Re: [Freesurfer] volume to surface registration

2018-05-14 Thread Wang, Zhuonan 
Thanks for the reply!

Zhuonan

发件人: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] 代表 Douglas N. Greve 
[dgr...@mgh.harvard.edu]
发送时间: 2018年5月14日 15:02
收件人: freesurfer@nmr.mgh.harvard.edu
主题: Re: [Freesurfer] volume to surface registration

Probably best to run recon-all on the mni152, then sample your 152 data
onto the surface, then use the surface-based registration.


On 05/10/2018 01:06 PM, Wang, Zhuonan wrote:
> Hi Team,
>
> I have a functional image which located in the FSL volume-based
> template(MNI152), and now I wanna to register this image to FS-based
> surface template (MNI305).
>
> How can I do this?
> Please let me know how to do this!
>
>
> PS: I'm not sure that the MNI152 is same as the FS's MNI152.
>
>
> Dataset File:MNI152_T1_1mm_brain.nii
> Identifier Code: NII_MkcC7NBmrrzYGzBC6bOpTA  Creation Date: Thu May 10
> 13:01:49 2018
> Template Space:  MNI
> Dataset Type:Anat Bucket (-abuc)
> Byte Order:  LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
> Storage Mode:NIFTI
> Storage Space:   14,442,064 (14 million [mega]) bytes
> Geometry String: "MATRIX(1,0,0,-90,0,-1,0,126,0,0,1,-72):182,218,182"
> Data Axes Tilt:  Plumb
> Data Axes Orientation:
>   first  (x) = Right-to-Left
>   second (y) = Posterior-to-Anterior
>   third  (z) = Inferior-to-Superior   [-orient RPI]
> R-to-L extent:   -90.000 [R] -to-91.000 [L] -step- 1.000 mm
> [182 voxels]
> A-to-P extent:   -91.000 [A] -to-   126.000 [P] -step- 1.000 mm
> [218 voxels]
> I-to-S extent:   -72.000 [I] -to-   109.000 [S] -step- 1.000 mm
> [182 voxels]
>
>
> Thank you!
> Zhuonan
>
>
>
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Re: [Freesurfer] volume to surface registration

2018-05-14 Thread Douglas N. Greve 
Probably best to run recon-all on the mni152, then sample your 152 data 
onto the surface, then use the surface-based registration.


On 05/10/2018 01:06 PM, Wang, Zhuonan wrote:
> Hi Team,
>
> I have a functional image which located in the FSL volume-based 
> template(MNI152), and now I wanna to register this image to FS-based 
> surface template (MNI305).
>
> How can I do this?
> Please let me know how to do this!
>
>
> PS: I'm not sure that the MNI152 is same as the FS's MNI152.
>
>
> Dataset File:    MNI152_T1_1mm_brain.nii
> Identifier Code: NII_MkcC7NBmrrzYGzBC6bOpTA  Creation Date: Thu May 10 
> 13:01:49 2018
> Template Space:  MNI
> Dataset Type:    Anat Bucket (-abuc)
> Byte Order:  LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
> Storage Mode:    NIFTI
> Storage Space:   14,442,064 (14 million [mega]) bytes
> Geometry String: "MATRIX(1,0,0,-90,0,-1,0,126,0,0,1,-72):182,218,182"
> Data Axes Tilt:  Plumb
> Data Axes Orientation:
>   first  (x) = Right-to-Left
>   second (y) = Posterior-to-Anterior
>   third  (z) = Inferior-to-Superior   [-orient RPI]
> R-to-L extent:   -90.000 [R] -to-    91.000 [L] -step- 1.000 mm 
> [182 voxels]
> A-to-P extent:   -91.000 [A] -to-   126.000 [P] -step- 1.000 mm 
> [218 voxels]
> I-to-S extent:   -72.000 [I] -to-   109.000 [S] -step- 1.000 mm 
> [182 voxels]
>
>
> Thank you!
> Zhuonan
>
>
>
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> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] Volume to Surface mapping looks great for Vols created in FSL but not SPM

2018-02-15 Thread Douglas N Greve 
should be the same as when you use --regheader with tkregister


On 02/09/2018 11:24 PM, Rita Elena Loiotile wrote:
> Hi,
>
> I just noticed that when I open my volume file in tksurfer using 
> --overlay it gives a better volume to surface mapping than when I do 
> mri_vol2surf. Do you know what .dat file is used implicitly when 
> tksurfer is called with a volume overlay?  It also seems to work well 
> when the subject is fsaverage and when it is 32k_fs_LR. Thank you.
>
> On Wed, Apr 5, 2017 at 9:54 AM, Douglas Greve 
> > wrote:
>
> If you have a 3mm MNI152 space, then you should run bbregister to
> fsaverage to create a new register.dat file. Alternatively, you
> can register it directly to 32k_fs_LR and cut out the middle man
> (make sure to use --9 to account for scaling). Please ignore my
> comment about fsaverage. In that case it was actually fine.
>
>
>
> On 4/4/17 9:40 PM, Rita Elena Loiotile wrote:
>> Hi Doug,
>>
>> Thanks for the email.  It is in 3mm space, so I guess I should
>> reslice.  Can you please clarify the comment about fsaverage? 
>> Does the --mni152reg flag not apply to that subject?  I'm not
>> sure what you mean about the inclusion indicating ambiguity.
>>
>> Thanks again,
>> Rita
>>
>> On Tue, Apr 4, 2017 at 9:21 PM, Douglas Greve
>> > wrote:
>>
>> The --mni152reg flag is only appropriate if the mov file is
>> in the 2mm mni152 space. The inclusion of fsaverage as the
>> source subject indicates some ambiguity about this
>>
>>
>> On 4/3/17 1:56 PM, Rita Elena Loiotile wrote:
>>> Hi,
>>>
>>> I'm trying to compare analyses that I've done entirely on
>>> the surface to analyses I've done in the volume.  I'm
>>> comparing the analyses by projecting the volume analyses to
>>> the surface (HCP's 32k_fs_LR).
>>>
>>> The commands I'm using are:
>>> mri_vol2surf --mov $niftiFile --mni152reg --hemi ${hemi}
>>> --projfrac-max 0 1 0.2 --o ${giftiFile}.$hemi.gii;
>>> mri_surf2surf --srcsubject fsaverage --srcsurfval
>>> ${giftiFile}.$hemi.gii --trgsubject 32k_fs_LR --trgsurfval
>>> ${giftiFile}.$hemi.gii --hemi ${hemi};It seems that the FSL
>>> volumes look identical to the surface analysis, when mapped.
>>> (Our surface analysis is mainly FSL-based, so this makes sense.)
>>> The SPM mapping, however, looks very odd. It isn't just that
>>> the intensity differs, but the localization of high
>>> intensity areas also varies. It seems that everything is
>>> shifted a bit superior and, possibly, posterior to the true
>>> location (as seen on the surface analysis).
>>> I'm wondering if I'm doing anything obviously wrong in my
>>> command usage. The brains were normalized to the MNI ICBM
>>> 152 template in SPM. I *think* it's suitable to use the
>>> -mni152reg flag in the command.
>>>
>>> I can attach pictures of the comparison if you'd like.
>>>
>>> Thanks in advance,
>>> Rita
>>>
>>>
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>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> 
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> 
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Re: [Freesurfer] Volume to Surface mapping looks great for Vols created in FSL but not SPM

