[Freesurfer] can not find module 'dev'

[Yun Wang]

Dear All,

I recently tried to gain  access the read-only CVS source-code repository, 
however, I have this kind of error:

cvs server: cannot find module `dev' - ignored
cvs [checkout aborted]: cannot expand modules

anyone have idea what is going on here? 

Thank you so much!



Best,

Yun Wang

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[Freesurfer] can not find module 'dev'

[Yun Wang]

Dear All,

I recently tried to gain  access the read-only CVS source-code repository, 
however, I have this kind of error:

cvs server: cannot find module `dev' - ignored
cvs [checkout aborted]: cannot expand modules

anyone have idea what is going on here? 

Thank you so much!



Best,

Yun Wang

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[Freesurfer] can not find module 'dev'

[Yun Wang]

Dear All,

I recently tried to gain  access the read-only CVS source-code repository, 
however, I have this kind of error:

cvs server: cannot find module `dev' - ignored
cvs [checkout aborted]: cannot expand modules

anyone have idea what is going on here? 

Thank you so much!



Best,

Yun Wang

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[Freesurfer] How to register the workshop at Boston

[Yun Wang]

Dear All,


I am new to Freesurfer, so I want to take the Freesurfer Workshops at Boston 
this April. But It appears I have passed the deadline to register. Does anyone 
know how to make it happen?


Thanks!


Yun Wang
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Re: [Freesurfer] recon-all pipeline for (sub-millimeter) 7T data

[Yun Wang]

Hi,

I recently using Freesurfer 6 beta version to recon high resolution data with 
the -cm flag, however,   the program exit with error.
total defect index = 0

\n mris_euler_number ../surf/rh.orig \n

Darwin AlbertStekiiMac 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29 02:26:53 
PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64



recon-all -s HIP001_3d exited with ERRORS at Thu Oct 22 08:15:53 CDT 2015

Attached is the whole log history. 

Thanks for any idea!

Yun 

> On Oct 18, 2015, at 14:10, Bruce Fischl  wrote:
> 
> you can use the -cm flag, but you might want to try out a beta of v6 instead 
> of 5.3
> On Sun, 18 Oct 2015, Yun Wang wrote:
> 
>> Glad to hear this ! So how should I specify high resolution structure using 
>> recon-all command?
>> 
>> 
>>> On Oct 17, 2015, at 10:09, Bruce Fischl  wrote:
>>> 
>>> High resolution fMRI has always been supported. V6 beta has better support 
>>> for high-resolution structurals. If your fMRI is higher than 1mm isotropic 
>>> then having higher res structurals (and hence denser cortical meshes) might 
>>> be useful
>>> 
>>> cheers
>>> Bruce
>>> 
>>> 
>>> 
>>> On Sat, 17 Oct 2015, Yun Wang wrote:
>>> 
>>>> Can the recon-all for high resolution fMRI data be used in V6 beta 
>>>> freesurfer now? If
>>>> so, how to use it?
>>>> 
>>>> On Jun 25, 2015, at 13:36, Allison Moreau 
>>>> 
>>>> wrote:
>>>> Hi Falk and Thomas,
>>>> We are actually working on testing the -hires flag now for the v6 release. 
>>>> We
>>>> intend to release it with v6.
>>>> -Allison
>>>> On 06/25/2015 07:09 AM, Falk Lüsebrink wrote:
>>>> Hi Thomas,
>>>> 
>>>> this looks like a really nice script and a lot better than my own. In the
>>>> upcoming release of FreeSurfer v.6 my work-around probably is not needed
>>>> anymore. However, I haven’t been able to have a look at the dev release yet
>>>> and whether the standard recon-all features a flag to process high
>>>> resolution data.
>>>> 
>>>> Best,
>>>> Falk
>>>> 
>>>> P.S. Following your instructions one will definitely become a coffee
>>>> junkie. :D
>>>> 
>>>> Von: freesurfer-boun...@nmr.mgh.harvard.edu 
>>>> [mailto:freesurfer-boun...@nmr.mgh.harvard
>>>> .edu] Im Auftrag von Emmerling Thomas (PSYCHOLOGY)
>>>> Gesendet: Mittwoch, 24. Juni 2015 14:35
>>>> An: freesurfer@nmr.mgh.harvard.edu
>>>> Betreff: [Freesurfer] recon-all pipeline for (sub-millimeter) 7T data
>>>> 
>>>> Hello!
>>>> 
>>>> I wrote a bash script some time ago to process data acquired at a
>>>> sub-millimeter resolution following the nice wiki entry of Falk Lüsebrink
>>>> (https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon). I thought it might
>>>> be helpful for others, too, as there are some questions about it in the
>>>> mailing list archives, so here it
>>>> is: https://github.com/thomastweets/freesurfer-7t-pipeline. I am happy
>>>> about any comments!
>>>> 
>>>> Best,
>>>> Thomas
>>>> ___
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>> ___
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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 
>>>> error
>>>> but does not contain patient information, please contact the sender and 
>>>> properly
>>>> dispose of the e-mail.
>>> ___
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>>> 
>>> 
>>> The information in this e-mail is intended only 

Re: [Freesurfer] recon-all pipeline for (sub-millimeter) 7T data

[Yun Wang]

It works pretty well, thanks ! 

