subject:"Re\: \[Freesurfer\] mri_surf2vol cannot recognize the type of surf\/lh.inflated"

Re: [Freesurfer] mri_surf2vol cannot recognize the type of surf/lh.inflated

2017-05-15 Thread Ruopeng Wang

Not sure if I followed. Does the look up table have the labels at all?

> On May 15, 2017, at 7:46 PM, Bruce Fischl  wrote:
> 
> hmm, not sure. Ruopeng?
> 
> On Mon, 15 May 2017, Lukas Pezenka wrote:
> 
>> Thank you. The tip about Christophe's parcellation was very helpful - I
>> can actually see the sulcal labels in freesurfer when loading
>> aparc.a2009s+aparc volume. Oddly enough, when I check the "show existing
>> labels only" box, none of them is displayed - I wonder why that is?
>> 
>> I should, in any case, be able to build the map now. Thank you!
>> 
>> Best regards,
>> 
>> Lukas
>> 
>> On 15.05.2017 18:38, Bruce Fischl wrote:
>>> no, they shouldn't be labeled as 0. You can create your own though,
>>> possibly using Christophe's parcellation instead of the aparc.annot
>>> (check in recon-all.cmd to see how to run it). Christophe's has sulci
>>> labeled separately so might be better for your purposes. Or you could
>>> create your own from your own label(s)
>>> On Mon, 15 May 2017, Lukas Pezenka
>>> wrote:
>>> 
 Hi Bruce,
 
 not sure - from what I see, sulci are labelled as 0 in the wmparc, are
 they not? In my understanding, only gyri are actually labelled... I
 might as well get that totally wrong, though, so sorry if I do...
 
 Best regards,
 
 Lukas
 
 
 On 15.05.2017 15:53, Bruce Fischl wrote:
> Hi Lukas
> 
> lh.sulc is not a surface - it's a scalar field over the surface. Have you
> looked at the wmparc? Does it not fill your needs?
> 
> cheers
> Bruce
> 
> 
> On Mon, 15
> May 2017, Lukas Pezenka wrote:
> 
>> Hi all,
>> 
>> here's my follow-up: I've now tried to use mris_fill on my lh.sulc.
>> However, I got the error message that "there are many more faces than
>> vertices". Running recon-all on this dataset takes 30+ hours on my
>> machine, hence I don't want to do it again unless it is absolutely
>> necessary.
>> 
>> Can anybody recommend another way (or a solution to either my
>> mri_surf2vol or mris_fill problems) of obtaining a binary sulcus mask?
>> I'm in desperate need of one..
>> 
>> Best regards,
>> 
>> Lukas
>> 
>> 
>> On 12.05.2017 16:18, Lukas Pezenka wrote:
>>> Hi all,
>>> 
>>> I need a volume that maps my sulci. So first I've run recon-all on my
>>> data. Worked like a charm. Visual verification in freeview shows that
>>> the inflated surface looks just about right (although it does not seem
>>> to be registered to the aparc+aseg volume). However, when I try to run
>>> mri_surf2vol, I get the error message "ERROR: cannot recognize the type
>>> of surf/lh.inflated".
>>> 
>>> My precise syntax was mri_surf2vol --o out.nii --identity casestudy2
>>> --surf inflated --hemi --lh --surfval surf/lh.inflated
>>> 
>>> Can anyone advise me on this?
>>> 
>>> Best regards,
>>> 
>>> Lukas
>>> 
>>> PS :I'm running on FS version 5.3.0.
>>> PPS: Is it possible to achieve this from freeview rather than from the
>>> command line?
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> 
>>> 
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>>> it is
>>> addressed. If you believe this e-mail was sent to you in error and the 
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>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you 
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>>> but does not contain patient information, please contact the sender and 
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>>> dispose of the e-mail.
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>> 
>> 
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Re: [Freesurfer] mri_surf2vol cannot recognize the type of surf/lh.inflated

2017-05-15 Thread Bruce Fischl

hmm, not sure. Ruopeng?