2018-02-09 Thread Rita Elena Loiotile 
Hi,

I just noticed that when I open my volume file in tksurfer using --overlay
it gives a better volume to surface mapping than when I do mri_vol2surf.
Do you know what .dat file is used implicitly when tksurfer is called with
a volume overlay?  It also seems to work well when the subject is fsaverage
and when it is 32k_fs_LR. Thank you.

On Wed, Apr 5, 2017 at 9:54 AM, Douglas Greve 
wrote:

> If you have a 3mm MNI152 space, then you should run bbregister to
> fsaverage to create a new register.dat file. Alternatively, you can
> register it directly to 32k_fs_LR and cut out the middle man (make sure to
> use --9 to account for scaling). Please ignore my comment about fsaverage.
> In that case it was actually fine.
>
>
>
> On 4/4/17 9:40 PM, Rita Elena Loiotile wrote:
>
> Hi Doug,
>
> Thanks for the email.  It is in 3mm space, so I guess I should reslice.
> Can you please clarify the comment about fsaverage?  Does the --mni152reg
> flag not apply to that subject?  I'm not sure what you mean about the
> inclusion indicating ambiguity.
>
> Thanks again,
> Rita
>
> On Tue, Apr 4, 2017 at 9:21 PM, Douglas Greve 
> wrote:
>
>> The --mni152reg flag is only appropriate if the mov file is in the 2mm
>> mni152 space. The inclusion of fsaverage as the source subject indicates
>> some ambiguity about this
>>
>> On 4/3/17 1:56 PM, Rita Elena Loiotile wrote:
>>
>> Hi,
>>
>> I'm trying to compare analyses that I've done entirely on the surface to
>> analyses I've done in the volume.  I'm comparing the analyses by projecting
>> the volume analyses to the surface (HCP's 32k_fs_LR).
>>
>> The commands I'm using are:
>> mri_vol2surf --mov $niftiFile --mni152reg --hemi ${hemi} --projfrac-max 0
>> 1 0.2 --o ${giftiFile}.$hemi.gii;
>> mri_surf2surf --srcsubject fsaverage --srcsurfval ${giftiFile}.$hemi.gii
>> --trgsubject 32k_fs_LR --trgsurfval ${giftiFile}.$hemi.gii --hemi ${hemi};
>> It seems that the FSL volumes look identical to the surface analysis, when
>> mapped. (Our surface analysis is mainly FSL-based, so this makes sense.)
>> The SPM mapping, however, looks very odd. It isn't just that the
>> intensity differs, but the localization of high intensity areas also
>> varies. It seems that everything is shifted a bit superior and, possibly,
>> posterior to the true location (as seen on the surface analysis).
>> I'm wondering if I'm doing anything obviously wrong in my command usage.
>> The brains were normalized to the MNI ICBM 152 template in SPM. I *think*
>> it's suitable to use the -mni152reg flag in the command.
>>
>> I can attach pictures of the comparison if you'd like.
>>
>> Thanks in advance,
>> Rita
>>
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
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>> du/mailman/listinfo/freesurfer The information in this e-mail is
>> intended only for the person to whom it is addressed. If you believe this
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>> information, please contact the Partners Compliance HelpLine at
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>> 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] volume vs surface-based and surface smoothing

2017-10-12 Thread Douglas N Greve 
The surface is created during recon-all. rawfunc2surf-sess resamples the 
volumetric fMRI onto the surface.


On 10/12/2017 01:42 PM, Alissa Stafford wrote:
> Thanks Matt! Does rawfunc2surf-sess create the surface and smooth?
>
> From: <freesurfer-boun...@nmr.mgh.harvard.edu 
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Matt 
> Glasser <m...@ma-tea.com <mailto:m...@ma-tea.com>>
> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu 
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> Date: Thursday, October 12, 2017 at 1:39 PM
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu 
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> Subject: Re: [Freesurfer] volume vs surface-based and surface smoothing
>
> Volume-based registration is fine with subject as you have the same 
> brain that you are registering (ideally such registrations are 6 DOF 
> rigid registrations and any image distortions are corrected for). 
>  Surface-based registration is better when comparing across subjects 
> due to the variability in cortical folding patterns and locations of 
> areas relative to folds across subjects.  Smoothing is best done on 
> the surface if it is done at all.  Smoothing in the volume harms one’s 
> spatial localization precision much more than smoothing on the surface 
> for an equivalent FWMH in mm.  It is worth keeping in mind that 
> smoothing on the surface does still blur across cortical areal 
> boundaries, however, so for many analyses it may be better to average 
> within cortical areas rather than to smooth a lot.
>
> Peace,
>
> Matt.
>
> From: <freesurfer-boun...@nmr.mgh.harvard.edu 
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Alissa 
> Stafford <alissa.staff...@jhu.edu <mailto:alissa.staff...@jhu.edu>>
> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu 
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> Date: Thursday, October 12, 2017 at 12:29 PM
> To: "Freesurfer@nmr.mgh.harvard.edu 
> <mailto:Freesurfer@nmr.mgh.harvard.edu>" 
> <Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> Subject: [Freesurfer] volume vs surface-based and surface smoothing
>
> Hello,
>
> I am trying to understand the preprocessing functions to successfully 
> complete surface-based analysis. I am confused about what is happening 
> on the volume level and when exactly the surface is being created. My 
> questions revolve around register-sess and rawfunc2surf-sess.
>
> Registration has 2 parts:
> 1: the native anatomical space is registered with the fsaverage space. 
> This is happening during recon-all.
> 2: native functional data is registered with the native anatomical 
> data. This is happening during register-sess in preprocess-sess.
> Aren’t these both volume-based registrations? If not when are the 
> surfaces created? My concern is that it is volume-based and I was 
> under the impression from this article: 
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/ , that all 
> registrations should be done on the surface.
>
> I am also confused about rawfunc2surf-sess. I believe up until this 
> function in preprocess-sess, everything has been done in the volume so 
> this is the first step that is done in the surface, is that correct? 
> And then does this do smoothing? I realized it has a fwhm input option 
> so it must smooth. So is this where the functional data is now 
> expressed in the surface and it also smooths? Or does surfsmooth-sess 
> need to be run in addition to rawfunc2surf-sess?
>
> I basically just want to be making sure I understand when registration 
> is volume-based or surface-based and when it’s appropriate to use 
> volume-based. And I was using the rawfunc2surf function assuming it 
> was for smoothing, but I am not so sure if this only creates the 
> surface or also smooths.
>
> Thanks,
> Alissa
> ___ Freesurfer mailing 
> list Freesurfer@nmr.mgh.harvard.edu 
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> 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 
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> you in error but does not contain patient information, please contact 
> the sender and properly dispose of the e-mail.
>
>
> _