> On Oct 18, 2015, at 14:10, Bruce Fischl  wrote:
> 
> you can use the -cm flag, but you might want to try out a beta of v6 instead 
> of 5.3
> On Sun, 18 Oct 2015, Yun Wang wrote:
> 
>> Glad to hear this ! So how should I specify high resolution structure using 
>> recon-all command?
>> 
>> 
>>> On Oct 17, 2015, at 10:09, Bruce Fischl  wrote:
>>> 
>>> High resolution fMRI has always been supported. V6 beta has better support 
>>> for high-resolution structurals. If your fMRI is higher than 1mm isotropic 
>>> then having higher res structurals (and hence denser cortical meshes) might 
>>> be useful
>>> 
>>> cheers
>>> Bruce
>>> 
>>> 
>>> 
>>> On Sat, 17 Oct 2015, Yun Wang wrote:
>>> 
>>>> Can the recon-all for high resolution fMRI data be used in V6 beta 
>>>> freesurfer now? If
>>>> so, how to use it?
>>>> 
>>>> On Jun 25, 2015, at 13:36, Allison Moreau 
>>>> 
>>>> wrote:
>>>> Hi Falk and Thomas,
>>>> We are actually working on testing the -hires flag now for the v6 release. 
>>>> We
>>>> intend to release it with v6.
>>>> -Allison
>>>> On 06/25/2015 07:09 AM, Falk Lüsebrink wrote:
>>>> Hi Thomas,
>>>> 
>>>> this looks like a really nice script and a lot better than my own. In the
>>>> upcoming release of FreeSurfer v.6 my work-around probably is not needed
>>>> anymore. However, I haven’t been able to have a look at the dev release yet
>>>> and whether the standard recon-all features a flag to process high
>>>> resolution data.
>>>> 
>>>> Best,
>>>> Falk
>>>> 
>>>> P.S. Following your instructions one will definitely become a coffee
>>>> junkie. :D
>>>> 
>>>> Von: freesurfer-boun...@nmr.mgh.harvard.edu 
>>>> [mailto:freesurfer-boun...@nmr.mgh.harvard
>>>> .edu] Im Auftrag von Emmerling Thomas (PSYCHOLOGY)
>>>> Gesendet: Mittwoch, 24. Juni 2015 14:35
>>>> An: freesurfer@nmr.mgh.harvard.edu
>>>> Betreff: [Freesurfer] recon-all pipeline for (sub-millimeter) 7T data
>>>> 
>>>> Hello!
>>>> 
>>>> I wrote a bash script some time ago to process data acquired at a
>>>> sub-millimeter resolution following the nice wiki entry of Falk Lüsebrink
>>>> (https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon). I thought it might
>>>> be helpful for others, too, as there are some questions about it in the
>>>> mailing list archives, so here it
>>>> is: https://github.com/thomastweets/freesurfer-7t-pipeline. I am happy
>>>> about any comments!
>>>> 
>>>> Best,
>>>> Thomas
>>>> ___
>>>> 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
>>>> 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.
>>> ___
>>> 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.
>> 
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
>> 
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> 
> 
> 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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Re: [Freesurfer] recon-all pipeline for (sub-millimeter) 7T data

[Yun Wang]

Glad to hear this ! So how should I specify high resolution structure using 
recon-all command?


> On Oct 17, 2015, at 10:09, Bruce Fischl  wrote:
> 
> High resolution fMRI has always been supported. V6 beta has better support 
> for high-resolution structurals. If your fMRI is higher than 1mm isotropic 
> then having higher res structurals (and hence denser cortical meshes) might 
> be useful
> 
> cheers
> Bruce
> 
> 
> 
> On Sat, 17 Oct 2015, Yun Wang wrote:
> 
>> Can the recon-all for high resolution fMRI data be used in V6 beta 
>> freesurfer now? If
>> so, how to use it?
>> 
>>  On Jun 25, 2015, at 13:36, Allison Moreau 
>>  wrote:
>> Hi Falk and Thomas,
>> We are actually working on testing the -hires flag now for the v6 release. We
>> intend to release it with v6.
>> -Allison 
>> On 06/25/2015 07:09 AM, Falk Lüsebrink wrote:
>>  Hi Thomas,
>>  
>> this looks like a really nice script and a lot better than my own. In the
>> upcoming release of FreeSurfer v.6 my work-around probably is not needed
>> anymore. However, I haven’t been able to have a look at the dev release yet
>> and whether the standard recon-all features a flag to process high
>> resolution data.
>>  
>> Best,
>> Falk
>>  
>> P.S. Following your instructions one will definitely become a coffee
>> junkie. :D
>>  
>> Von: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [mailto:freesurfer-boun...@nmr.mgh.harvard
>> .edu] Im Auftrag von Emmerling Thomas (PSYCHOLOGY)
>> Gesendet: Mittwoch, 24. Juni 2015 14:35
>> An: freesurfer@nmr.mgh.harvard.edu
>> Betreff: [Freesurfer] recon-all pipeline for (sub-millimeter) 7T data
>>  
>> Hello!
>>  
>> I wrote a bash script some time ago to process data acquired at a
>> sub-millimeter resolution following the nice wiki entry of Falk Lüsebrink
>> (https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon). I thought it might
>> be helpful for others, too, as there are some questions about it in the
>> mailing list archives, so here it
>> is: https://github.com/thomastweets/freesurfer-7t-pipeline. I am happy
>> about any comments!
>>  
>> Best,
>> Thomas
>> ___
>> 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
>> 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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> 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] recon-all pipeline for (sub-millimeter) 7T data

[Yun Wang]

Can the recon-all for high resolution fMRI data be used in V6 beta freesurfer 
now? If so, how to use it?


