subject:"Re\: \[HCP\-Users\] Human\-Macaque deformation map in wb

Re: [HCP-Users] Human-Macaque deformation map in wb_view?

2018-04-15 Thread Saad Jbabdi

Hi - that worked! Thank you so much John.

Cheers
Saad

On 12 Apr 2018, at 17:00, Harwell, John
> wrote:

So it is a shape file. Follow the same instructions as before except for the
second step that has been updated to set the File Type to GIFTI Shape File.

In Caret5:
* Select File Menu -> Save Data File
* In the Save Data File Dialog, set the File Type to GIFTI Shape File
(*.shape.gii)
* Change the File Name so that it ends in “.shape.gii” (may want to click the
File Name button to choose the name with a file selection dialog)
* Verify that the Encoding is XML.
* Click the Save button.

Note that GIFTI func and shape are the same format and you can rename from
.shape.gii to .func.gii.

Alternatively, if you can find the Caret Shape File in a terminal window,
“wb_import”, included with the Workbench distribution, can be used to convert
data files from Caret format to a Workbench compatible format.

wb_import -data-file
CONVERT DATA FILE TO WORKBENCH FORMAT
wb_import -data-file
[-allow-overwrite]
[-structure structure-name]
[-area-color-filearea-color-file-name]
[-border-color-file border-color-file-name]
[-foci-color-filefoci-color-file-name]
]

On Apr 12, 2018, at 10:24 AM, Saad Jbabdi
> wrote:

This one

On 12 Apr 2018, at 15:21, Harwell, John
> wrote:

Do you know the name and type of the file displayed as the primary overlay on
the surface? It should be selected in Primary Overlay on the Display Control’s
Overlay/Underlay - Surface page.

On Apr 12, 2018, at 7:41 AM, Saad Jbabdi
> wrote:

Hi John

When I follow your steps it produces an empty func file:

http://www.nitrc.org/frs/download.php/1594/gifti.dtd;>
http://www.w3.org/2001/XMLSchema-instance;

xsi:noNamespaceSchemaLocation="http://brainvis.wustl.edu/caret6/xml_schemas/GIFTI_Caret.xsd;
Version="1.0"
NumberOfDataArrays="0">

On 11 Apr 2018, at 19:24, Harwell, John
> wrote:

In Caret5:
* Select File Menu -> Save Data File
* In the Save Data File Dialog, set the File Type to GIFTI Functional File
(*.func.gii)
* Change the File Name so that it ends in “.func.gii” (may want to click the
File Name button to choose the name with a file selection dialog)
* Verify that the Encoding is XML.
* Click the Save button.

This should create a GIFTI functional file that can be loaded into wb_view.

John H

On Apr 11, 2018, at 12:47 PM, Saad Jbabdi
> wrote:

Hi Matt

Thanks. But I am not sure I was clear enough so let me rephrase: is there a way
to somehow export the attached map from Caret into a func.gi file that I can
open in wb_view?

Thanks!
Saad

On 11 Apr 2018, at 16:36, Glasser, Matthew
> wrote:

Hi Saad,

Not that I am aware of. Probably better to generate distortion maps (e.g.
isotropic and anisotropic strains).

Matt.

On 4/11/18, 10:28 AM,
"hcp-users-boun...@humanconnectome.org
on behalf of
Saad Jbabdi"

on behalf of
saad.jba...@ndcn.ox.ac.uk> wrote:

Hi all,

Is there a way to load Caret¹s PALS-F99 deformation map onto wb_view?

Thanks
Saad

___
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HCP-Users@humanconnectome.org
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Re: [HCP-Users] Human-Macaque deformation map in wb_view?

2018-04-12 Thread Harwell, John

So it is a shape file.  Follow the same instructions as before except for the 
second step that has been updated to set the File Type to GIFTI Shape File.

In Caret5:
* Select File Menu -> Save Data File
* In the Save Data File Dialog, set the File Type to GIFTI Shape File 
(*.shape.gii)
* Change the File Name so that it ends in “.shape.gii” (may want to click the 
File Name button to choose the name with a file selection dialog)
* Verify that the Encoding is XML.
* Click the Save button.

Note that GIFTI func and shape are the same format and you can rename from 
.shape.gii to .func.gii.

