Re: [HCP-Users] Obtaining the MNI coordinates of cluster peaks in the melodic_IC.dscalar.nii ICA maps

[James Morrow]

Thanks Tim and Matt for the detailed responses.


I agree that mapping to volumes is sub-optimal. Our goal is to identify
coords to be used as targets for brain stimulation with TMS. We need MNI
coords for neuronavigation. Given the extent of the TMS field, we have some
tolerance for imprecisions in the mapping.



Can I clarify – was the ICA run on the volumes and then later mapped on to
surfaces, or was it performed on the surface data? If the former, are the
original volumetric results for the ICA of each subject available anywhere
in .nii format?


Cheers,

James

*James Morrow*
Research assistant
Brain & Mental Health Laboratory

*Monash Institute of Cognitive and Clinical Neurosciences*
School of Psychological Sciences
Monash University
c/o MBI, 770 Blackburn Road
Clayton VIC 3800
Australia

T: 03 9902 9768
E: james.mor...@monash.edu 
www.med.monash.edu.au/psych/bmh/




On 3 August 2017 at 07:00, Timothy Coalson  wrote:

> As Matt said, "MNI coordinates" of functionally-aligned cortical surface
> features don't have much meaning, similar to how T1w-aligned MNI space
> volumes don't have good cortical functional alignment (except in a few
> low-variability regions).  We have shown that group average surface
> coordinates do not follow the MNI cortical ribbon (see attached image that
> simply shows the average white and pial contours on top of the MNI
> nonlinear template).  The ICA maps themselves are also more informative
> than just the vertices at their peaks.
>
> Surface group results should not be turned into volumetric files, group
> average surfaces do not have much folding left in them, and as such they do
> not match the MNI template anymore - this is due to folding
> incompatibilities between subjects, but also due to using functional
> surface registration instead of folding patterns.  Using the individual
> surfaces to map to the volume and then averaging across them would spread
> your data out just as badly as doing volume-based analysis of cortex, so
> this is also highly discouraged.
>
> Despite strongly advising you not to do what you outlined, I will tell you
> what commands you would need.  The -cifti-extrema command will output a map
> with 1s and -1s at each local extrema.  The surface it uses is for neighbor
> information and distance computation - this isn't as critical as
> coordinates are, as it merely sets the maximum possible density of extrema
> (what you could get from a very noisy map).  You will need to use a
> threshold or other method to exclude local extrema that are outside the
> high-valued area.  We use midthickness surfaces for this kind of thing (and
> when doing some important spatial operation, we use corrected vertex areas
> to compensate for the loss of folding in group average surfaces, see
> -metric-smoothing).
>
> You can extract the coordinates of a surface file with
> -surface-coordinates-to-metric, and you can use -cifti-separate on the
> -cifti-extrema result to get those as metric files, so that the indices
> will match, so that you can use them in matlab or some other tool for
> ad-hoc analysis (alternatively, use -cifti-create-dense-from-template to
> put the surface coordinates into a cifti file).  Since we advise not to do
> this with any group data, you are on your own here (finding the coordinates
> in a bunch of individuals and averaging those will give exactly the same
> bad answer, reflecting the fact that many/most functional areas have
> notably different MNI coordinates in each individual).
>
> Tim
>
>
> On Tue, Aug 1, 2017 at 7:46 PM, James Morrow 
> wrote:
>
>> Hi,
>>
>>
>> We have recently downloaded the HCP900 Parcellation + Timeseries +
>> Netmats (820 Subjects) dataset.
>>
>>
>>
>> We would like to obtain the MNI coordinates of cluster peaks in the
>> melodic_IC.dscalar.nii ICA maps.
>>
>>
>>
>> Is there any way to do this?
>>
>>
>>
>> Is the –cifti-extrema function of wb_command the correct command? It
>> requires a surface file, but I’m not sure which would be most appropriate
>> for the group ICA results.
>>
>>
>>
>> Alternatively, would there be a way to convert the dscalar file into a
>> standard volumetric nii so that I can use standard FSL tools?
>>
>>
>> Thanks
>>
>>
>> James Morrow
>>
>> ___
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>
>
>

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Re: [HCP-Users] Obtaining the MNI coordinates of cluster peaks in the melodic_IC.dscalar.nii ICA maps

[Timothy Coalson]

On Wed, Aug 2, 2017 at 6:02 PM, James Morrow 
wrote:

> Thanks Tim and Matt for the detailed responses.
>
>
> I agree that mapping to volumes is sub-optimal. Our goal is to identify
> coords to be used as targets for brain stimulation with TMS. We need MNI
> coords for neuronavigation. Given the extent of the TMS field, we have some
> tolerance for imprecisions in the mapping.
>

I see.  We generally get asked these questions in the context of fMRI
analysis, hence our reluctance.

