote:
>
>> Dear Matt and Tim,
>>
>> Thanks for your help.
>>
>> I moved the midthickness-new-out surface from the wb_shortcuts
>> -freesurfer-resample-prep command back into the FreeSurfer volume space,
>> by converting from RAS to voxel coordinates. This surface seemed to line up
>> perfectly with the orig.nii anatomical in conformed FreeSurfer space. When
>> I overlay the group average (s1200) myelin map on the midthickness-new-out
>> surface it looks like it lines up great with the gyri/sulci.
>>
>> From this I understand that the surface mesh is overlaid in such a way as
>> to impose anatomical correspondence between the native and HCP average
>> brains, but the midthickness-new-out surface is still aligned with the
>> native (conformed) brain. Is this correct?
>>
>
> You are close, and the issue might only be terminology, and Matt mostly
> covered it.  Surface registration doesn't change the shape of the brain,
> but group averaging surfaces does change the shape - group average surfaces
> don't look like a normal brain, they are much smoother.  I wouldn't call it
> "anatomical correspondence" between the HCP average surface and the
> subject, because to me that implies that the coordinates of the surfaces
> line up (which they won't).  The thing that is usually most important is
> what registration was used to generate the registered sphere - in this
> case, it sounds like you used the freesurfer-generated registered sphere,
> so your registration type is freesurfer.  This determines what kind of
> correspondence you have across subjects processed the same way (for group
> analysis).
>
> Both midthickness-current-out and midthickness-new-out will align with the
> same volume files, the only difference between them is in how they fit
> triangles to the contour of the surface (how many triangles, how they are
> numbered, how much they vary in size...).  Specifically,
> midthickness-new-out will have the same number of triangles, with each
> triangle in a corresponding location, across all subjects you do this
> procedure with, so you can therefore combine vertexwise data across such
> subjects.  Additionally, because you used our atlas resampling from
> freesurfer to fs_LR, you are now set up to compare across hemispheres, or
> to HCP data, without much additional effort.
>
>
>> I managed to get the Nearest-Neighbour-like mapping I wanted done in
>> Matlab. When I display this on the group average surfaces, it also looks
>> pretty good. I just want to check that the workbench steps I have taken are
>> correct.
>>
>> Best wishes,
>>
>> Sean
>>
>> On 3 January 2018 at 17:19, Timothy Coalson <tsc...@mst.edu> wrote:
>>
>>> The fs_LR 32k spheres use a resolution (vertex spacing) that is suitable
>>> for 2mm fMRI data, but it sounds like you are using structural-resolution
>>> voxels.  As Matt says, I would put the fs_LR surface into your volume
>>> space, and do only a single mapping, because nearest neighbor or enclosing
>>> voxel mapping is extremely lossy - additionally, I would use the 164k
>>> spheres instead.
>>>
>>> Other forms of resampling, meant for continuous data, are not as lossy
>>> because they can approximate the underlying function, but "voxel identity"
>>> is not a continuous function.  I don't know exactly what you are doing, but
>>> I would suggest mapping the data that *is* continuous onto fs_LR registered
>>> surfaces, and then re-posing your "element identity" as vertex indices,
>>> rather than T1w voxels.  If this doesn't let you do what you want, then
>>> maybe you can do per-subject independent volume analysis, and then map the
>>> results of that onto the individual's surface before combining across
>>> subjects?
>>>
>>> If you want to explain your bigger-picture goal, we might have other
>>> useful suggestions.
>>>
>>> Tim
>>>
>>>
>>> On Wed, Jan 3, 2018 at 11:58 AM, Glasser, Matthew <glass...@wustl.edu>
>>> wrote:
>>>
>>>> I think I would probably resample the subject’s own FS_LR registered
>>>> surfaces into the FreeSurfer space (an exact transformation) and then do a
>>>> single mapping from volume to surface.  You would need to figure out the
>>>> affine matrix that describes this tr

[HCP-Users] volume to average surface with Nearest Neighbour interpolation

[Seán Froudist Walsh]

Dear HCP experts,

I am interested in mapping individual voxels in a subject's FreeSurfer
conformed space (orig.nii) onto the HCP template (fsaverage_LR) while
maintaining the original voxel values.

All of the voxels lie within the LH cortical ribbon in the (conformed)
volume space. There are 186 voxels with non-zero values that act as unique
identifiers, with all other voxels having a value of zero.

I have prepared the native FreeSurfer to HCP transformations, then
performed volume-to-surface mapping of the sample data, and finally applied
the FreeSurfer-to-HCP transform to the sample data. I have tried to
identify the options that perform something like Nearest Neighbour
assignment, as I need to maintain the original values as identifiers. The
problem I am facing is that volume-to-surface mapping as done below reduces
the number of non-zero voxels/vertices from 186 to 94, and the
Freesufer-to-HCP resampling reduces the number of non-zero vertices further
from 94 to 13 non-zero points.

I would greatly appreciate your guidance as to the best way to achieve my
desired goal of obtaining all 186 vertices with their original values onto
the HCP template. Should I map each voxel to the closest voxel on the
FreeSurfer WM surface, or something similar?

The commands I used are shown below.

Many thanks,

Sean

wb_shortcuts -freesurfer-resample-prep lh.white.surf.gii lh.pial.surf.gii
lh.sphere.FSave.reg.surf.gii
HCP_S1200_GroupAvg_v1/standard_mesh_atlases/resample_fsaverage/fs_LR-deformed_to-fsaverage.L.sphere.32k_fs_LR.surf.gii
lh.midthickness.surf.gii
${current_subject}.l.midthickness.32k_fs_LR.surf.gii
lh.sphere.HCP.reg.surf.gii

and then created a volume-to-surface mapping, while maintaining the
original voxel/vertex values using

wb_command -volume-to-surface-mapping '
{current_subject}_samples_LH_cortex.nii.gz
lh.midthickness.surf.gii   samples_native.shape.gii -enclosing



and then applied the transform using

wb_command -metric-resample samples_native.shape.gii
lh.sphere.HCP.reg.surf.gii
HCP_S1200_GroupAvg_v1/standard_mesh_atlases/resample_fsaverage/fs_LR-deformed_to-fsaverage.L.sphere.32k_fs_LR.surf.gii
BARYCENTRIC -largest {current_subject}_samples_HCP.shape.gii

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