On Mon, 15 May 2017, Lukas Pezenka wrote:

> Thank you. The tip about Christophe's parcellation was very helpful - I
> can actually see the sulcal labels in freesurfer when loading
> aparc.a2009s+aparc volume. Oddly enough, when I check the "show existing
> labels only" box, none of them is displayed - I wonder why that is?
>
> I should, in any case, be able to build the map now. Thank you!
>
> Best regards,
>
> Lukas
>
> On 15.05.2017 18:38, Bruce Fischl wrote:
>> no, they shouldn't be labeled as 0. You can create your own though,
>> possibly using Christophe's parcellation instead of the aparc.annot
>> (check in recon-all.cmd to see how to run it). Christophe's has sulci
>> labeled separately so might be better for your purposes. Or you could
>> create your own from your own label(s)
>> On Mon, 15 May 2017, Lukas Pezenka
>> wrote:
>>
>>> Hi Bruce,
>>>
>>> not sure - from what I see, sulci are labelled as 0 in the wmparc, are
>>> they not? In my understanding, only gyri are actually labelled... I
>>> might as well get that totally wrong, though, so sorry if I do...
>>>
>>> Best regards,
>>>
>>> Lukas
>>>
>>>
>>> On 15.05.2017 15:53, Bruce Fischl wrote:
 Hi Lukas

 lh.sulc is not a surface - it's a scalar field over the surface. Have you
 looked at the wmparc? Does it not fill your needs?

 cheers
 Bruce


 On Mon, 15
 May 2017, Lukas Pezenka wrote:

> Hi all,
>
> here's my follow-up: I've now tried to use mris_fill on my lh.sulc.
> However, I got the error message that "there are many more faces than
> vertices". Running recon-all on this dataset takes 30+ hours on my
> machine, hence I don't want to do it again unless it is absolutely
> necessary.
>
> Can anybody recommend another way (or a solution to either my
> mri_surf2vol or mris_fill problems) of obtaining a binary sulcus mask?
> I'm in desperate need of one..
>
> Best regards,
>
> Lukas
>
>
> On 12.05.2017 16:18, Lukas Pezenka wrote:
>> Hi all,
>>
>> I need a volume that maps my sulci. So first I've run recon-all on my
>> data. Worked like a charm. Visual verification in freeview shows that
>> the inflated surface looks just about right (although it does not seem
>> to be registered to the aparc+aseg volume). However, when I try to run
>> mri_surf2vol, I get the error message "ERROR: cannot recognize the type
>> of surf/lh.inflated".
>>
>> My precise syntax was mri_surf2vol --o out.nii --identity casestudy2
>> --surf inflated --hemi --lh --surfval surf/lh.inflated
>>
>> Can anyone advise me on this?
>>
>> Best regards,
>>
>> Lukas
>>
>> PS :I'm running on FS version 5.3.0.
>> PPS: Is it possible to achieve this from freeview rather than from the
>> command line?
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom 
>> it is
>> addressed. If you believe this e-mail was sent to you in error and the 
>> e-mail
>> contains patient information, please contact the Partners Compliance 
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you 
>> in error
>> but does not contain patient information, please contact the sender and 
>> properly
>> dispose of the e-mail.
>>
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>
>
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Re: [Freesurfer] mri_surf2vol cannot recognize the type of surf/lh.inflated

2017-05-15 Thread Lukas Pezenka

Thank you. The tip about Christophe's parcellation was very helpful - I 
can actually see the sulcal labels in freesurfer when loading 
aparc.a2009s+aparc volume. Oddly enough, when I check the "show existing 
labels only" box, none of them is displayed - I wonder why that is?

I should, in any case, be able to build the map now. Thank you!

