Re: [HCP-Users] Estimation of surface area

[Glasser, Matthew]

That is correct.  MNI space IS NOT the correct place to measure areas, volumes, 
thicknesses.

Peace,

Matt.

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>
Date: Wednesday, April 18, 2018 at 1:25 PM
To: "Paul, Subhadip" <subhadip.p...@kcl.ac.uk<mailto:subhadip.p...@kcl.ac.uk>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Estimation of surface area

Those commands look correct, however MNI space may not be the correct place to 
make these measurements, as the registration distorts the subject anatomy to 
match a template (and the template happens to be significantly larger than the 
average subject).  I suspect we do not actually recompute thickness in MNI 
space, so a thickness file in the MNINonLinear folder may simply be a copy from 
the T1w folder.  Similarly, I would expect that our released values for surface 
area are measured in T1w space, which is a rigidly aligned, distortion 
corrected scanner space, matching the true shape of the subject's brain.

Note that with cifti files, you can use -cifti-parcellate to do these per-area 
summaries for all areas at once, rather than one at a time.  You can use 
-cifti-convert -to-text to dump the data values after that (and 
-file-information will tell you the order of areas in the parcellated file).

Tim


On Wed, Apr 18, 2018 at 1:07 PM, Paul, Subhadip 
<subhadip.p...@kcl.ac.uk<mailto:subhadip.p...@kcl.ac.uk>> wrote:

Dear HCP users,

HCP  has released thickness, surface area values based on DK (Desikan-Killiany) 
atlas in a csv file. I would like to extract those values using Destrieux 
atlas. To verify, whether am I following the correct procedure, I have 
extracted regional cortical thickness data using MATLAB from the HCP directory 
(/HCP_1200/100206/MNINonLinear/Native/) using DK atlas and compared with HCP 
released values. The values are same. Now, I am using connectome-workbench to 
estimate regional surface area using DK atlas. However, the extracted value 
does not match with HCP provided value.

To extract the area of left bankssts area (key 1) from 
/HCP_1200/100206/MNINonLinear/Native/, I am using the following connectome 
workbench commands:

wb_command -gifti-label-to-roi 100206.L.aparc.native.label.gii roi.func.gii 
-key 1

wb_command -metric-weighted-stats roi.func.gii -sum -area-surface 
100206.L.midthickness.native.surf.gii -show-map-name

Could you please tell me whether am I using the correct commands? When I used 
*pial*.surf.gii or *white*.surf.gii instead of *midthickness*.surf.gii file in 
the second command, still the extracted value does not match with the HCP 
released value.

Once I figure out the correct approach, I would replace the *aparc.*.label.gii 
file in the first command, with *aparc.a2009s*.label.gii to extract surface 
area using Destrieux atlas.

Thanking you,

Subhadip



Subhadip Paul

King's College London

16 De Crespigny Park, London 
<https://maps.google.com/?q=16+De+Crespigny+Park,+London++SE5+8AF=gmail=g>
 SE5 
8AF<https://maps.google.com/?q=16+De+Crespigny+Park,+London++SE5+8AF=gmail=g>

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Re: [HCP-Users] Estimation of surface area

[Timothy Coalson]

Those commands look correct, however MNI space may not be the correct place
to make these measurements, as the registration distorts the subject
anatomy to match a template (and the template happens to be significantly
larger than the average subject).  I suspect we do not actually recompute
thickness in MNI space, so a thickness file in the MNINonLinear folder may
simply be a copy from the T1w folder.  Similarly, I would expect that our
released values for surface area are measured in T1w space, which is a
rigidly aligned, distortion corrected scanner space, matching the true
shape of the subject's brain.

Note that with cifti files, you can use -cifti-parcellate to do these
per-area summaries for all areas at once, rather than one at a time.  You
can use -cifti-convert -to-text to dump the data values after that (and
-file-information will tell you the order of areas in the parcellated file).

Tim


On Wed, Apr 18, 2018 at 1:07 PM, Paul, Subhadip 
wrote:

> Dear HCP users,
>
> HCP  has released thickness, surface area values based on DK
> (Desikan-Killiany) atlas in a csv file. I would like to extract those
> values using Destrieux atlas. To verify, whether am I following the correct
> procedure, I have extracted regional cortical thickness data using MATLAB
> from the HCP directory (/HCP_1200/100206/MNINonLinear/Native/) using DK
> atlas and compared with HCP released values. The values are same. Now, I am
> using connectome-workbench to estimate regional surface area using DK
> atlas. However, the extracted value does not match with HCP provided value.
>
> To extract the area of left bankssts area (key 1) from
> /HCP_1200/100206/MNINonLinear/Native/, I am using the following
> connectome workbench commands:
>
> wb_command -gifti-label-to-roi 100206.L.aparc.native.label.gii
> roi.func.gii -key 1
>
> wb_command -metric-weighted-stats roi.func.gii -sum -area-surface
> 100206.L.midthickness.native.surf.gii -show-map-name
>
> Could you please tell me whether am I using the correct commands? When I
> used *pial*.surf.gii or *white*.surf.gii instead of *midthickness*.surf.gii
> file in the second command, still the extracted value does not match with
> the HCP released value.
>
> Once I figure out the correct approach, I would replace the
> *aparc.*.label.gii file in the first command, with *aparc.a2009s*.label.gii
> to extract surface area using Destrieux atlas.
>
> Thanking you,
>
> Subhadip
>
>
> *Subhadip Paul*
>
> King's College London
>
> 16 De Crespigny Park, London
> SE5
> 8AF
> 
>
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>

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[HCP-Users] Estimation of surface area

[Paul, Subhadip]

Dear HCP users,

HCP  has released thickness, surface area values based on DK (Desikan-Killiany) 
atlas in a csv file. I would like to extract those values using Destrieux 
atlas. To verify, whether am I following the correct procedure, I have 
extracted regional cortical thickness data using MATLAB from the HCP directory 
(/HCP_1200/100206/MNINonLinear/Native/) using DK atlas and compared with HCP 
released values. The values are same. Now, I am using connectome-workbench to 
estimate regional surface area using DK atlas. However, the extracted value 
does not match with HCP provided value.

To extract the area of left bankssts area (key 1) from 
/HCP_1200/100206/MNINonLinear/Native/, I am using the following connectome 
workbench commands:

wb_command -gifti-label-to-roi 100206.L.aparc.native.label.gii roi.func.gii 
-key 1

wb_command -metric-weighted-stats roi.func.gii -sum -area-surface 
100206.L.midthickness.native.surf.gii -show-map-name

Could you please tell me whether am I using the correct commands? When I used 
*pial*.surf.gii or *white*.surf.gii instead of *midthickness*.surf.gii file in 
the second command, still the extracted value does not match with the HCP 
released value.

Once I figure out the correct approach, I would replace the *aparc.*.label.gii 
file in the first command, with *aparc.a2009s*.label.gii to extract surface 
area using Destrieux atlas.

Thanking you,

Subhadip



Subhadip Paul

King's College London

16 De Crespigny Park, London SE5 8AF

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