Re: [HCP-Users] surf2surf

2017-10-16 Thread Timothy Coalson 
If you mean that the public archive section also asks for a password, yes
it does, and we are aware.  We expected usage to decrease somewhat, so we
didn't really try to fix the issue.  We might want to revisit this decision.

Tim


On Mon, Oct 16, 2017 at 3:53 PM, Seán Froudist Walsh 
wrote:

> 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 <http://brainvis.wustl.edu/sum
>>> sdb/public/8293223_inter-atlas_deformation_maps.zip> info <
>>> http://brainvis.wustl.edu/sumsdb/public/ROOT/public/ATLAS_D
>>> ATA_SETS/HUMAN/CONTE69/Inter-atlas_deformation_mapsinter-atl
>>> as_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 o

Re: [HCP-Users] surf2surf

2017-10-16 Thread 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 <http://brainvis.wustl.edu/sum
>> 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 <http://www.neuroecologylab.org/>
>> @NeuroecologyLab
>>
&g

Re: [HCP-Users] surf2surf

2017-10-16 Thread Timothy Coalson 
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) 
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 <http://brainvis.wustl.edu/sumsdb/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_deformation_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 <http://www.neuroecologylab.org/>
> @NeuroecologyLab
>
> ___
> 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

2017-10-16 Thread Mars, R.B. (Rogier) 
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<mailto: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<http://www.neuroecologylab.org>
@NeuroecologyLab

On 15 Oct 2017, at 18:00, 
hcp-users-requ...@humanconnectome.org<mailto:hcp-users-requ...@humanconnectome.org>
 wrote:

Send HCP-Users mailing list submissions to
hcp-users@humanconnectome.org<mailto: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 
<http://brainvis.wustl.edu/sumsdb/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_deformation_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 <http://www.neuroecologylab.org/>
@NeuroecologyLab

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Re: [HCP-Users] surf2surf

2017-10-15 Thread David Van Essen 
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 

 info 

 
/ROOT/public/ATLAS_DATA_SETS/HUMAN/CONTE69/Inter-atlas_deformation_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
> 
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> 


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Re: [HCP-Users] surf2surf

2017-10-12 Thread Glasser, Matthew 
Hi Rogier,

Do you have a spherical registration between the surfaces?  You can use 
wb_command -metric-resample if you do.  If you want to use FreeSurfer tools for 
this, probably better to ask on the FreeSurfer list, as I am not as familiar 
with their tools that overlap with Connectome Workbench’s capabilities.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of "Mars, R.B. (Rogier)" 
mailto:r.m...@donders.ru.nl>>
Date: Thursday, October 12, 2017 at 10:27 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] surf2surf

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<http://www.neuroecologylab.org>
@NeuroecologyLab


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[HCP-Users] surf2surf

2017-10-12 Thread Mars, R.B. (Rogier) 
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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