How does the neuronavigation go from MNI coordinates to subject
coordinates, do you happen to have a reasonable T1w MRI scan of your
subjects?  I don't know how big the TMS field is, and I hadn't looked at
the distance from subject to group average surfaces before, but in one of
the HCP subjects, I got a maximum of 2cm distance from the group average
surface (using midthickness surfaces), which occurred in a few specific
locations, while 90% of the surface was 1cm distance or less.


> Can I clarify – was the ICA run on the volumes and then later mapped on to
> surfaces, or was it performed on the surface data? If the former, are the
> original volumetric results for the ICA of each subject available anywhere
> in .nii format?
>
>
> Cheers,
>
> James
>
> *James Morrow*
> Research assistant
> Brain & Mental Health Laboratory
>
> *Monash Institute of Cognitive and Clinical Neurosciences*
> School of Psychological Sciences
> Monash University
> c/o MBI, 770 Blackburn Road
> Clayton VIC 3800
> Australia
>
> T: 03 9902 9768
> E: james.mor...@monash.edu 
> www.med.monash.edu.au/psych/bmh/
>
> 
> 
>
> On 3 August 2017 at 07:00, Timothy Coalson  wrote:
>
>> As Matt said, "MNI coordinates" of functionally-aligned cortical surface
>> features don't have much meaning, similar to how T1w-aligned MNI space
>> volumes don't have good cortical functional alignment (except in a few
>> low-variability regions).  We have shown that group average surface
>> coordinates do not follow the MNI cortical ribbon (see attached image that
>> simply shows the average white and pial contours on top of the MNI
>> nonlinear template).  The ICA maps themselves are also more informative
>> than just the vertices at their peaks.
>>
>> Surface group results should not be turned into volumetric files, group
>> average surfaces do not have much folding left in them, and as such they do
>> not match the MNI template anymore - this is due to folding
>> incompatibilities between subjects, but also due to using functional
>> surface registration instead of folding patterns.  Using the individual
>> surfaces to map to the volume and then averaging across them would spread
>> your data out just as badly as doing volume-based analysis of cortex, so
>> this is also highly discouraged.
>>
>> Despite strongly advising you not to do what you outlined, I will tell
>> you what commands you would need.  The -cifti-extrema command will output a
>> map with 1s and -1s at each local extrema.  The surface it uses is for
>> neighbor information and distance computation - this isn't as critical as
>> coordinates are, as it merely sets the maximum possible density of extrema
>> (what you could get from a very noisy map).  You will need to use a
>> threshold or other method to exclude local extrema that are outside the
>> high-valued area.  We use midthickness surfaces for this kind of thing (and
>> when doing some important spatial operation, we use corrected vertex areas
>> to compensate for the loss of folding in group average surfaces, see
>> -metric-smoothing).
>>
>> You can extract the coordinates of a surface file with
>> -surface-coordinates-to-metric, and you can use -cifti-separate on the
>> -cifti-extrema result to get those as metric files, so that the indices
>> will match, so that you can use them in matlab or some other tool for
>> ad-hoc analysis (alternatively, use -cifti-create-dense-from-template to
>> put the surface coordinates into a cifti file).  Since we advise not to do
>> this with any group data, you are on your own here (finding the coordinates
>> in a bunch of individuals and averaging those will give exactly the same
>> bad answer, reflecting the fact that many/most functional areas have
>> notably different MNI coordinates in each individual).
>>
>> Tim
>>
>>
>> On Tue, Aug 1, 2017 at 7:46 PM, James Morrow 
>> wrote:
>>
>>> Hi,
>>>
>>>
>>> We have recently downloaded the HCP900 Parcellation + Timeseries +
>>> Netmats (820 Subjects) dataset.
>>>
>>>
>>>
>>> We would like to obtain the MNI coordinates of cluster peaks in the
>>> melodic_IC.dscalar.nii ICA maps.
>>>
>>>
>>>
>>> Is there any way to do this?
>>>
>>>
>>>
>>> Is the –cifti-extrema function of wb_command the correct command? It
>>> requires a surface file, but I’m not sure which would be most appropriate
>>> for the group ICA 

Re: [HCP-Users] Obtaining the MNI coordinates of cluster peaks in the melodic_IC.dscalar.nii ICA maps

[Glasser, Matthew]

They were run in the CIFTI greyordinates space.  As it turns out, ICA results 
from well aligned data look different from those of poorly aligned data, as one 
gets many components representing misalignment if the data are not well aligned.

Peace,

Matt.

From: James Morrow >
Date: Wednesday, August 2, 2017 at 6:02 PM
To: Timothy Coalson >, Matt Glasser 
>
Cc: "hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] Obtaining the MNI coordinates of cluster peaks in the 
melodic_IC.dscalar.nii ICA maps

Thanks Tim and Matt for the detailed responses.

I agree that mapping to volumes is sub-optimal. Our goal is to identify coords 
to be used as targets for brain stimulation with TMS. We need MNI coords for 
neuronavigation. Given the extent of the TMS field, we have some tolerance for 
imprecisions in the mapping.