> On Jun 25, 2015, at 13:36, Allison Moreau  
> wrote:
> 
> Hi Falk and Thomas,
> 
> We are actually working on testing the -hires flag now for the v6 release. We 
> intend to release it with v6.
> 
> -Allison 
> 
> On 06/25/2015 07:09 AM, Falk Lüsebrink wrote:
>> Hi Thomas,
>>  
>> this looks like a really nice script and a lot better than my own. In the 
>> upcoming release of FreeSurfer v.6 my work-around probably is not needed 
>> anymore. However, I haven’t been able to have a look at the dev release yet 
>> and whether the standard recon-all features a flag to process high 
>> resolution data.
>>  
>> Best,
>> Falk
>>  
>> P.S. Following your instructions one will definitely become a coffee junkie. 
>> :D
>>  
>> Von: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu 
>> ] Im Auftrag von Emmerling 
>> Thomas (PSYCHOLOGY)
>> Gesendet: Mittwoch, 24. Juni 2015 14:35
>> An: freesurfer@nmr.mgh.harvard.edu 
>> Betreff: [Freesurfer] recon-all pipeline for (sub-millimeter) 7T data
>>  
>> Hello!
>>  
>> I wrote a bash script some time ago to process data acquired at a 
>> sub-millimeter resolution following the nice wiki entry of Falk Lüsebrink 
>> (https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon 
>> ). I thought it might 
>> be helpful for others, too, as there are some questions about it in the 
>> mailing list archives, so here it is: 
>> https://github.com/thomastweets/freesurfer-7t-pipeline 
>> . I am happy about 
>> any comments!
>>  
>> Best,
>> Thomas
>> 
>> 
>> ___
>> 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 
> 
> 
> 
> 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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[Freesurfer] high resolution data using recon-all

[Yun Wang]

Hi All,

I have 7T high resolution data 0.625mm.  Is it  appropriate to process the data 
using recon-all ? If not, any idea?

Thanks!


Yun Wang
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[Freesurfer] Cortical Parcellation Atlas Question

[Yun Wang]

Hi All,


I am currently doing resting state fMRI functional connectivity across the 
cortical. Is it appropriate that I use Freesurfer cortical Parcellation altas 
such as Desikan-Killany Atlas to extract time series?


Thanks!

Yun
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Re: [Freesurfer] extract time series from surface vertices

[Yun Wang]

Thanks! It works! 
> On Oct 7, 2015, at 10:31, Yun Wang  wrote:
> 
> Thanks for your answer. But I am not so sure about what I am doing here, 
> could you please check here. The main idea is to extract ROI average time 
> series from different layer surface. 
> 
> what I have done
> 1 using mris_expand to get intermediate  layer,  such as lh. 
> white_outer0.16GM. 
> 2 using bbregister to register functional volume to anatomical volume. 
> 3 using mri_vol2surf to sample the functional data to the intermediate layer. 
> mri_vol2surf --mov filtered_func_data.nii.gz --out $SUBJECTS_DIR/lh_0.16.w 
> --out_type paint --srcreg register.dat --hemi lh --projfrac 0 --surf 
> white_outer0.16GM
> 
> after get lh_0.16.w, how should I use this file in mri_segstats function! 
> This is a overlay file, not a volume or surface. 
> 
> 
> Thanks!
> 
> 
> 
>> On Oct 5, 2015, at 18:38, Douglas Greve > <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>> 
>> mri_segstats with the label option. Specify --id 1 and use the --avgwf 
>> output option to get the full time course
>> 
>> On 10/5/15 1:34 PM, Yun Wang wrote:
>>> Hi All,
>>> 
>>> If I use mri_vol2surf to sample the functional volume onto surface, how can 
>>> I extract the time series  from surface vertices corresponding to certain 
>>> ROI or Label which were created by freesurfer.
>>> 
>>> Thanks!
>>> 
>>> Yun
>>> ___
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>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> 
>>> 
>> 
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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 
>> error
>> but does not contain patient information, please contact the sender and 
>> properly
>> dispose of the e-mail.
>> 
> 

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Re: [Freesurfer] extract time series from surface vertices

[Yun Wang]

Thanks for your answer. But I am not so sure about what I am doing here, could 
you please check here. The main idea is to extract ROI average time series from 
different layer surface. 

what I have done
1 using mris_expand to get intermediate  layer,  such as lh. white_outer0.16GM. 
2 using bbregister to register functional volume to anatomical volume. 
3 using mri_vol2surf to sample the functional data to the intermediate layer. 
mri_vol2surf --mov filtered_func_data.nii.gz --out $SUBJECTS_DIR/lh_0.16.w 
--out_type paint --srcreg register.dat --hemi lh --projfrac 0 --surf 
white_outer0.16GM

after get lh_0.16.w, how should I use this file in mri_segstats function! This 
is a overlay file, not a volume or surface. 


Thanks!



> On Oct 5, 2015, at 18:38, Douglas Greve  wrote:
> 
> mri_segstats with the label option. Specify --id 1 and use the --avgwf 
> output option to get the full time course
> 
> On 10/5/15 1:34 PM, Yun Wang wrote:
>> Hi All,
>> 
>> If I use mri_vol2surf to sample the functional volume onto surface, how can 
>> I extract the time series  from surface vertices corresponding to certain 
>> ROI or Label which were created by freesurfer.
>> 
>> Thanks!
>> 
>> Yun
>> ___
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[Freesurfer] extract time series from surface vertices

[Yun Wang]

Hi All,

If I use mri_vol2surf to sample the functional volume onto surface, how can I 
extract the time series  from surface vertices corresponding to certain ROI or 
Label which were created by freesurfer. 