Re: [Freesurfer] volume vs surface-based and surface smoothing

2017-10-12 Thread Matt Glasser 
My understanding of the FreeSurfer surface-based functional processing is
that it adheres to the below guidelines; however, I have not personally used
it so we¹ll have to see what the FreeSurfer experts say.

Peace,

Matt.

From:  <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alissa Stafford
<alissa.staff...@jhu.edu>
Reply-To:  Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date:  Thursday, October 12, 2017 at 12:42 PM
To:  Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject:  Re: [Freesurfer] volume vs surface-based and surface smoothing

Thanks Matt! Does rawfunc2surf-sess create the surface and smooth?

From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Matt Glasser
<m...@ma-tea.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, October 12, 2017 at 1:39 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] volume vs surface-based and surface smoothing

Volume-based registration is fine with subject as you have the same brain
that you are registering (ideally such registrations are 6 DOF rigid
registrations and any image distortions are corrected for).  Surface-based
registration is better when comparing across subjects due to the variability
in cortical folding patterns and locations of areas relative to folds across
subjects.  Smoothing is best done on the surface if it is done at all.
Smoothing in the volume harms one¹s spatial localization precision much more
than smoothing on the surface for an equivalent FWMH in mm.  It is worth
keeping in mind that smoothing on the surface does still blur across
cortical areal boundaries, however, so for many analyses it may be better to
average within cortical areas rather than to smooth a lot.

Peace,

Matt.

From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alissa Stafford
<alissa.staff...@jhu.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, October 12, 2017 at 12:29 PM
To: "Freesurfer@nmr.mgh.harvard.edu" <Freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] volume vs surface-based and surface smoothing

Hello,

I am trying to understand the preprocessing functions to successfully
complete surface-based analysis. I am confused about what is happening on
the volume level and when exactly the surface is being created. My questions
revolve around register-sess and rawfunc2surf-sess.

Registration has 2 parts:
1: the native anatomical space is registered with the fsaverage space. This
is happening during recon-all.
2: native functional data is registered with the native anatomical data.
This is happening during register-sess in preprocess-sess.
Aren¹t these both volume-based registrations? If not when are the surfaces
created? My concern is that it is volume-based and I was under the
impression from this article:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/ , that all
registrations should be done on the surface.

I am also confused about rawfunc2surf-sess. I believe up until this function
in preprocess-sess, everything has been done in the volume so this is the
first step that is done in the surface, is that correct? And then does this
do smoothing? I realized it has a fwhm input option so it must smooth. So is
this where the functional data is now expressed in the surface and it also
smooths? Or does surfsmooth-sess need to be run in addition to
rawfunc2surf-sess?

I basically just want to be making sure I understand when registration is
volume-based or surface-based and when it¹s appropriate to use volume-based.
And I was using the rawfunc2surf function assuming it was for smoothing, but
I am not so sure if this only creates the surface or also smooths.

Thanks,
Alissa
___ Freesurfer mailing list
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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
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and properly dispose of th

Re: [Freesurfer] volume vs surface-based and surface smoothing

2017-10-12 Thread Alissa Stafford 
Thanks Matt! Does rawfunc2surf-sess create the surface and smooth?

From: 
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Matt Glasser <m...@ma-tea.com<mailto:m...@ma-tea.com>>
Reply-To: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, October 12, 2017 at 1:39 PM
To: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] volume vs surface-based and surface smoothing

Volume-based registration is fine with subject as you have the same brain that 
you are registering (ideally such registrations are 6 DOF rigid registrations 
and any image distortions are corrected for).  Surface-based registration is 
better when comparing across subjects due to the variability in cortical 
folding patterns and locations of areas relative to folds across subjects.  
Smoothing is best done on the surface if it is done at all.  Smoothing in the 
volume harms one’s spatial localization precision much more than smoothing on 
the surface for an equivalent FWMH in mm.  It is worth keeping in mind that 
smoothing on the surface does still blur across cortical areal boundaries, 
however, so for many analyses it may be better to average within cortical areas 
rather than to smooth a lot.

Peace,

Matt.

From: 
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Alissa Stafford 
<alissa.staff...@jhu.edu<mailto:alissa.staff...@jhu.edu>>
Reply-To: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, October 12, 2017 at 12:29 PM
To: "Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>" 
<Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] volume vs surface-based and surface smoothing

Hello,

I am trying to understand the preprocessing functions to successfully complete 
surface-based analysis. I am confused about what is happening on the volume 
level and when exactly the surface is being created. My questions revolve 
around register-sess and rawfunc2surf-sess.

Registration has 2 parts:
1: the native anatomical space is registered with the fsaverage space. This is 
happening during recon-all.
2: native functional data is registered with the native anatomical data. This 
is happening during register-sess in preprocess-sess.
Aren’t these both volume-based registrations? If not when are the surfaces 
created? My concern is that it is volume-based and I was under the impression 
from this article:  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/ , 
that all registrations should be done on the surface.

I am also confused about rawfunc2surf-sess. I believe up until this function in 
preprocess-sess, everything has been done in the volume so this is the first 
step that is done in the surface, is that correct? And then does this do 
smoothing? I realized it has a fwhm input option so it must smooth. So is this 
where the functional data is now expressed in the surface and it also smooths? 
Or does surfsmooth-sess need to be run in addition to rawfunc2surf-sess?

I basically just want to be making sure I understand when registration is 
volume-based or surface-based and when it’s appropriate to use volume-based. 
And I was using the rawfunc2surf function assuming it was for smoothing, but I 
am not so sure if this only creates the surface or also smooths.

