Re: [HCP-Users] create borders based on .dlabel files

[Timothy Coalson]

The -label-to-border command requires gifti label files, as it does one
surface at a time - there is not a cifti version of this command (because
border files are surface only and single hemisphere, and there is no
equivalent volume operation).  So, first -cifti-separate to get gifti label
files:

wb_command -cifti-separate melodic_IC_ftb.dlabel.nii -label CORTEX_LEFT
test.L.label.gii -label CORTEX_RIGHT test.R.label.gii

Then you can use -label-to-border:

wb_command
-label-to-border Q1-Q6_R440.L.inflated.32k_fs_LR.surf.gii test.L.label.gii
test.L.border
wb_command
-label-to-border Q1-Q6_R440.R.inflated.32k_fs_LR.surf.gii test.R.label.gii
test.R.border

Note that cifti files generally can only be used with operations that begin
with -cifti (there are some exceptions, like -nifti-information,
-file-information, -set-map-names, -add-to-spec-file, -file-convert, ...)

Tim


On Mon, Nov 30, 2015 at 3:34 PM, Yizhou Ma  wrote:

> Dear HCP experts,
>
> I am trying to create borders based on HCP's .dlabel files. I am working
> on the FTB labels in the ICA PTN results. The reference surface I use is
> the R440 template, inflated surface. Here's the command I used:
>
> wb_command -label-to-border Q1-Q6_R440.L.inflated.32k_fs_LR.surf.gii
> melodic_IC_ftb.dlabel.nii test.border
>
> I got the following error message:
>
> ERROR: Parse Error while reading melodic_IC_ftb.dlabel.nii: error occurred
> while parsing element line number: 1 column number: 1
>
> Could somebody please help me with this?
>
> Thank you very much,
> Cherry
>
> ___
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> HCP-Users@humanconnectome.org
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>

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Re: [HCP-Users] create borders based on .dlabel files

[Timothy Coalson]

When displaying them in the GUI, select the "border" input mode, select
"edit" in the added toolbar, make sure "properties" is depressed, then
click on a border, then you get a popup where you can edit border colors.
Then, save the file from the GUI and it will have those colors.

There is currently no command to set border colors, but the
-label-to-border command will use the label color as the output border
color.  Unfortunately it looks like -border-merge may not currently
preserve colors (there can be conflicts between files that I'd need to
figure out what to do with).

Tim


On Mon, Nov 30, 2015 at 4:30 PM, Yizhou Ma  wrote:

> This worked for me. Thanks!
>
> And how can I change the display of the border? Like the color and width?
> I used -border-merge to merge all the borders and
> -border-export-color-table to get the color table. Is there a way I can
> save a border file with my own color table?
>
> Thanks,
> Cherry
>
> On Mon, Nov 30, 2015 at 4:01 PM, Timothy Coalson  wrote:
>
>> The -label-to-border command requires gifti label files, as it does one
>> surface at a time - there is not a cifti version of this command (because
>> border files are surface only and single hemisphere, and there is no
>> equivalent volume operation).  So, first -cifti-separate to get gifti label
>> files:
>>
>> wb_command -cifti-separate melodic_IC_ftb.dlabel.nii -label CORTEX_LEFT
>> test.L.label.gii -label CORTEX_RIGHT test.R.label.gii
>>
>> Then you can use -label-to-border:
>>
>> wb_command
>> -label-to-border Q1-Q6_R440.L.inflated.32k_fs_LR.surf.gii test.L.label.gii
>> test.L.border
>> wb_command
>> -label-to-border Q1-Q6_R440.R.inflated.32k_fs_LR.surf.gii test.R.label.gii
>> test.R.border
>>
>> Note that cifti files generally can only be used with operations that
>> begin with -cifti (there are some exceptions, like -nifti-information,
>> -file-information, -set-map-names, -add-to-spec-file, -file-convert, ...)
>>
>> Tim
>>
>>
>> On Mon, Nov 30, 2015 at 3:34 PM, Yizhou Ma  wrote:
>>
>>> Dear HCP experts,
>>>
>>> I am trying to create borders based on HCP's .dlabel files. I am working
>>> on the FTB labels in the ICA PTN results. The reference surface I use is
>>> the R440 template, inflated surface. Here's the command I used:
>>>
>>> wb_command -label-to-border Q1-Q6_R440.L.inflated.32k_fs_LR.surf.gii
>>> melodic_IC_ftb.dlabel.nii test.border
>>>
>>> I got the following error message:
>>>
>>> ERROR: Parse Error while reading melodic_IC_ftb.dlabel.nii: error
>>> occurred while parsing element line number: 1 column number: 1
>>>
>>> Could somebody please help me with this?
>>>
>>> Thank you very much,
>>> Cherry
>>>
>>> ___
>>> HCP-Users mailing list
>>> HCP-Users@humanconnectome.org
>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>
>>
>>
>