Thanks!

Yun
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Re: [Freesurfer] different layer ROI

[Yun Wang]

Oh, so after I get the different layers’ functional data,  using which function 
to extract V1 ROI value ? I am not so familiar with freesurfer, excuse me with 
my ignorance. 


> On Sep 25, 2015, at 11:45, Bruce Fischl  wrote:
> 
> projdist would be 0 since you want to sample right on the surface location. I 
> don't think you need a mask
> On Fri, 25 Sep 2015, Yun Wang wrote:
> 
>> Thanks! Again I want to make sure when using mri_vol2surf for my case
>> the options
>> 
>> —surf   :  my layer surface  ?
>> —projdist : how should I use this?
>> —mask:the label that I want use V1?
>> 
>> 
>> 
>> 
>>> On Sep 25, 2015, at 11:18, Bruce Fischl  wrote:
>>> 
>>> Hi Yun
>>> 
>>> just specify the surface you want in mri_vol2surf to generate a time series 
>>> per-vertex on each surface, then you can average each of those within the 
>>> V1 ROI if you want.
>>> 
>>> cheers
>>> Bruce
>>> 
>>> 
>>> 
>>> On Fri, 25 Sep 2015, Yun Wang wrote:
>>> 
>>>> But the question is how to sample different layer surface ’s functional 
>>>> data in one or multiple ROI.
>>>> 
>>>> Thanks!
>>>> 
>>>> Yun
>>>> 
>>>> 
>>>>> On Sep 25, 2015, at 10:59, Bruce Fischl  
>>>>> wrote:
>>>>> 
>>>>> you want to extract the time series from an fMRI volume in say "deep" and 
>>>>> "superficial" V1? If so, then I think what you want is 3 intermediate 
>>>>> surfaces between white and pial, then sample using surfaces 1 and 3 (but 
>>>>> not 2, which would be the boundary between the top half and the bottom 
>>>>> half).
>>>>> 
>>>>> cheers
>>>>> Bruce
>>>>> 
>>>>> On Fri, 25 Sep 2015, Yun Wang wrote:
>>>>> 
>>>>>> Hi All,
>>>>>> 
>>>>>> I have two questions:
>>>>>> 
>>>>>> 1   I have used mris_expand to get additional two layer surface 
>>>>>> between white and pial surface. what I want to do next : using label 
>>>>>> such as V1 as ROI, then get different layer ROI in V1. How can I get it?
>>>>>> 
>>>>>> 2 After I get layers’ ROI, I want to extract the time series . Anyone 
>>>>>> have idea?
>>>>>> 
>>>>>> 
>>>>>> Thanks!
>>>>>> 
>>>>>> Yun Wang
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>>>>>> 
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Re: [Freesurfer] different layer ROI

[Yun Wang]

Thanks! Again I want to make sure when using mri_vol2surf for my case 
the options
 
—surf   :  my layer surface  ?
—projdist : how should I use this?
—mask:the label that I want use V1? 




> On Sep 25, 2015, at 11:18, Bruce Fischl  wrote:
> 
> Hi Yun
> 
> just specify the surface you want in mri_vol2surf to generate a time series 
> per-vertex on each surface, then you can average each of those within the V1 
> ROI if you want.
> 
> cheers
> Bruce
> 
> 
> 
> On Fri, 25 Sep 2015, Yun Wang wrote:
> 
>> But the question is how to sample different layer surface ’s functional data 
>> in one or multiple ROI.
>> 
>> Thanks!
>> 
>> Yun
>> 
>> 
>>> On Sep 25, 2015, at 10:59, Bruce Fischl  wrote:
>>> 
>>> you want to extract the time series from an fMRI volume in say "deep" and 
>>> "superficial" V1? If so, then I think what you want is 3 intermediate 
>>> surfaces between white and pial, then sample using surfaces 1 and 3 (but 
>>> not 2, which would be the boundary between the top half and the bottom 
>>> half).
>>> 
>>> cheers
>>> Bruce
>>> 
>>> On Fri, 25 Sep 2015, Yun Wang wrote:
>>> 
>>>> Hi All,
>>>> 
>>>> I have two questions:
>>>> 
>>>> 1   I have used mris_expand to get additional two layer surface 
>>>> between white and pial surface. what I want to do next : using label such 
>>>> as V1 as ROI, then get different layer ROI in V1. How can I get it?
>>>> 
>>>> 2 After I get layers’ ROI, I want to extract the time series . Anyone have 
>>>> idea?
>>>> 
>>>> 
>>>> Thanks!
>>>> 
>>>> Yun Wang
>>>> ___
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>>>> 
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Re: [Freesurfer] different layer ROI

[Yun Wang]

But the question is how to sample different layer surface ’s functional data in 
one or multiple ROI.

Thanks!

Yun


> On Sep 25, 2015, at 10:59, Bruce Fischl  wrote:
> 
> you want to extract the time series from an fMRI volume in say "deep" and 
> "superficial" V1? If so, then I think what you want is 3 intermediate 
> surfaces between white and pial, then sample using surfaces 1 and 3 (but not 
> 2, which would be the boundary between the top half and the bottom half).
> 
> cheers
> Bruce
> 
> On Fri, 25 Sep 2015, Yun Wang wrote:
> 
>> Hi All,
>> 
>> I have two questions:
>> 
>> 1   I have used mris_expand to get additional two layer surface between 
>> white and pial surface. what I want to do next : using label such as V1 as 
>> ROI, then get different layer ROI in V1. How can I get it?
>> 
>> 2 After I get layers’ ROI, I want to extract the time series . Anyone have 
>> idea?
>> 
>> 
>> Thanks!
>> 
>> Yun Wang
>> ___
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[Freesurfer] different layer ROI

[Yun Wang]

Hi All,

I have two questions:

1   I have used mris_expand to get additional two layer surface between 
white and pial surface. what I want to do next : using label such as V1 as ROI, 
then get different layer ROI in V1. How can I get it?