Best regards,

Lukas

On 15.05.2017 18:38, Bruce Fischl wrote:
> no, they shouldn't be labeled as 0. You can create your own though,
> possibly using Christophe's parcellation instead of the aparc.annot
> (check in recon-all.cmd to see how to run it). Christophe's has sulci
> labeled separately so might be better for your purposes. Or you could
> create your own from your own label(s)
> On Mon, 15 May 2017, Lukas Pezenka
> wrote:
>
>> Hi Bruce,
>>
>> not sure - from what I see, sulci are labelled as 0 in the wmparc, are
>> they not? In my understanding, only gyri are actually labelled... I
>> might as well get that totally wrong, though, so sorry if I do...
>>
>> Best regards,
>>
>> Lukas
>>
>>
>> On 15.05.2017 15:53, Bruce Fischl wrote:
>>> Hi Lukas
>>>
>>> lh.sulc is not a surface - it's a scalar field over the surface. Have you
>>> looked at the wmparc? Does it not fill your needs?
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Mon, 15
>>> May 2017, Lukas Pezenka wrote:
>>>
 Hi all,

 here's my follow-up: I've now tried to use mris_fill on my lh.sulc.
 However, I got the error message that "there are many more faces than
 vertices". Running recon-all on this dataset takes 30+ hours on my
 machine, hence I don't want to do it again unless it is absolutely
 necessary.

 Can anybody recommend another way (or a solution to either my
 mri_surf2vol or mris_fill problems) of obtaining a binary sulcus mask?
 I'm in desperate need of one..

 Best regards,

 Lukas


 On 12.05.2017 16:18, Lukas Pezenka wrote:
> Hi all,
>
> I need a volume that maps my sulci. So first I've run recon-all on my
> data. Worked like a charm. Visual verification in freeview shows that
> the inflated surface looks just about right (although it does not seem
> to be registered to the aparc+aseg volume). However, when I try to run
> mri_surf2vol, I get the error message "ERROR: cannot recognize the type
> of surf/lh.inflated".
>
> My precise syntax was mri_surf2vol --o out.nii --identity casestudy2
> --surf inflated --hemi --lh --surfval surf/lh.inflated
>
> Can anyone advise me on this?
>
> Best regards,
>
> Lukas
>
> PS :I'm running on FS version 5.3.0.
> PPS: Is it possible to achieve this from freeview rather than from the
> command line?
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it 
> is
> addressed. If you believe this e-mail was sent to you in error and the 
> e-mail
> contains patient information, please contact the Partners Compliance 
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
>
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Re: [Freesurfer] mri_surf2vol cannot recognize the type of surf/lh.inflated

2017-05-15 Thread Bruce Fischl

no, they shouldn't be labeled as 0. You can create your own though, 
possibly using Christophe's parcellation instead of the aparc.annot 
(check in recon-all.cmd to see how to run it). Christophe's has sulci 
labeled separately so might be better for your purposes. Or you could 
create your own from your own label(s)
On Mon, 15 May 2017, Lukas Pezenka 
wrote:

> Hi Bruce,
>
> not sure - from what I see, sulci are labelled as 0 in the wmparc, are
> they not? In my understanding, only gyri are actually labelled... I
> might as well get that totally wrong, though, so sorry if I do...
>
> Best regards,
>
> Lukas
>
>
> On 15.05.2017 15:53, Bruce Fischl wrote:
>> Hi Lukas
>>
>> lh.sulc is not a surface - it's a scalar field over the surface. Have you
>> looked at the wmparc? Does it not fill your needs?
>>
>> cheers
>> Bruce
>>
>>
>> On Mon, 15
>> May 2017, Lukas Pezenka wrote:
>>
>>> Hi all,
>>>
>>> here's my follow-up: I've now tried to use mris_fill on my lh.sulc.
>>> However, I got the error message that "there are many more faces than
>>> vertices". Running recon-all on this dataset takes 30+ hours on my
>>> machine, hence I don't want to do it again unless it is absolutely
>>> necessary.
>>>
>>> Can anybody recommend another way (or a solution to either my
>>> mri_surf2vol or mris_fill problems) of obtaining a binary sulcus mask?
>>> I'm in desperate need of one..
>>>
>>> Best regards,
>>>
>>> Lukas
>>>
>>>
>>> On 12.05.2017 16:18, Lukas Pezenka wrote:
 Hi all,

 I need a volume that maps my sulci. So first I've run recon-all on my
 data. Worked like a charm. Visual verification in freeview shows that
 the inflated surface looks just about right (although it does not seem
 to be registered to the aparc+aseg volume). However, when I try to run
 mri_surf2vol, I get the error message "ERROR: cannot recognize the type
 of surf/lh.inflated".