Thanks,
Alissa
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Re: [Freesurfer] volume vs surface-based and surface smoothing

2017-10-12 Thread Matt Glasser 
Volume-based registration is fine with subject as you have the same brain
that you are registering (ideally such registrations are 6 DOF rigid
registrations and any image distortions are corrected for).  Surface-based
registration is better when comparing across subjects due to the variability
in cortical folding patterns and locations of areas relative to folds across
subjects.  Smoothing is best done on the surface if it is done at all.
Smoothing in the volume harms one¹s spatial localization precision much more
than smoothing on the surface for an equivalent FWMH in mm.  It is worth
keeping in mind that smoothing on the surface does still blur across
cortical areal boundaries, however, so for many analyses it may be better to
average within cortical areas rather than to smooth a lot.

Peace,

Matt.

From:   on behalf of Alissa Stafford

Reply-To:  Freesurfer support list 
Date:  Thursday, October 12, 2017 at 12:29 PM
To:  "Freesurfer@nmr.mgh.harvard.edu" 
Subject:  [Freesurfer] volume vs surface-based and surface smoothing

Hello,

I am trying to understand the preprocessing functions to successfully
complete surface-based analysis. I am confused about what is happening on
the volume level and when exactly the surface is being created. My questions
revolve around register-sess and rawfunc2surf-sess.

Registration has 2 parts:
1: the native anatomical space is registered with the fsaverage space. This
is happening during recon-all.
2: native functional data is registered with the native anatomical data.
This is happening during register-sess in preprocess-sess.
Aren¹t these both volume-based registrations? If not when are the surfaces
created? My concern is that it is volume-based and I was under the
impression from this article:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/ , that all
registrations should be done on the surface.

I am also confused about rawfunc2surf-sess. I believe up until this function
in preprocess-sess, everything has been done in the volume so this is the
first step that is done in the surface, is that correct? And then does this
do smoothing? I realized it has a fwhm input option so it must smooth. So is
this where the functional data is now expressed in the surface and it also
smooths? Or does surfsmooth-sess need to be run in addition to
rawfunc2surf-sess?

I basically just want to be making sure I understand when registration is
volume-based or surface-based and when it¹s appropriate to use volume-based.
And I was using the rawfunc2surf function assuming it was for smoothing, but
I am not so sure if this only creates the surface or also smooths.

Thanks,
Alissa
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Re: [Freesurfer] Volume to Surface mapping looks great for Vols created in FSL but not SPM

2017-04-05 Thread Douglas Greve 
If you have a 3mm MNI152 space, then you should run bbregister to 
fsaverage to create a new register.dat file. Alternatively, you can 
register it directly to 32k_fs_LR and cut out the middle man (make sure 
to use --9 to account for scaling). Please ignore my comment about 
fsaverage. In that case it was actually fine.




On 4/4/17 9:40 PM, Rita Elena Loiotile wrote:

Hi Doug,

Thanks for the email.  It is in 3mm space, so I guess I should 
reslice.  Can you please clarify the comment about fsaverage?  Does 
the --mni152reg flag not apply to that subject?  I'm not sure what you 
mean about the inclusion indicating ambiguity.


Thanks again,
Rita

On Tue, Apr 4, 2017 at 9:21 PM, Douglas Greve 
> wrote:


The --mni152reg flag is only appropriate if the mov file is in the
2mm mni152 space. The inclusion of fsaverage as the source subject
indicates some ambiguity about this


On 4/3/17 1:56 PM, Rita Elena Loiotile wrote:

Hi,

I'm trying to compare analyses that I've done entirely on the
surface to analyses I've done in the volume.  I'm comparing the
analyses by projecting the volume analyses to the surface (HCP's
32k_fs_LR).

The commands I'm using are:
mri_vol2surf --mov $niftiFile --mni152reg --hemi ${hemi}
--projfrac-max 0 1 0.2 --o ${giftiFile}.$hemi.gii;
mri_surf2surf --srcsubject fsaverage --srcsurfval
${giftiFile}.$hemi.gii --trgsubject 32k_fs_LR --trgsurfval
${giftiFile}.$hemi.gii --hemi ${hemi};It seems that the FSL
volumes look identical to the surface analysis, when mapped. (Our
surface analysis is mainly FSL-based, so this makes sense.)
The SPM mapping, however, looks very odd. It isn't just that the
intensity differs, but the localization of high intensity areas
also varies. It seems that everything is shifted a bit superior
and, possibly, posterior to the true location (as seen on the
surface analysis).
I'm wondering if I'm doing anything obviously wrong in my command
usage. The brains were normalized to the MNI ICBM 152 template in
SPM. I *think* it's suitable to use the -mni152reg flag in the
command.

I can attach pictures of the comparison if you'd like.

Thanks in advance,
Rita


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Re: [Freesurfer] Volume to Surface mapping looks great for Vols created in FSL but not SPM

2017-04-04 Thread Rita Elena Loiotile 
Hi Doug,

Thanks for the email.  It is in 3mm space, so I guess I should reslice.
Can you please clarify the comment about fsaverage?  Does the --mni152reg
flag not apply to that subject?  I'm not sure what you mean about the
inclusion indicating ambiguity.

Thanks again,
Rita

On Tue, Apr 4, 2017 at 9:21 PM, Douglas Greve 
wrote:

> The --mni152reg flag is only appropriate if the mov file is in the 2mm
> mni152 space. The inclusion of fsaverage as the source subject indicates
> some ambiguity about this
>
> On 4/3/17 1:56 PM, Rita Elena Loiotile wrote:
>
> Hi,
>
> I'm trying to compare analyses that I've done entirely on the surface to
> analyses I've done in the volume.  I'm comparing the analyses by projecting
> the volume analyses to the surface (HCP's 32k_fs_LR).
>
> The commands I'm using are:
> mri_vol2surf --mov $niftiFile --mni152reg --hemi ${hemi} --projfrac-max 0
> 1 0.2 --o ${giftiFile}.$hemi.gii;
> mri_surf2surf --srcsubject fsaverage --srcsurfval ${giftiFile}.$hemi.gii
> --trgsubject 32k_fs_LR --trgsurfval ${giftiFile}.$hemi.gii --hemi ${hemi};
> It seems that the FSL volumes look identical to the surface analysis, when
> mapped. (Our surface analysis is mainly FSL-based, so this makes sense.)
> The SPM mapping, however, looks very odd. It isn't just that the intensity
> differs, but the localization of high intensity areas also varies. It seems
> that everything is shifted a bit superior and, possibly, posterior to the
> true location (as seen on the surface analysis).
> I'm wondering if I'm doing anything obviously wrong in my command usage.
> The brains were normalized to the MNI ICBM 152 template in SPM. I *think*
> it's suitable to use the -mni152reg flag in the command.
>
> I can attach pictures of the comparison if you'd like.
>
> Thanks in advance,
> Rita
>
>
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> addressed. If you believe this e-mail was sent to you in error and the
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> properly
> dispose of the e-mail.
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Re: [Freesurfer] Volume to Surface mapping looks great for Vols created in FSL but not SPM

2017-04-04 Thread Douglas Greve 
The --mni152reg flag is only appropriate if the mov file is in the 2mm 
mni152 space. The inclusion of fsaverage as the source subject indicates 
some ambiguity about this



On 4/3/17 1:56 PM, Rita Elena Loiotile wrote:

Hi,

I'm trying to compare analyses that I've done entirely on the surface 
to analyses I've done in the volume.  I'm comparing the analyses by 
projecting the volume analyses to the surface (HCP's 32k_fs_LR).