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Re: [HCP-Users] create borders based on .dlabel files

[Yizhou Ma]

So I can either edit in wb_view or save a label file with the colors I
want. Thanks!

On Mon, Nov 30, 2015 at 4:59 PM, Timothy Coalson  wrote:

> When displaying them in the GUI, select the "border" input mode, select
> "edit" in the added toolbar, make sure "properties" is depressed, then
> click on a border, then you get a popup where you can edit border colors.
> Then, save the file from the GUI and it will have those colors.
>
> There is currently no command to set border colors, but the
> -label-to-border command will use the label color as the output border
> color.  Unfortunately it looks like -border-merge may not currently
> preserve colors (there can be conflicts between files that I'd need to
> figure out what to do with).
>
> Tim
>
>
> On Mon, Nov 30, 2015 at 4:30 PM, Yizhou Ma  wrote:
>
>> This worked for me. Thanks!
>>
>> And how can I change the display of the border? Like the color and width?
>> I used -border-merge to merge all the borders and
>> -border-export-color-table to get the color table. Is there a way I can
>> save a border file with my own color table?
>>
>> Thanks,
>> Cherry
>>
>> On Mon, Nov 30, 2015 at 4:01 PM, Timothy Coalson  wrote:
>>
>>> The -label-to-border command requires gifti label files, as it does one
>>> surface at a time - there is not a cifti version of this command (because
>>> border files are surface only and single hemisphere, and there is no
>>> equivalent volume operation).  So, first -cifti-separate to get gifti label
>>> files:
>>>
>>> wb_command -cifti-separate melodic_IC_ftb.dlabel.nii -label CORTEX_LEFT
>>> test.L.label.gii -label CORTEX_RIGHT test.R.label.gii
>>>
>>> Then you can use -label-to-border:
>>>
>>> wb_command
>>> -label-to-border Q1-Q6_R440.L.inflated.32k_fs_LR.surf.gii test.L.label.gii
>>> test.L.border
>>> wb_command
>>> -label-to-border Q1-Q6_R440.R.inflated.32k_fs_LR.surf.gii test.R.label.gii
>>> test.R.border
>>>
>>> Note that cifti files generally can only be used with operations that
>>> begin with -cifti (there are some exceptions, like -nifti-information,
>>> -file-information, -set-map-names, -add-to-spec-file, -file-convert, ...)
>>>
>>> Tim
>>>
>>>
>>> On Mon, Nov 30, 2015 at 3:34 PM, Yizhou Ma  wrote:
>>>
 Dear HCP experts,

 I am trying to create borders based on HCP's .dlabel files. I am
 working on the FTB labels in the ICA PTN results. The reference surface I
 use is the R440 template, inflated surface. Here's the command I used:

 wb_command -label-to-border Q1-Q6_R440.L.inflated.32k_fs_LR.surf.gii
 melodic_IC_ftb.dlabel.nii test.border

 I got the following error message:

 ERROR: Parse Error while reading melodic_IC_ftb.dlabel.nii: error
 occurred while parsing element line number: 1 column number: 1

 Could somebody please help me with this?

 Thank you very much,
 Cherry

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

>>>
>>>
>>
>

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