2 After I get layers’ ROI, I want to extract the time series . Anyone have idea?


Thanks! 

Yun Wang
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Re: [Freesurfer] Basic questions regarding of layers

[Yun Wang]

Thanks for your answer! Truly help me a lot!  

> On Sep 8, 2015, at 07:17, Bruce Fischl  wrote:
> 
> Hi Yun
> 
> 1. No, the surfaces are not binary. They exist in in a continuum, so aren't 
> limited by the resolution of the underlying volumes. You should be able to 
> visualize them over the volumes using
> 
> freeview -v  -f 
> 
> 2. mri_compute_layer_fractions computes the volume fractions of each 
> compartment in each voxel (e.g. it's 20% white matter and 80% in the first 
> compartment of gray matter), then mris_compute_layer_intensities uses these 
> volume fractions and sets up a linear systems of equations to solve for the 
> "unmixed" intensities of each layer. It does so by pooling voxels across 
> space so you sacrifice some tangential resolution. Note that this of course 
> does not resolve the issue of super-resolution, which can't work in 
> band-limited MRI acquisitions. Still, at 1mm you should be able to get a 
> reasonable 2-layer estimate.
> 
> Note also that you can directly visualize the outputs of both steps. 
> mri_compute_layer_fractions will output a multi-frame volume, where each 
> frame contains the volume fraction of each compartment (starting from white 
> matter in frame 0 I believe).
> 
> Sorry, we've never had time to properly document this.
> 
> cheers
> Bruce
> 
> On Mon, 7 Sep 2015, Yun Wang wrote:
> 
>> 
>>  Hi All, 
>> I have some basic questions regarding of layers surface in freesurfer.
>> The main idea is to extract the time series between different layers. 
>> 1 After recon -all, I got white surface and pial surface, then I use
>> mri_expand to get 3 additional layers’ surface between white surface
>> and pial surface. Is the layer’s surface binary? After I convert the
>> layers’ surface to volume using mri_surf2vol, There is no significant
>> difference between the  layers because of the resolution. So I am
>> thinking this would be the wrong to do it?
>> 2 I believe there are two functions: mri_compute_layer_fractions,
>> mris_compute_layer_intensities, which are supposed to solve the
>> intensity problem. But I have no idea how to use it in the light of
>> lacking explanation. What is the difference between the two functions
>> and partial  volume correction function(mri_compute_volume_fractions,
>> mri_compute_volume_intensities). 
>> Appreciate your brain’s sparks! 
>> Best,
>> Yun Wang
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[Freesurfer] Basic questions regarding of layers

[Yun Wang]

> 
> 
> Hi All, 
> 
> 
> I have some basic questions regarding of layers surface in freesurfer. The 
> main idea is to extract the time series between different layers. 
> 
> 1 After recon -all, I got white surface and pial surface, then I use 
> mri_expand to get 3 additional layers’ surface between white surface and pial 
> surface. Is the layer’s surface binary? After I convert the layers’ surface 
> to volume using mri_surf2vol, There is no significant difference between the  
> layers because of the resolution. So I am thinking this would be the wrong to 
> do it?
> 
> 2 I believe there are two functions: mri_compute_layer_fractions, 
> mris_compute_layer_intensities, which are supposed to solve the intensity 
> problem. But I have no idea how to use it in the light of lacking 
> explanation. What is the difference between the two functions and partial  
> volume correction function(mri_compute_volume_fractions, 
> mri_compute_volume_intensities). 
> 
> 
> Appreciate your brain’s sparks! 
> 
> 
> 
> 
> Best,
> 
> Yun Wang
> 
> 
> 
> 
> 
> 
> 

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Re: [Freesurfer] two functions' purpose and usage

[Yun Wang]

Anyone knows this? 


> On Sep 2, 2015, at 11:12, Yun Wang  wrote:
> 
> Hi all experts,
> 
> 
> I have questions about two functions purposes and usages. 
> 
> 
> mri_compute_layer_fractions and mris_compute_layer_intensities. 
> 
> 
> mri_compute_layer_fractions [options]   
> 
> 1   Which registration file ?
> 2  which input volume?
> 3 options?
> mris_compute_layer_intensities [options]   volume fractions file>  
> 
> 1 input intensity volume means fMRI ?
> 
> 
> Appreciate your idea! 
> 
> 
> Yun Wang
> 
> 

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[Freesurfer] two functions' purpose and usage

[Yun Wang]

Hi all experts,


I have questions about two functions purposes and usages. 


mri_compute_layer_fractions and mris_compute_layer_intensities. 


mri_compute_layer_fractions [options]   

1   Which registration file ?
2  which input volume?
3 options?
mris_compute_layer_intensities [options]

1 input intensity volume means fMRI ?


Appreciate your idea! 


Yun Wang


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Re: [Freesurfer] mri_compute_layer_fractions

[Yun Wang]

After I try the code:
mri_compute_layer_fractions -nlayers 4

$SUBJECTS_DIR/fMRI/register.lta  
$SUBJECTS_DIR/fMRI/HIP001_rest_preproc_norm.nii test.mgz



open test.mgz using freeview like this!  Not binarize according different 
layers! Also the frontal part of the brain is missing! 