 My precise syntax was mri_surf2vol --o out.nii --identity casestudy2
 --surf inflated --hemi --lh --surfval surf/lh.inflated

 Can anyone advise me on this?

 Best regards,

 Lukas

 PS :I'm running on FS version 5.3.0.
 PPS: Is it possible to achieve this from freeview rather than from the
 command line?
 ___
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

 The information in this e-mail is intended only for the person to whom it 
 is
 addressed. If you believe this e-mail was sent to you in error and the 
 e-mail
 contains patient information, please contact the Partners Compliance 
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you in 
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 properly
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Re: [Freesurfer] mri_surf2vol cannot recognize the type of surf/lh.inflated

2017-05-15 Thread Douglas N Greve

You need to use a valid output format like mgh, mgz, nii, etc (eg, 
surf/lh.inflated.mgh). Also, you should not run vol2surf mapping to the 
inflated surface as this surface is mostly outside the head. Use the 
default white surface and then visualize on the inflated only

On 05/12/2017 10:18 AM, Lukas Pezenka wrote:
> Hi all,
>
> I need a volume that maps my sulci. So first I've run recon-all on my
> data. Worked like a charm. Visual verification in freeview shows that
> the inflated surface looks just about right (although it does not seem
> to be registered to the aparc+aseg volume). However, when I try to run
> mri_surf2vol, I get the error message "ERROR: cannot recognize the type
> of surf/lh.inflated".
>
> My precise syntax was mri_surf2vol --o out.nii --identity casestudy2
> --surf inflated --hemi --lh --surfval surf/lh.inflated
>
> Can anyone advise me on this?
>
> Best regards,
>
> Lukas
>
> PS :I'm running on FS version 5.3.0.
> PPS: Is it possible to achieve this from freeview rather than from the
> command line?
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] mri_surf2vol cannot recognize the type of surf/lh.inflated

2017-05-15 Thread Lukas Pezenka

Hi Bruce,

not sure - from what I see, sulci are labelled as 0 in the wmparc, are 
they not? In my understanding, only gyri are actually labelled... I 
might as well get that totally wrong, though, so sorry if I do...

Best regards,

Lukas


On 15.05.2017 15:53, Bruce Fischl wrote:
> Hi Lukas
>
> lh.sulc is not a surface - it's a scalar field over the surface. Have you
> looked at the wmparc? Does it not fill your needs?
>
> cheers
> Bruce
>
>
> On Mon, 15
> May 2017, Lukas Pezenka wrote:
>
>> Hi all,
>>
>> here's my follow-up: I've now tried to use mris_fill on my lh.sulc.
>> However, I got the error message that "there are many more faces than
>> vertices". Running recon-all on this dataset takes 30+ hours on my
>> machine, hence I don't want to do it again unless it is absolutely
>> necessary.
>>
>> Can anybody recommend another way (or a solution to either my
>> mri_surf2vol or mris_fill problems) of obtaining a binary sulcus mask?
>> I'm in desperate need of one..
>>
>> Best regards,
>>
>> Lukas
>>
>>
>> On 12.05.2017 16:18, Lukas Pezenka wrote:
>>> Hi all,
>>>
>>> I need a volume that maps my sulci. So first I've run recon-all on my
>>> data. Worked like a charm. Visual verification in freeview shows that
>>> the inflated surface looks just about right (although it does not seem
>>> to be registered to the aparc+aseg volume). However, when I try to run
>>> mri_surf2vol, I get the error message "ERROR: cannot recognize the type
>>> of surf/lh.inflated".
>>>
>>> My precise syntax was mri_surf2vol --o out.nii --identity casestudy2
>>> --surf inflated --hemi --lh --surfval surf/lh.inflated
>>>
>>> Can anyone advise me on this?
>>>
>>> Best regards,
>>>
>>> Lukas
>>>
>>> PS :I'm running on FS version 5.3.0.
>>> PPS: Is it possible to achieve this from freeview rather than from the
>>> command line?
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom it is
>>> addressed. If you believe this e-mail was sent to you in error and the 
>>> e-mail
>>> contains patient information, please contact the Partners Compliance 
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>>> error
>>> but does not contain patient information, please contact the sender and 
>>> properly
>>> dispose of the e-mail.
>>>
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Re: [Freesurfer] mri_surf2vol cannot recognize the type of surf/lh.inflated