Can I clarify – was the ICA run on the volumes and then later mapped on to 
surfaces, or was it performed on the surface data? If the former, are the 
original volumetric results for the ICA of each subject available anywhere in 
.nii format?

Cheers,
James

James Morrow
Research assistant
Brain & Mental Health Laboratory

Monash Institute of Cognitive and Clinical Neurosciences
School of Psychological Sciences
Monash University
c/o MBI, 770 Blackburn Road
Clayton VIC 3800
Australia

T: 03 9902 9768
E: james.mor...@monash.edu
www.med.monash.edu.au/psych/bmh/

[http://www.med.monash.edu.au/assets/images/psych/bmh/bannerbmh.jpg]
[http://med.monash.edu.au/psych/email-sig/miccn-email-sig.jpg]

On 3 August 2017 at 07:00, Timothy Coalson 
> wrote:
As Matt said, "MNI coordinates" of functionally-aligned cortical surface 
features don't have much meaning, similar to how T1w-aligned MNI space volumes 
don't have good cortical functional alignment (except in a few low-variability 
regions).  We have shown that group average surface coordinates do not follow 
the MNI cortical ribbon (see attached image that simply shows the average white 
and pial contours on top of the MNI nonlinear template).  The ICA maps 
themselves are also more informative than just the vertices at their peaks.

Surface group results should not be turned into volumetric files, group average 
surfaces do not have much folding left in them, and as such they do not match 
the MNI template anymore - this is due to folding incompatibilities between 
subjects, but also due to using functional surface registration instead of 
folding patterns.  Using the individual surfaces to map to the volume and then 
averaging across them would spread your data out just as badly as doing 
volume-based analysis of cortex, so this is also highly discouraged.

Despite strongly advising you not to do what you outlined, I will tell you what 
commands you would need.  The -cifti-extrema command will output a map with 1s 
and -1s at each local extrema.  The surface it uses is for neighbor information 
and distance computation - this isn't as critical as coordinates are, as it 
merely sets the maximum possible density of extrema (what you could get from a 
very noisy map).  You will need to use a threshold or other method to exclude 
local extrema that are outside the high-valued area.  We use midthickness 
surfaces for this kind of thing (and when doing some important spatial 
operation, we use corrected vertex areas to compensate for the loss of folding 
in group average surfaces, see -metric-smoothing).

You can extract the coordinates of a surface file with 
-surface-coordinates-to-metric, and you can use -cifti-separate on the 
-cifti-extrema result to get those as metric files, so that the indices will 
match, so that you can use them in matlab or some other tool for ad-hoc 
analysis (alternatively, use -cifti-create-dense-from-template to put the 
surface coordinates into a cifti file).  Since we advise not to do this with 
any group data, you are on your own here (finding the coordinates in a bunch of 
individuals and averaging those will give exactly the same bad answer, 
reflecting the fact that many/most functional areas have notably different MNI 
coordinates in each individual).

Tim


On Tue, Aug 1, 2017 at 7:46 PM, James Morrow 
> wrote:
Hi,

We have recently downloaded the HCP900 Parcellation + Timeseries + Netmats (820 
Subjects) dataset.

We would like to obtain the MNI coordinates of cluster peaks in the 
melodic_IC.dscalar.nii ICA maps.

Is there any way to do this?

Is the –cifti-extrema function of wb_command the correct command? It requires a 
surface 

Re: [HCP-Users] Obtaining the MNI coordinates of cluster peaks in the melodic_IC.dscalar.nii ICA maps

[Glasser, Matthew]

This is challenging for several reasons: Standard volumetric data don’t have 
good alignment of cortical areas, and cortical areas are complex patches on a 
convoluted surface not 3D points, so MNI coordinates are not especially 
meaningful as a way of determining if results are the same across studies.  
Additionally, while it is possible to average surfaces across subjects and 
generate average surface coordinates, these have substantial biases in them.  
Really the only place where you have good surface/volume correspondence is at 
the level of individual subjects and averaging and smoothing in the volume as 
is traditionally done is quite harmful to brain imaging data.

Peace,

Matt.

From: 
>
 on behalf of James Morrow 
>
Date: Tuesday, August 1, 2017 at 7:46 PM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] Obtaining the MNI coordinates of cluster peaks in the 
melodic_IC.dscalar.nii ICA maps

Hi,

We have recently downloaded the HCP900 Parcellation + Timeseries + Netmats (820 
Subjects) dataset.

We would like to obtain the MNI coordinates of cluster peaks in the 
melodic_IC.dscalar.nii ICA maps.

Is there any way to do this?

Is the –cifti-extrema function of wb_command the correct command? It requires a 
surface file, but I’m not sure which would be most appropriate for the group 
ICA results.

Alternatively, would there be a way to convert the dscalar file into a standard 
volumetric nii so that I can use standard FSL tools?

Thanks

James Morrow


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