> On Sep 1, 2015, at 11:49, Bruce Fischl  wrote:
> 
> you can use -n  to change the name of the surfaces, and -nlayers  to 
> specify the number of layers it computes (# of surfaces = 1+number of layers 
> I think)
> On Tue, 1 Sep 2015, Yun Wang wrote:
> 
>> Thanks! But it looks this script keeps looking for the lh.gwdist00N forever,
>> here is the error message: 
>> mri_compute_layer_fractions: could not load lh surface 5 
>> from/Users/emilyUS/Documents/Cortical_layer/Data/anatomical/Rest-Anatomical/out
>> put/surf/lh.gwdist005
>> I do not have lh.gwdist005. How can I set up the number in this code?
>> 
>>  On Sep 1, 2015, at 11:08, Bruce Fischl
>>   wrote:
>> no, you just need to name them in the way that
>> mri_compute_layer_fractions is expecting (e.g. lh.gwdist000 for white,
>> etc...)
>> On Tue, 1 Sep 2015, Yun Wang wrote:
>> 
>>  I do have 5 intermediate surfaces, should I combine them
>>  together?
>> 
>>On Sep 1, 2015, at 10:43, Bruce Fischl
>> wrote:
>> 
>>you need to use mris_expand to generate the
>>family of intermediate surfaces
>> 
>>cheers
>>Bruce
>>On Tue, 1 Sep 2015, Yun Wang wrote:
>> 
>>  Hi all experts,
>>  I have the error message when
>>  trying to use
>>   mri_compute_layer_fractions.
>>  mri_compute_layer_fractions
>>  $SUBJECTS_DIR/fMRI/register.lta
>>  $SUBJECTS_DIR/white_lh.mgz  test
>>  reading 
>> registrationfile/Users/emilyUS/Documents/Cortical_layer/Data/anatomical/Rest-Anatomical
>>  /fMR
>>  I/register.lta
>>  regio_read_register: loading lta
>>  regio_read_register: loading lta
>>  
>> readingvolume/Users/emilyUS/Documents/Cortical_layer/Data/anatomical/Rest-Anatomic
>>  al/out
>>  put/mri/aseg.mgz
>>  reading laminar surfaces from
>>  gwdist.?
>>      
>> readingsurface/Users/emilyUS/Documents/Cortical_layer/Data/anatomical/Rest-Anatomi
>>  cal/out
>>  put/surf/lh.gwdist000
>>  Anyone know the gwdist? how I can
>>  get it?
>>  Thanks!
>>  Yun Wang
>> 
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Re: [Freesurfer] mri_compute_layer_fractions

[Yun Wang]

Thanks! But it looks this script keeps looking for the lh.gwdist00N forever, 
here is the error message: 

mri_compute_layer_fractions: could not load lh surface 5 from 
/Users/emilyUS/Documents/Cortical_layer/Data/anatomical/Rest-Anatomical/output/surf/lh.gwdist005

I do not have lh.gwdist005. How can I set up the number in this code?

> On Sep 1, 2015, at 11:08, Bruce Fischl  wrote:
> 
> no, you just need to name them in the way that 
> mri_compute_layer_fractions is expecting (e.g. lh.gwdist000 for white, 
> etc...)
> On Tue, 1 Sep 2015, Yun Wang wrote:
> 
>> I do have 5 intermediate surfaces, should I combine them together?
>> 
>>> On Sep 1, 2015, at 10:43, Bruce Fischl  wrote:
>>> 
>>> you need to use mris_expand to generate the family of intermediate surfaces
>>> 
>>> 
>>> cheers
>>> Bruce
>>> On Tue, 1 Sep 2015, Yun Wang wrote:
>>> 
>>>> Hi all experts,
>>>> I have the error message when trying to use  mri_compute_layer_fractions.
>>>> mri_compute_layer_fractions $SUBJECTS_DIR/fMRI/register.lta
>>>> $SUBJECTS_DIR/white_lh.mgz  test
>>>> reading registration 
>>>> file/Users/emilyUS/Documents/Cortical_layer/Data/anatomical/Rest-Anatomical/fMR
>>>> I/register.lta
>>>> regio_read_register: loading lta
>>>> regio_read_register: loading lta
>>>> reading 
>>>> volume/Users/emilyUS/Documents/Cortical_layer/Data/anatomical/Rest-Anatomical/out
>>>> put/mri/aseg.mgz
>>>> reading laminar surfaces from gwdist.?
>>>> reading 
>>>> surface/Users/emilyUS/Documents/Cortical_layer/Data/anatomical/Rest-Anatomical/out
>>>> put/surf/lh.gwdist000
>>>> Anyone know the gwdist? how I can get it?
>>>> Thanks!
>>>> Yun Wang
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Re: [Freesurfer] mri_compute_layer_fractions

[Yun Wang]

I use the mris_expand like this:

mris_expand -thickness lh.white 0.2lh.white_outer0.2GM 

  mris_expand -thickness lh.white 0.4 lh.white_outer_0.4GM

mris_expand -thickness lh.white 0.6lh.white_outer0.6GM 

 mris_expand -thickness lh.white 0.8 lh.white_outer_0.8GM


anything wrong?