The commands I'm using are:
mri_vol2surf --mov $niftiFile --mni152reg --hemi ${hemi} 
--projfrac-max 0 1 0.2 --o ${giftiFile}.$hemi.gii;
mri_surf2surf --srcsubject fsaverage --srcsurfval 
${giftiFile}.$hemi.gii --trgsubject 32k_fs_LR --trgsurfval 
${giftiFile}.$hemi.gii --hemi ${hemi};It seems that the FSL volumes 
look identical to the surface analysis, when mapped. (Our surface 
analysis is mainly FSL-based, so this makes sense.)
The SPM mapping, however, looks very odd. It isn't just that the 
intensity differs, but the localization of high intensity areas also 
varies. It seems that everything is shifted a bit superior and, 
possibly, posterior to the true location (as seen on the surface 
analysis).
I'm wondering if I'm doing anything obviously wrong in my command 
usage. The brains were normalized to the MNI ICBM 152 template in SPM. 
I *think* it's suitable to use the -mni152reg flag in the command.


I can attach pictures of the comparison if you'd like.

Thanks in advance,
Rita


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Re: [Freesurfer] Volume to Surface

2016-10-11 Thread Crawford, Anna 
When I do this for PET data for example and use the bbregister-generated.dat 
file, will that be with --srcreg bbregister-generated.dat ? If so, will I still 
use --regheader  ?

Thank you,
Anna

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Friday, September 30, 2016 1:17 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Volume to Surface

yes, that's right. You will use mri_vol2surf with the identity matrix
with the parcellation, but some bbregister-generated .dat file with PET
data.

cheers
Bruce

On Fri, 30 Sep 2016, Crawford, Anna wrote:

> No problem. I'm not exactly sure, but I think I just want a surface overlay
> so mri_vol2surf would be what I want. Right now, I am just trying to get
> down the generic way of how to do it which is why I went with trying to
> overlay the parcellation onto the inflated surface. Later, I will have
> different modalities such as PET that I will want to overlay on the inflated
> surface that will already be registered to the MRI. So I just wanted to get
> the proper workflow of how to get a volume overlayed onto the surface if
> that makes sense.
>
> Thank you,
> Anna
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much
> [trisanna.sprung-m...@mail.mcgill.ca]
> Sent: Friday, September 30, 2016 10:48 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Volume to Surface
>
> Sorry - always helps to read the whole question :D
>
> So, you are trying to create an inflated white surface? As far as I know
> this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and
> inflated surfaces that are the pial pushed outwards.
>
> Also, "mri_vol2surf" creates surface overlays on surfaces that already
> exist.
>
> Trisanna
>
> --
> Ph.D. Candidate McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna <crawf...@ccf.org> wrote:
>   I already ran recall-all. I am trying to create a different
>   surface not created using recon-all.
>
>   Anna
>
> 
>   From: freesurfer-boun...@nmr.mgh.harvard.edu
>   [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna
>       Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca]
>   Sent: Friday, September 30, 2016 10:40 AM
>   To: Freesurfer support list
>   Subject: Re: [Freesurfer] Volume to Surface
>
> You have to run recon-all to get the surfaces of a volume.
>
> Trisanna
>
> --
> Ph.D. Candidate McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna <crawf...@ccf.org>
> wrote:
>   Hello,
>
>   I am trying to take nay volume that is registered and
>   create an inflated surface. I am trying to use
>   mri_vol2surf. I am having problems with the registration
>   source. From the examples I could fine, it should be
>   --srcreg *.dat. The only *.dat file I have is segment.dat
>   which does not work. I also tried using the white matter
>   volume which also didn't work. My input and output is
>   below. Could you offer some guidance on the registration
>   file?
>
>   Thank you,
>   Anna
>
>   mri_vol2surf --src
>   
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz
>   --out
>   
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh
>   --srcreg
>   
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat
>   --hemi lh --surf white --out_type paint
>   INFO: output format is paint
>   srcvol =
>   
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz
>   srcreg =
>   
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat
>   srcregold = 0
>   srcwarp unspecified
>   surf = white
>   hemi = lh
>   reshape = 0
>   interp = nearest
>   float2int = round
>   GetProjMax = 0
>   INFO: float2int code = 0
>   INFO: changing type to float
>   Done loading volume
>   regio_read_register(): Success
>   Error reading betplaneres from
>   
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat
>
> ===
>
> Please consider th

Re: [Freesurfer] Volume to Surface

2016-09-30 Thread Douglas N Greve 
Right. It is working and the overlay does not look right because of the 
color scheme


