Re: [Freesurfer] label to surface

2020-07-10 Thread Sam W 
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Hi Doug,
I'm using this command:
mri_label2label --srclabel lh.fusiform.label --trglabel output.label --s
sub01 --regmethod surface --hemi lh --outmask outmask.gii
Best regards,
Sam


On Fri, Jul 10, 2020 at 9:48 PM Douglas N. Greve 
wrote:

> what's your mri_label2label command?
>
> On 7/10/2020 3:05 PM, Sam W wrote:
>
> External Email - Use Caution
> Hi Doug and Tim,
> I'm running probtrackx with freesurfer surfaces as seeds. However
> probtrackx requires a file that contains both the whole surface file (eg,
> lh.pial) as well as the overlay (the scalar values associated with the
> vertices of the roi).
> I can create such a file with FSL's label2surf command which creates a
> gifti file that encodes both the surface and the overlay.
> My question is whether I can do the same with freesurfer? Running
> probtrackx with the overlay from mri_label2label --outmask does not work.
> It also needs the associated pial or white surface.
> Best regards,
> Sam
>
>
> On Fri, Jul 10, 2020 at 4:29 PM Douglas N. Greve 
> wrote:
>
>> what do you mean merge with the pial?
>>
>> On 7/9/2020 8:07 PM, Sam W wrote:
>>
>> External Email - Use Caution
>> It works great Doug, thanks a lot!
>> Can I ask you a follow up question please? I created the overlay with
>> mri_label2label using --outmask as you suggested, but now I'd like to merge
>> that overlay with the pial surface (lh.pial). Is there a tool I can use to
>> achieve that result?
>> Best regards,
>> Sam
>>
>>
>> On Thu, Jul 9, 2020 at 7:31 PM Douglas N. Greve 
>> wrote:
>>
>>> Use mri_label2label with the --outmask option
>>>
>>> On 7/8/2020 10:14 PM, Sam W wrote:
>>>
>>> External Email - Use Caution
>>> Hi,
>>> Is there a way to convert a label file into a surface/overlay? Thank you!
>>> Best regards,
>>> Sam
>>>
>>> ___
>>> Freesurfer mailing 
>>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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Re: [Freesurfer] label to surface

2020-07-10 Thread Douglas N. Greve 

what's your mri_label2label command?

On 7/10/2020 3:05 PM, Sam W wrote:


External Email - Use Caution

Hi Doug and Tim,
I'm running probtrackx with freesurfer surfaces as seeds. However 
probtrackx requires a file that contains both the whole surface file 
(eg, lh.pial) as well as the overlay (the scalar values associated 
with the vertices of the roi).
I can create such a file with FSL's label2surf command which creates a 
gifti file that encodes both the surface and the overlay.
My question is whether I can do the same with freesurfer? Running 
probtrackx with the overlay from mri_label2label --outmask does not 
work. It also needs the associated pial or white surface.

Best regards,
Sam


On Fri, Jul 10, 2020 at 4:29 PM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:


what do you mean merge with the pial?

On 7/9/2020 8:07 PM, Sam W wrote:


External Email - Use Caution

It works great Doug, thanks a lot!
Can I ask you a follow up question please? I created the overlay
with mri_label2label using --outmask as you suggested, but now
I'd like to merge that overlay with the pial surface (lh.pial).
Is there a tool I can use to achieve that result?
Best regards,
Sam


On Thu, Jul 9, 2020 at 7:31 PM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:

Use mri_label2label with the --outmask option

On 7/8/2020 10:14 PM, Sam W wrote:


External Email - Use Caution

Hi,
Is there a way to convert a label file into a
surface/overlay? Thank you!
Best regards,
Sam

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Re: [Freesurfer] label to surface

2020-07-10 Thread Sam W 
External Email - Use Caution

Hi Doug and Tim,
I'm running probtrackx with freesurfer surfaces as seeds. However
probtrackx requires a file that contains both the whole surface file (eg,
lh.pial) as well as the overlay (the scalar values associated with the
vertices of the roi).
I can create such a file with FSL's label2surf command which creates a
gifti file that encodes both the surface and the overlay.
My question is whether I can do the same with freesurfer? Running
probtrackx with the overlay from mri_label2label --outmask does not work.
It also needs the associated pial or white surface.
Best regards,
Sam