> On Sep 1, 2015, at 10:47, Yun Wang  wrote:
> 
> I do have 5 intermediate surfaces, should I combine them together?
> 
>> On Sep 1, 2015, at 10:43, Bruce Fischl  wrote:
>> 
>> you need to use mris_expand to generate the family of intermediate surfaces
>> 
>> 
>> cheers
>> Bruce
>> On Tue, 1 Sep 2015, Yun Wang wrote:
>> 
>>> Hi all experts,
>>> I have the error message when trying to use  mri_compute_layer_fractions. 
>>> mri_compute_layer_fractions $SUBJECTS_DIR/fMRI/register.lta
>>> $SUBJECTS_DIR/white_lh.mgz  test
>>> reading registration 
>>> file/Users/emilyUS/Documents/Cortical_layer/Data/anatomical/Rest-Anatomical/fMR
>>> I/register.lta
>>> regio_read_register: loading lta
>>> regio_read_register: loading lta
>>> reading 
>>> volume/Users/emilyUS/Documents/Cortical_layer/Data/anatomical/Rest-Anatomical/out
>>> put/mri/aseg.mgz
>>> reading laminar surfaces from gwdist.?
>>> reading 
>>> surface/Users/emilyUS/Documents/Cortical_layer/Data/anatomical/Rest-Anatomical/out
>>> put/surf/lh.gwdist000
>>> Anyone know the gwdist? how I can get it?
>>> Thanks!
>>> Yun Wang
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Re: [Freesurfer] mri_compute_layer_fractions

[Yun Wang]

I do have 5 intermediate surfaces, should I combine them together?

> On Sep 1, 2015, at 10:43, Bruce Fischl  wrote:
> 
> you need to use mris_expand to generate the family of intermediate surfaces
> 
> 
> cheers
> Bruce
> On Tue, 1 Sep 2015, Yun Wang wrote:
> 
>> Hi all experts,
>> I have the error message when trying to use  mri_compute_layer_fractions. 
>> mri_compute_layer_fractions $SUBJECTS_DIR/fMRI/register.lta
>> $SUBJECTS_DIR/white_lh.mgz  test
>> reading registration 
>> file/Users/emilyUS/Documents/Cortical_layer/Data/anatomical/Rest-Anatomical/fMR
>> I/register.lta
>> regio_read_register: loading lta
>> regio_read_register: loading lta
>> reading 
>> volume/Users/emilyUS/Documents/Cortical_layer/Data/anatomical/Rest-Anatomical/out
>> put/mri/aseg.mgz
>> reading laminar surfaces from gwdist.?
>> reading 
>> surface/Users/emilyUS/Documents/Cortical_layer/Data/anatomical/Rest-Anatomical/out
>> put/surf/lh.gwdist000
>> Anyone know the gwdist? how I can get it?
>> Thanks!
>> Yun Wang
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[Freesurfer] mri_compute_layer_fractions

[Yun Wang]

Hi all experts,

I have the error message when trying to use  mri_compute_layer_fractions. 

mri_compute_layer_fractions $SUBJECTS_DIR/fMRI/register.lta 
$SUBJECTS_DIR/white_lh.mgz  test
reading registration file 
/Users/emilyUS/Documents/Cortical_layer/Data/anatomical/Rest-Anatomical/fMRI/register.lta
regio_read_register: loading lta
regio_read_register: loading lta
reading volume 
/Users/emilyUS/Documents/Cortical_layer/Data/anatomical/Rest-Anatomical/output/mri/aseg.mgz
reading laminar surfaces from gwdist.?
reading surface 
/Users/emilyUS/Documents/Cortical_layer/Data/anatomical/Rest-Anatomical/output/surf/lh.gwdist000


Anyone know the gwdist? how I can get it?

Thanks!

Yun Wang

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Re: [Freesurfer] making ROI after bbregister

[Yun Wang]

Usage: mri_compute_layer_fractions [options]   


What is  ? ? 

> On Aug 26, 2015, at 10:37, Bruce Fischl  wrote:
> 
> we have toold for doing this but they aren't documented (mris_expand, 
> mri_compute_layer_fractions, mris_compute_layer_intensities). This is what 
> Rebecca Shafee used in her recent two-compartment paper
> 
> http://www.ncbi.nlm.nih.gov/pubmed/25449739 
> <http://www.ncbi.nlm.nih.gov/pubmed/25449739>
> 
> cheers
> Bruce
> 
> 
> On Wed, 26 Aug 2015, Douglas Greve wrote:
> 
>> I'm not sure what you mean. bbregister does not divide gm into layers.
>> Can you elaborate on what you have done and trying to do?
>> 
>> On 8/26/15 11:02 AM, Yun Wang wrote:
>>> Dear all experts,
>>> 
>>> 
>>> I am currently dividing the gray matter into 6 different layers using 
>>> bbregister, however, does anyone know how to make the space between layers 
>>> into ROIs? Thanks! Appreciating your idea.
>>> 
>>> Yun
>>> 
>>> 
>>> 
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[Freesurfer] making ROI after bbregister

[Yun Wang]

Dear all experts,


I am currently dividing the gray matter into 6 different layers using 
bbregister, however, does anyone know how to make the space between layers into 
ROIs? Thanks! Appreciating your idea. 

Yun 



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Re: [Freesurfer] how to make ROI using surface

[Yun Wang]

Hi Bruce,

Can you tell me how I can use mis_compute_layer_fractions ? I found it in 
dev_binary in 
http://ftp.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/snowleopard-i686/
 
<http://ftp.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/snowleopard-i686/>.
 

Thanks!