Alternatively, if you can find the Caret Shape File in a terminal window, 
“wb_import”, included with the Workbench distribution, can be used to convert 
data files from Caret format to a Workbench compatible format.

wb_import -data-file
   CONVERT DATA FILE TO WORKBENCH FORMAT
  wb_import -data-file
 [-allow-overwrite]
 [-structure  structure-name]
 [-area-color-filearea-color-file-name]
 [-border-color-file  border-color-file-name]
 [-foci-color-filefoci-color-file-name]
 ]

On Apr 12, 2018, at 10:24 AM, Saad Jbabdi 
> wrote:

This one

On 12 Apr 2018, at 15:21, Harwell, John 
> wrote:

Do you know the name and type of the file displayed as the primary overlay on 
the surface?  It should be selected in Primary Overlay on the Display Control’s 
Overlay/Underlay - Surface page.

On Apr 12, 2018, at 7:41 AM, Saad Jbabdi 
> wrote:

Hi John

When I follow your steps it produces an empty func file:

http://www.nitrc.org/frs/download.php/1594/gifti.dtd;>
http://www.w3.org/2001/XMLSchema-instance;

xsi:noNamespaceSchemaLocation="http://brainvis.wustl.edu/caret6/xml_schemas/GIFTI_Caret.xsd;
  Version="1.0"
  NumberOfDataArrays="0">

On 11 Apr 2018, at 19:24, Harwell, John 
> wrote:

In Caret5:
* Select File Menu -> Save Data File
* In the Save Data File Dialog, set the File Type to GIFTI Functional File 
(*.func.gii)
* Change the File Name so that it ends in “.func.gii” (may want to click the 
File Name button to choose the name with a file selection dialog)
* Verify that the Encoding is XML.
* Click the Save button.

This should create a GIFTI functional file that can be loaded into wb_view.

John H

On Apr 11, 2018, at 12:47 PM, Saad Jbabdi 
> wrote:

Hi Matt

Thanks. But I am not sure I was clear enough so let me rephrase: is there a way 
to somehow export the attached map from Caret into a func.gi file that I can 
open in wb_view?

Thanks!
Saad

On 11 Apr 2018, at 16:36, Glasser, Matthew 
> wrote:

Hi Saad,

Not that I am aware of.  Probably better to generate distortion maps (e.g.
isotropic and anisotropic strains).

Matt.

On 4/11/18, 10:28 AM, 
"hcp-users-boun...@humanconnectome.org
 on behalf of
Saad Jbabdi" 

 on behalf of
saad.jba...@ndcn.ox.ac.uk> wrote:

Hi all,

Is there a way to load Caret¹s PALS-F99 deformation map onto wb_view?

Thanks
Saad

___
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HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
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Re: [HCP-Users] Human-Macaque deformation map in wb_view?

2018-04-12 Thread Harwell, John

Do you know the name and type of the file displayed as the primary overlay on 
the surface?  It should be selected in Primary Overlay on the Display Control’s 
Overlay/Underlay - Surface page.

On Apr 12, 2018, at 7:41 AM, Saad Jbabdi 
> wrote:

Hi John

When I follow your steps it produces an empty func file:

http://www.nitrc.org/frs/download.php/1594/gifti.dtd;>
http://www.w3.org/2001/XMLSchema-instance;

xsi:noNamespaceSchemaLocation="http://brainvis.wustl.edu/caret6/xml_schemas/GIFTI_Caret.xsd;
  Version="1.0"
  NumberOfDataArrays="0">

On 11 Apr 2018, at 19:24, Harwell, John 
> wrote:

In Caret5:
* Select File Menu -> Save Data File
* In the Save Data File Dialog, set the File Type to GIFTI Functional File 
(*.func.gii)
* Change the File Name so that it ends in “.func.gii” (may want to click the 
File Name button to choose the name with a file selection dialog)
* Verify that the Encoding is XML.
* Click the Save button.

This should create a GIFTI functional file that can be loaded into wb_view.

John H

On Apr 11, 2018, at 12:47 PM, Saad Jbabdi 
> wrote:

Hi Matt

Thanks. But I am not sure I was clear enough so let me rephrase: is there a way 
to somehow export the attached map from Caret into a func.gi file that I can 
open in wb_view?

Thanks!
Saad

On 11 Apr 2018, at 16:36, Glasser, Matthew 
> wrote:

Hi Saad,

Not that I am aware of.  Probably better to generate distortion maps (e.g.
isotropic and anisotropic strains).

Matt.

On 4/11/18, 10:28 AM, 
"hcp-users-boun...@humanconnectome.org
 on behalf of
Saad Jbabdi" 

 on behalf of
saad.jba...@ndcn.ox.ac.uk> wrote:

Hi all,

Is there a way to load Caret¹s PALS-F99 deformation map onto wb_view?