On Fri, Jul 10, 2020 at 4:29 PM Douglas N. Greve 
wrote:

> what do you mean merge with the pial?
>
> On 7/9/2020 8:07 PM, Sam W wrote:
>
> External Email - Use Caution
> It works great Doug, thanks a lot!
> Can I ask you a follow up question please? I created the overlay with
> mri_label2label using --outmask as you suggested, but now I'd like to merge
> that overlay with the pial surface (lh.pial). Is there a tool I can use to
> achieve that result?
> Best regards,
> Sam
>
>
> On Thu, Jul 9, 2020 at 7:31 PM Douglas N. Greve 
> wrote:
>
>> Use mri_label2label with the --outmask option
>>
>> On 7/8/2020 10:14 PM, Sam W wrote:
>>
>> External Email - Use Caution
>> Hi,
>> Is there a way to convert a label file into a surface/overlay? Thank you!
>> Best regards,
>> Sam
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] label to surface

2020-07-10 Thread Douglas N. Greve 

what do you mean merge with the pial?

On 7/9/2020 8:07 PM, Sam W wrote:


External Email - Use Caution

It works great Doug, thanks a lot!
Can I ask you a follow up question please? I created the overlay with 
mri_label2label using --outmask as you suggested, but now I'd like to 
merge that overlay with the pial surface (lh.pial). Is there a tool I 
can use to achieve that result?

Best regards,
Sam


On Thu, Jul 9, 2020 at 7:31 PM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:


Use mri_label2label with the --outmask option

On 7/8/2020 10:14 PM, Sam W wrote:


External Email - Use Caution

Hi,
Is there a way to convert a label file into a surface/overlay?
Thank you!
Best regards,
Sam

___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] label to surface

2020-07-10 Thread Tim Schäfer 
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It should just work when displayed on the pial surface, the vertex indices are 
equivalent. Did you try it?

Or what exactly do you mean by 'merging' with the pial surface?

Tim

> On July 10, 2020 at 2:07 AM Sam W  wrote:
> 
> 
> External Email - Use Caution
> 
> It works great Doug, thanks a lot!
> Can I ask you a follow up question please? I created the overlay with
> mri_label2label using --outmask as you suggested, but now I'd like to merge
> that overlay with the pial surface (lh.pial). Is there a tool I can use to
> achieve that result?
> Best regards,
> Sam
> 
> 
> On Thu, Jul 9, 2020 at 7:31 PM Douglas N. Greve 
> wrote:
> 
> > Use mri_label2label with the --outmask option
> >
> > On 7/8/2020 10:14 PM, Sam W wrote:
> >
> > External Email - Use Caution
> > Hi,
> > Is there a way to convert a label file into a surface/overlay? Thank you!
> > Best regards,
> > Sam
> >
> > ___
> > Freesurfer mailing 
> > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] label to surface

2020-07-09 Thread Sam W 
External Email - Use Caution

It works great Doug, thanks a lot!
Can I ask you a follow up question please? I created the overlay with
mri_label2label using --outmask as you suggested, but now I'd like to merge
that overlay with the pial surface (lh.pial). Is there a tool I can use to
achieve that result?
Best regards,
Sam


On Thu, Jul 9, 2020 at 7:31 PM Douglas N. Greve 
wrote:

> Use mri_label2label with the --outmask option
>
> On 7/8/2020 10:14 PM, Sam W wrote:
>
> External Email - Use Caution
> Hi,
> Is there a way to convert a label file into a surface/overlay? Thank you!
> Best regards,
> Sam
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] label to surface

2020-07-09 Thread Douglas N. Greve 

Use mri_label2label with the --outmask option

On 7/8/2020 10:14 PM, Sam W wrote:


External Email - Use Caution

Hi,
Is there a way to convert a label file into a surface/overlay? Thank you!
Best regards,
Sam

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[Freesurfer] label to surface

2020-07-08 Thread Sam W 
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Hi,
Is there a way to convert a label file into a surface/overlay? Thank you!
Best regards,
Sam
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