2017-05-15 Thread Bruce Fischl

Hi Lukas

lh.sulc is not a surface - it's a scalar field over the surface. Have you 
looked at the wmparc? Does it not fill your needs?

cheers
Bruce


On Mon, 15 
May 2017, Lukas Pezenka wrote:

> Hi all,
>
> here's my follow-up: I've now tried to use mris_fill on my lh.sulc.
> However, I got the error message that "there are many more faces than
> vertices". Running recon-all on this dataset takes 30+ hours on my
> machine, hence I don't want to do it again unless it is absolutely
> necessary.
>
> Can anybody recommend another way (or a solution to either my
> mri_surf2vol or mris_fill problems) of obtaining a binary sulcus mask?
> I'm in desperate need of one..
>
> Best regards,
>
> Lukas
>
>
> On 12.05.2017 16:18, Lukas Pezenka wrote:
>> Hi all,
>>
>> I need a volume that maps my sulci. So first I've run recon-all on my
>> data. Worked like a charm. Visual verification in freeview shows that
>> the inflated surface looks just about right (although it does not seem
>> to be registered to the aparc+aseg volume). However, when I try to run
>> mri_surf2vol, I get the error message "ERROR: cannot recognize the type
>> of surf/lh.inflated".
>>
>> My precise syntax was mri_surf2vol --o out.nii --identity casestudy2
>> --surf inflated --hemi --lh --surfval surf/lh.inflated
>>
>> Can anyone advise me on this?
>>
>> Best regards,
>>
>> Lukas
>>
>> PS :I'm running on FS version 5.3.0.
>> PPS: Is it possible to achieve this from freeview rather than from the
>> command line?
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
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Re: [Freesurfer] mri_surf2vol cannot recognize the type of surf/lh.inflated

2017-05-15 Thread Lukas Pezenka

Hi all,

here's my follow-up: I've now tried to use mris_fill on my lh.sulc. 
However, I got the error message that "there are many more faces than 
vertices". Running recon-all on this dataset takes 30+ hours on my 
machine, hence I don't want to do it again unless it is absolutely 
necessary.

Can anybody recommend another way (or a solution to either my 
mri_surf2vol or mris_fill problems) of obtaining a binary sulcus mask? 
I'm in desperate need of one..

Best regards,

Lukas


On 12.05.2017 16:18, Lukas Pezenka wrote:
> Hi all,
>
> I need a volume that maps my sulci. So first I've run recon-all on my
> data. Worked like a charm. Visual verification in freeview shows that
> the inflated surface looks just about right (although it does not seem
> to be registered to the aparc+aseg volume). However, when I try to run
> mri_surf2vol, I get the error message "ERROR: cannot recognize the type
> of surf/lh.inflated".
>
> My precise syntax was mri_surf2vol --o out.nii --identity casestudy2
> --surf inflated --hemi --lh --surfval surf/lh.inflated
>
> Can anyone advise me on this?
>
> Best regards,
>
> Lukas
>
> PS :I'm running on FS version 5.3.0.
> PPS: Is it possible to achieve this from freeview rather than from the
> command line?
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Re: [Freesurfer] mri_surf2vol cannot recognize the type of surf/lh.inflated

Re: [Freesurfer] mri_surf2vol cannot recognize the type of surf/lh.inflated

Re: [Freesurfer] mri_surf2vol cannot recognize the type of surf/lh.inflated

Re: [Freesurfer] mri_surf2vol cannot recognize the type of surf/lh.inflated

Re: [Freesurfer] mri_surf2vol cannot recognize the type of surf/lh.inflated

Re: [Freesurfer] mri_surf2vol cannot recognize the type of surf/lh.inflated

Re: [Freesurfer] mri_surf2vol cannot recognize the type of surf/lh.inflated

Re: [Freesurfer] mri_surf2vol cannot recognize the type of surf/lh.inflated

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