Thanks
Saad

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
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HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

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Re: [HCP-Users] Human-Macaque deformation map in wb_view?

2018-04-12 Thread Saad Jbabdi

Hi John

When I follow your steps it produces an empty func file:

http://www.nitrc.org/frs/download.php/1594/gifti.dtd;>
http://www.w3.org/2001/XMLSchema-instance;

xsi:noNamespaceSchemaLocation="http://brainvis.wustl.edu/caret6/xml_schemas/GIFTI_Caret.xsd;
  Version="1.0"
  NumberOfDataArrays="0">

On 11 Apr 2018, at 19:24, Harwell, John 
> wrote:

In Caret5:
* Select File Menu -> Save Data File
* In the Save Data File Dialog, set the File Type to GIFTI Functional File 
(*.func.gii)
* Change the File Name so that it ends in “.func.gii” (may want to click the 
File Name button to choose the name with a file selection dialog)
* Verify that the Encoding is XML.
* Click the Save button.

This should create a GIFTI functional file that can be loaded into wb_view.

John H

On Apr 11, 2018, at 12:47 PM, Saad Jbabdi 
> wrote:

Hi Matt

Thanks. But I am not sure I was clear enough so let me rephrase: is there a way 
to somehow export the attached map from Caret into a func.gi file that I can 
open in wb_view?

Thanks!
Saad

On 11 Apr 2018, at 16:36, Glasser, Matthew 
> wrote:

Hi Saad,

Not that I am aware of.  Probably better to generate distortion maps (e.g.
isotropic and anisotropic strains).

Matt.

On 4/11/18, 10:28 AM, 
"hcp-users-boun...@humanconnectome.org
 on behalf of
Saad Jbabdi" 

 on behalf of
saad.jba...@ndcn.ox.ac.uk> wrote:

Hi all,

Is there a way to load Caret¹s PALS-F99 deformation map onto wb_view?

Thanks
Saad

___
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

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Re: [HCP-Users] Human-Macaque deformation map in wb_view?

2018-04-11 Thread Harwell, John

In Caret5:
* Select File Menu -> Save Data File
* In the Save Data File Dialog, set the File Type to GIFTI Functional File 
(*.func.gii)
* Change the File Name so that it ends in “.func.gii” (may want to click the 
File Name button to choose the name with a file selection dialog)
* Verify that the Encoding is XML.
* Click the Save button.

This should create a GIFTI functional file that can be loaded into wb_view.

John H

On Apr 11, 2018, at 12:47 PM, Saad Jbabdi 
> wrote:

Hi Matt

Thanks. But I am not sure I was clear enough so let me rephrase: is there a way 
to somehow export the attached map from Caret into a func.gi file that I can 
open in wb_view?

Thanks!
Saad

On 11 Apr 2018, at 16:36, Glasser, Matthew 
> wrote:

Hi Saad,

Not that I am aware of.  Probably better to generate distortion maps (e.g.
isotropic and anisotropic strains).

Matt.

On 4/11/18, 10:28 AM, 
"hcp-users-boun...@humanconnectome.org
 on behalf of
Saad Jbabdi" 

 on behalf of
saad.jba...@ndcn.ox.ac.uk> wrote:

Hi all,

Is there a way to load Caret¹s PALS-F99 deformation map onto wb_view?

Thanks
Saad

___
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

___
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HCP-Users@humanconnectome.org
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Re: [HCP-Users] Human-Macaque deformation map in wb_view?

2018-04-11 Thread Glasser, Matthew

Hi Saad,

Not that I am aware of.  Probably better to generate distortion maps (e.g.
isotropic and anisotropic strains).

Matt.

On 4/11/18, 10:28 AM, "hcp-users-boun...@humanconnectome.org on behalf of
Saad Jbabdi"  wrote:

>Hi all,
>
>Is there a way to load Caret¹s PALS-F99 deformation map onto wb_view?
>
>Thanks
>Saad
>
>
>
>___
>HCP-Users mailing list
>HCP-Users@humanconnectome.org
>http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
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Re: [HCP-Users] Human-Macaque deformation map in wb_view?

Re: [HCP-Users] Human-Macaque deformation map in wb_view?

Re: [HCP-Users] Human-Macaque deformation map in wb_view?

Re: [HCP-Users] Human-Macaque deformation map in wb_view?

Re: [HCP-Users] Human-Macaque deformation map in wb_view?

Re: [HCP-Users] Human-Macaque deformation map in wb_view?

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