Yun 

> On Jul 2, 2015, at 14:39, Bruce Fischl  wrote:
> 
> they are binaries. What version of FreeSurfer do you have, and what 
> hardware/software environment?
> 
> On Thu, 2 Jul 2015, Yun Wang wrote:
> 
>> I could not find the function, can you tell me why and how I use this 
>> function? Thanks!
>> 
>> 
>>> On Jul 2, 2015, at 14:30, Bruce Fischl  wrote:
>>> 
>>> Hi Yun Wang
>>> 
>>> if you've run mris_expand you will need to run mris_compute_layer_fractions 
>>> I believe (and mris_compute_layer_intensities if you want to account for 
>>> partial volume effects)
>>> 
>>> cheers
>>> Bruce
>>> 
>>> On Thu, 2 Jul 2015, Yun Wang wrote:
>>> 
>>>> Hi All,
>>>> 
>>>> 
>>>> I am trying to segment gray matters (anatomical) into 5 layers and then 
>>>> extracting different layers’ functional MRI data. I have got 5 surfaces 
>>>> using mir_expand function and finish the registration of fMRI to 
>>>> anatomical data. I want to make 5 masks and then extract the time series, 
>>>> does anyone know how to make ROI using surface?
>>>> 
>>>> 
>>>> Thanks!
>>>> 
>>>> 
>>>> Yun Wang
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Re: [Freesurfer] how to make ROI using surface

[Yun Wang]

freesurfer-Darwin-lion-stable-pub-v5.3.0 version

I use Mac Pro OS X Yosemite



> On Jul 2, 2015, at 14:39, Bruce Fischl  wrote:
> 
> they are binaries. What version of FreeSurfer do you have, and what 
> hardware/software environment?
> 
> On Thu, 2 Jul 2015, Yun Wang wrote:
> 
>> I could not find the function, can you tell me why and how I use this 
>> function? Thanks!
>> 
>> 
>>> On Jul 2, 2015, at 14:30, Bruce Fischl  wrote:
>>> 
>>> Hi Yun Wang
>>> 
>>> if you've run mris_expand you will need to run mris_compute_layer_fractions 
>>> I believe (and mris_compute_layer_intensities if you want to account for 
>>> partial volume effects)
>>> 
>>> cheers
>>> Bruce
>>> 
>>> On Thu, 2 Jul 2015, Yun Wang wrote:
>>> 
>>>> Hi All,
>>>> 
>>>> 
>>>> I am trying to segment gray matters (anatomical) into 5 layers and then 
>>>> extracting different layers’ functional MRI data. I have got 5 surfaces 
>>>> using mir_expand function and finish the registration of fMRI to 
>>>> anatomical data. I want to make 5 masks and then extract the time series, 
>>>> does anyone know how to make ROI using surface?
>>>> 
>>>> 
>>>> Thanks!
>>>> 
>>>> 
>>>> Yun Wang
>>>> ___
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>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>> 
>>>> 
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Re: [Freesurfer] how to make ROI using surface

[Yun Wang]

I could not find the function, can you tell me why and how I use this function? 
Thanks! 


> On Jul 2, 2015, at 14:30, Bruce Fischl  wrote:
> 
> Hi Yun Wang
> 
> if you've run mris_expand you will need to run mris_compute_layer_fractions I 
> believe (and mris_compute_layer_intensities if you want to account for 
> partial volume effects)
> 
> cheers
> Bruce
> 
> On Thu, 2 Jul 2015, Yun Wang wrote:
> 
>> Hi All,
>> 
>> 
>> I am trying to segment gray matters (anatomical) into 5 layers and then 
>> extracting different layers’ functional MRI data. I have got 5 surfaces 
>> using mir_expand function and finish the registration of fMRI to anatomical 
>> data. I want to make 5 masks and then extract the time series, does anyone 
>> know how to make ROI using surface?
>> 
>> 
>> Thanks!
>> 
>> 
>> Yun Wang
>> ___
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[Freesurfer] how to make ROI using surface

[Yun Wang]

Hi All,


I am trying to segment gray matters (anatomical) into 5 layers and then 
extracting different layers’ functional MRI data. I have got 5 surfaces using 
mir_expand function and finish the registration of fMRI to anatomical data. I 
want to make 5 masks and then extract the time series, does anyone know how to 
make ROI using surface? 


Thanks!


Yun Wang
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Re: [Freesurfer] (no subject)

[Yun wang]

Thanks! 

Yun Wang

> On Jun 22, 2015, at 7:40 AM, Bruce Fischl  wrote:
> 
> Hi
> 
> you can use mris_expand to do this, although of course we just divide up the 
> space evenly since we don't know where the actual laminar boundaries are.
> 
> cheers
> Bruce
> 
> p.s. e.g.:
> 
> mris_expand -t -n 6 lh.white lh.expanded
> 
> 
> will write out 6 intermediate surfaces
> 
>> On Mon, 15 Jun 2015, Yun Wang wrote:
>> 
>> Hi,
>> I am pretty new to the Freesurfer. I want to get the idea how the freesurfer
>> differentiate 6 layers. I have already get the pial/ gray matter,gray/matt
>> white matter, thickness map, then how to calculate and form the laminars? 
>> Thanks! 
>> --
>> Yun Wang
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[Freesurfer] (no subject)

[Yun Wang]

Hi,

I am pretty new to the Freesurfer. I want to get the idea how the
freesurfer differentiate 6 layers. I have already get the pial/ gray
matter,gray/matt white matter, thickness map, then how to calculate and
form the laminars?

Thanks!

-- 
Yun Wang
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