On 09/30/2016 05:16 PM, Crawford, Anna wrote:
> I'm not sure where to find the 140 220 220 0, but when I scrolled over what 
> would seem to be the superior temporal area,I did have a value of 1030 which 
> changed as I moved to different areas. I added the $h.aparc.annot annotations 
> to confirm the locations and then compared to the .txt file for a few 
> locations in the brain. The location numbers for my overlay matched the 
> region of the brain. So, this seems as it worked properly. It is just a 
> matter of color scheme not matching right?
>
> Thank you,
> Anna
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Friday, September 30, 2016 4:44 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Volume to Surface
>
> examine the actual values. They should be constants that correspond to
> the values in $FREESURFER_HOME/FreeSurferColorLUT.txt, eg, left superior
> temporal gyrus should be
>
> 1030ctx-lh-superiortemporal 140 220 220 0
>
> On 09/30/2016 04:15 PM, Crawford, Anna wrote:
>> I did the same thing usng aparc+aseg.mgz and added --projfrac 0.5 and I got 
>> a similar type of surface to the one I had sent.
>>
>> mri_vol2surf --src 
>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/aparc+aseg.mgz
>>  --out 
>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.aparc+asegS.mgh
>>  --regheader segfs --hemi lh --surf white --out_type mgh --projfrac 0.5
>> srcvol = 
>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/aparc+aseg.mgz
>> srcreg unspecified
>> srcregold = 0
>> srcwarp unspecified
>> surf = white
>> hemi = lh
>> ProjFrac = 0.5
>> thickness = thickness
>> reshape = 0
>> interp = nearest
>> float2int = round
>> GetProjMax = 0
>> INFO: float2int code = 0
>> INFO: changing type to float
>> Done loading volume
>> Computing registration from header.
>> Using 
>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/mri/orig.mgz as 
>> target reference.
>> Reading surface 
>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/surf/lh.white
>> Done reading source surface
>> Reading thickness 
>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/surf/lh.thickness
>> Done
>> Mapping Source Volume onto Source Subject Surface
>>1 0.5 0.5 0.5
>> using old
>> Done mapping volume to surface
>> Number of source voxels hit = 73174
>> Writing to 
>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.aparc+asegS.mgh
>> Dim: 115984 1 1
>>
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Friday, September 30, 2016 3:52 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Volume to Surface
>>
>> You should use aparc+aseg.mgz and set the --projfrac 0.5. This should
>> produce something with the same information as the ?h.aparc.annot
>> (though the color scale will be different)
>>
>>
>> On 09/30/2016 03:51 PM, Crawford, Anna wrote:
>>> I was just using the wmparc as an example to get a volume overlay onto the 
>>> surface. I chose that one just to see the parcellated surface similar to 
>>> the volume.
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>>> [gr...@nmr.mgh.harvard.edu]
>>> Sent: Friday, September 30, 2016 3:41 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] Volume to Surface
>>>
>>> I can't tell from that image if it is right. Why are you mapping the
>>> wmparc to the surface? The wmparc will have segmentation boundaries
>>> right at the surface, so the actual value there will be unpredicatable.
>>>
>>>
>>> On 09/30/2016 03:31 PM, Crawford, Anna wrote:
>>>> Thank you everyone for your help! I do have a follow up question. I 
>>>> believe this did what I wanted and is what I will want to do for PET data 
>>>> for example. When I did the wmparc to the surface, I was expecting to  see 
>>>> the different areas mapped o

Re: [Freesurfer] Volume to Surface

2016-09-30 Thread Crawford, Anna 
I'm not sure where to find the 140 220 220 0, but when I scrolled over what 
would seem to be the superior temporal area,I did have a value of 1030 which 
changed as I moved to different areas. I added the $h.aparc.annot annotations 
to confirm the locations and then compared to the .txt file for a few locations 
in the brain. The location numbers for my overlay matched the region of the 
brain. So, this seems as it worked properly. It is just a matter of color 
scheme not matching right?

Thank you,
Anna

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, September 30, 2016 4:44 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Volume to Surface

examine the actual values. They should be constants that correspond to
the values in $FREESURFER_HOME/FreeSurferColorLUT.txt, eg, left superior
temporal gyrus should be

1030ctx-lh-superiortemporal 140 220 220 0

On 09/30/2016 04:15 PM, Crawford, Anna wrote:
> I did the same thing usng aparc+aseg.mgz and added --projfrac 0.5 and I got a 
> similar type of surface to the one I had sent.
>
> mri_vol2surf --src 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/aparc+aseg.mgz 
> --out 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.aparc+asegS.mgh
>  --regheader segfs --hemi lh --surf white --out_type mgh --projfrac 0.5
> srcvol = 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/aparc+aseg.mgz
> srcreg unspecified
> srcregold = 0
> srcwarp unspecified
> surf = white
> hemi = lh
> ProjFrac = 0.5
> thickness = thickness
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
> INFO: changing type to float
> Done loading volume
> Computing registration from header.
>Using 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/mri/orig.mgz as 
> target reference.
> Reading surface 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/surf/lh.white
> Done reading source surface
> Reading thickness 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/surf/lh.thickness
> Done
> Mapping Source Volume onto Source Subject Surface
>   1 0.5 0.5 0.5
> using old
> Done mapping volume to surface
> Number of source voxels hit = 73174
> Writing to 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.aparc+asegS.mgh
> Dim: 115984 1 1
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Friday, September 30, 2016 3:52 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Volume to Surface
>
> You should use aparc+aseg.mgz and set the --projfrac 0.5. This should
> produce something with the same information as the ?h.aparc.annot
> (though the color scale will be different)
>
>
> On 09/30/2016 03:51 PM, Crawford, Anna wrote:
>> I was just using the wmparc as an example to get a volume overlay onto the 
>> surface. I chose that one just to see the parcellated surface similar to the 
>> volume.
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Friday, September 30, 2016 3:41 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Volume to Surface
>>
>> I can't tell from that image if it is right. Why are you mapping the
>> wmparc to the surface? The wmparc will have segmentation boundaries
>> right at the surface, so the actual value there will be unpredicatable.
>>
>>
>> On 09/30/2016 03:31 PM, Crawford, Anna wrote:
>>> Thank you everyone for your help! I do have a follow up question. I believe 
>>> this did what I wanted and is what I will want to do for PET data for 
>>> example. When I did the wmparc to the surface, I was expecting to  see the 
>>> different areas mapped out similar to the volume. I have attached a screen 
>>> capture of what it looks like. Can someone confirm that this seems to be 
>>> correct and I was just expecting the wrong thing? I suspect this is the 
>>> case since to see the different areas in the volume you use the look up 
>>> table for the color map and that is not an option for the surface overlay.
>>>
>>> Thank you all again for your feedback!
>>>
>>> Anna
>>> 
>>> From: frees

Re: [Freesurfer] Volume to Surface

2016-09-30 Thread Douglas N Greve 
examine the actual values. They should be constants that correspond to 
the values in $FREESURFER_HOME/FreeSurferColorLUT.txt, eg, left superior 
temporal gyrus should be

1030ctx-lh-superiortemporal 140 220 220 0

On 09/30/2016 04:15 PM, Crawford, Anna wrote:
> I did the same thing usng aparc+aseg.mgz and added --projfrac 0.5 and I got a 
> similar type of surface to the one I had sent.
>
> mri_vol2surf --src 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/aparc+aseg.mgz 
> --out 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.aparc+asegS.mgh
>  --regheader segfs --hemi lh --surf white --out_type mgh --projfrac 0.5
> srcvol = 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/aparc+aseg.mgz
> srcreg unspecified
> srcregold = 0
> srcwarp unspecified
> surf = white
> hemi = lh
> ProjFrac = 0.5
> thickness = thickness
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
> INFO: changing type to float
> Done loading volume
> Computing registration from header.
>Using 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/mri/orig.mgz as 
> target reference.
> Reading surface 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/surf/lh.white
> Done reading source surface
> Reading thickness 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/surf/lh.thickness
> Done
> Mapping Source Volume onto Source Subject Surface
>   1 0.5 0.5 0.5
> using old
> Done mapping volume to surface
> Number of source voxels hit = 73174
> Writing to 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.aparc+asegS.mgh
> Dim: 115984 1 1
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Friday, September 30, 2016 3:52 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Volume to Surface
>
> You should use aparc+aseg.mgz and set the --projfrac 0.5. This should
> produce something with the same information as the ?h.aparc.annot
> (though the color scale will be different)
>
>
> On 09/30/2016 03:51 PM, Crawford, Anna wrote:
>> I was just using the wmparc as an example to get a volume overlay onto the 
>> surface. I chose that one just to see the parcellated surface similar to the 
>> volume.
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Friday, September 30, 2016 3:41 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Volume to Surface
>>
>> I can't tell from that image if it is right. Why are you mapping the
>> wmparc to the surface? The wmparc will have segmentation boundaries
>> right at the surface, so the actual value there will be unpredicatable.
>>
>>
>> On 09/30/2016 03:31 PM, Crawford, Anna wrote:
>>> Thank you everyone for your help! I do have a follow up question. I believe 
>>> this did what I wanted and is what I will want to do for PET data for 
>>> example. When I did the wmparc to the surface, I was expecting to  see the 
>>> different areas mapped out similar to the volume. I have attached a screen 
>>> capture of what it looks like. Can someone confirm that this seems to be 
>>> correct and I was just expecting the wrong thing? I suspect this is the 
>>> case since to see the different areas in the volume you use the look up 
>>> table for the color map and that is not an option for the surface overlay.
>>>
>>> Thank you all again for your feedback!
>>>
>>> Anna
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>>> [gr...@nmr.mgh.harvard.edu]
>>> Sent: Friday, September 30, 2016 2:42 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] Volume to Surface
>>>
>>> Anna, try removing --out_type paint and instead specify the output file
>>> as wmparcSlh.mgh
>>>
>>> Trisanna, thanks so much for chipping in!
>>>
>>>
>>>
>>> On 09/30/2016 01:14 PM, Trisanna Sprung-Much wrote:
>>>> Ok so this is where my knowledge might be limited because you did a
>>>> slightly different thing than me by specifying the output type as
>>>> "paint

Re: [Freesurfer] Volume to Surface

2016-09-30 Thread Crawford, Anna 
I did the same thing usng aparc+aseg.mgz and added --projfrac 0.5 and I got a 
similar type of surface to the one I had sent.

mri_vol2surf --src 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/aparc+aseg.mgz 
--out 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.aparc+asegS.mgh
 --regheader segfs --hemi lh --surf white --out_type mgh --projfrac 0.5
srcvol = 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/aparc+aseg.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
ProjFrac = 0.5
thickness = thickness
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
Computing registration from header.
  Using 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/mri/orig.mgz as 
target reference.
Reading surface 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/surf/lh.white
Done reading source surface
Reading thickness 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/surf/lh.thickness
Done
Mapping Source Volume onto Source Subject Surface
 1 0.5 0.5 0.5
using old
Done mapping volume to surface
Number of source voxels hit = 73174
Writing to 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.aparc+asegS.mgh
Dim: 115984 1 1


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, September 30, 2016 3:52 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Volume to Surface

You should use aparc+aseg.mgz and set the --projfrac 0.5. This should
produce something with the same information as the ?h.aparc.annot
(though the color scale will be different)


On 09/30/2016 03:51 PM, Crawford, Anna wrote:
> I was just using the wmparc as an example to get a volume overlay onto the 
> surface. I chose that one just to see the parcellated surface similar to the 
> volume.
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Friday, September 30, 2016 3:41 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Volume to Surface
>
> I can't tell from that image if it is right. Why are you mapping the
> wmparc to the surface? The wmparc will have segmentation boundaries
> right at the surface, so the actual value there will be unpredicatable.
>
>
> On 09/30/2016 03:31 PM, Crawford, Anna wrote:
>> Thank you everyone for your help! I do have a follow up question. I believe 
>> this did what I wanted and is what I will want to do for PET data for 
>> example. When I did the wmparc to the surface, I was expecting to  see the 
>> different areas mapped out similar to the volume. I have attached a screen 
>> capture of what it looks like. Can someone confirm that this seems to be 
>> correct and I was just expecting the wrong thing? I suspect this is the case 
>> since to see the different areas in the volume you use the look up table for 
>> the color map and that is not an option for the surface overlay.
>>
>> Thank you all again for your feedback!
>>
>> Anna
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Friday, September 30, 2016 2:42 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Volume to Surface
>>
>> Anna, try removing --out_type paint and instead specify the output file
>> as wmparcSlh.mgh
>>
>> Trisanna, thanks so much for chipping in!
>>
>>
>>
>> On 09/30/2016 01:14 PM, Trisanna Sprung-Much wrote:
>>> Ok so this is where my knowledge might be limited because you did a
>>> slightly different thing than me by specifying the output type as
>>> "paint" - that is what the .w format is. This is a label, I believe
>>> and needs to be loaded as such.
>>>
>>> What happens if you try to remove the "output_type" and try to load
>>> the result as an overlay?
>>>
>>> --
>>> Ph.D. Candidate
>>> McGill University
>>> Integrated Program in Neuroscience
>>> Psychology
>>>
>>>
>>> On Fri, Sep 30, 2016 at 1:00 PM, Crawford, Anna <crawf...@ccf.org
>>> <mailto:crawf...@ccf.org>> wrote:
>>>
>>>   Thank you! So good news, that worked and created wmparcSlh.w
>>>
>>>   I'm not sure what the .w means. When I tr

Re: [Freesurfer] Volume to Surface

2016-09-30 Thread Douglas N Greve 
You should use aparc+aseg.mgz and set the --projfrac 0.5. This should 
produce something with the same information as the ?h.aparc.annot 
(though the color scale will be different)


On 09/30/2016 03:51 PM, Crawford, Anna wrote:
> I was just using the wmparc as an example to get a volume overlay onto the 
> surface. I chose that one just to see the parcellated surface similar to the 
> volume.
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Friday, September 30, 2016 3:41 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Volume to Surface
>
> I can't tell from that image if it is right. Why are you mapping the
> wmparc to the surface? The wmparc will have segmentation boundaries
> right at the surface, so the actual value there will be unpredicatable.
>
>
> On 09/30/2016 03:31 PM, Crawford, Anna wrote:
>> Thank you everyone for your help! I do have a follow up question. I believe 
>> this did what I wanted and is what I will want to do for PET data for 
>> example. When I did the wmparc to the surface, I was expecting to  see the 
>> different areas mapped out similar to the volume. I have attached a screen 
>> capture of what it looks like. Can someone confirm that this seems to be 
>> correct and I was just expecting the wrong thing? I suspect this is the case 
>> since to see the different areas in the volume you use the look up table for 
>> the color map and that is not an option for the surface overlay.
>>
>> Thank you all again for your feedback!
>>
>> Anna
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Friday, September 30, 2016 2:42 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Volume to Surface
>>
>> Anna, try removing --out_type paint and instead specify the output file
>> as wmparcSlh.mgh
>>
>> Trisanna, thanks so much for chipping in!
>>
>>
>>
>> On 09/30/2016 01:14 PM, Trisanna Sprung-Much wrote:
>>> Ok so this is where my knowledge might be limited because you did a
>>> slightly different thing than me by specifying the output type as
>>> "paint" - that is what the .w format is. This is a label, I believe
>>> and needs to be loaded as such.
>>>
>>> What happens if you try to remove the "output_type" and try to load
>>> the result as an overlay?
>>>
>>> --
>>> Ph.D. Candidate
>>> McGill University
>>> Integrated Program in Neuroscience
>>> Psychology
>>>
>>>
>>> On Fri, Sep 30, 2016 at 1:00 PM, Crawford, Anna <crawf...@ccf.org
>>> <mailto:crawf...@ccf.org>> wrote:
>>>
>>>   Thank you! So good news, that worked and created wmparcSlh.w
>>>
>>>   I'm not sure what the .w means. When I try to load it onto the
>>>   surface, I get an error: "Failed to load Surface overlay."
>>>
>>>   Thank you,
>>>   Anna
>>>   
>>> ------------
>>>   *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>>>   <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
>>>   [freesurfer-boun...@nmr.mgh.harvard.edu
>>>   <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of
>>>   Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca
>>>   <mailto:trisanna.sprung-m...@mail.mcgill.ca>]
>>>   *Sent:* Friday, September 30, 2016 12:51 PM
>>>
>>>   *To:* Freesurfer support list
>>>   *Subject:* Re: [Freesurfer] Volume to Surface
>>>
>>>   My apologies, I meant "--regheader subject"
>>>
>>>   --
>>>   Ph.D. Candidate
>>>   McGill University
>>>   Integrated Program in Neuroscience
>>>   Psychology
>>>
>>>
>>>   On Fri, Sep 30, 2016 at 12:46 PM, Crawford, Anna <crawf...@ccf.org
>>>   <mailto:crawf...@ccf.org>> wrote:
>>>
>>>   Yeah, I get Error: Option unknown for --regmethod
>>>
>>>   Anna
>>>   
>>> 
>>>   *From:* freesurfer-boun...@nmr.

Re: [Freesurfer] Volume to Surface

2016-09-30 Thread Crawford, Anna 
I was just using the wmparc as an example to get a volume overlay onto the 
surface. I chose that one just to see the parcellated surface similar to the 
volume. 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, September 30, 2016 3:41 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Volume to Surface

I can't tell from that image if it is right. Why are you mapping the
wmparc to the surface? The wmparc will have segmentation boundaries
right at the surface, so the actual value there will be unpredicatable.


On 09/30/2016 03:31 PM, Crawford, Anna wrote:
> Thank you everyone for your help! I do have a follow up question. I believe 
> this did what I wanted and is what I will want to do for PET data for 
> example. When I did the wmparc to the surface, I was expecting to  see the 
> different areas mapped out similar to the volume. I have attached a screen 
> capture of what it looks like. Can someone confirm that this seems to be 
> correct and I was just expecting the wrong thing? I suspect this is the case 
> since to see the different areas in the volume you use the look up table for 
> the color map and that is not an option for the surface overlay.
>
> Thank you all again for your feedback!
>
> Anna
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Friday, September 30, 2016 2:42 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Volume to Surface
>
> Anna, try removing --out_type paint and instead specify the output file
> as wmparcSlh.mgh
>
> Trisanna, thanks so much for chipping in!
>
>
>
> On 09/30/2016 01:14 PM, Trisanna Sprung-Much wrote:
>> Ok so this is where my knowledge might be limited because you did a
>> slightly different thing than me by specifying the output type as
>> "paint" - that is what the .w format is. This is a label, I believe
>> and needs to be loaded as such.
>>
>> What happens if you try to remove the "output_type" and try to load
>> the result as an overlay?
>>
>> --
>> Ph.D. Candidate
>> McGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Fri, Sep 30, 2016 at 1:00 PM, Crawford, Anna <crawf...@ccf.org
>> <mailto:crawf...@ccf.org>> wrote:
>>
>>  Thank you! So good news, that worked and created wmparcSlh.w
>>
>>  I'm not sure what the .w means. When I try to load it onto the
>>  surface, I get an error: "Failed to load Surface overlay."
>>
>>  Thank you,
>>  Anna
>>  
>>  *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>>  <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
>>  [freesurfer-boun...@nmr.mgh.harvard.edu
>>      <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of
>>  Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca
>>  <mailto:trisanna.sprung-m...@mail.mcgill.ca>]
>>  *Sent:* Friday, September 30, 2016 12:51 PM
>>
>>  *To:* Freesurfer support list
>>  *Subject:* Re: [Freesurfer] Volume to Surface
>>
>>  My apologies, I meant "--regheader subject"
>>
>>  --
>>  Ph.D. Candidate
>>  McGill University
>>  Integrated Program in Neuroscience
>>  Psychology
>>
>>
>>  On Fri, Sep 30, 2016 at 12:46 PM, Crawford, Anna <crawf...@ccf.org
>>  <mailto:crawf...@ccf.org>> wrote:
>>
>>  Yeah, I get Error: Option unknown for --regmethod
>>
>>  Anna
>>  
>> 
>>      *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>>  <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
>>  [freesurfer-boun...@nmr.mgh.harvard.edu
>>  <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of
>>  Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca
>>  <mailto:trisanna.sprung-m...@mail.mcgill.ca>]
>>  *Sent:* Friday, September 30, 2016 12:41 PM
>>
>>  *To:* Freesurfer support list
>>  *Subject:* Re: [Freesurfer] Volume to Surface
>>
>>  hmmm, yup not sure there. Did you try "--regmethod subject"
>>
>&g

Re: [Freesurfer] Volume to Surface

2016-09-30 Thread Douglas N Greve 
I can't tell from that image if it is right. Why are you mapping the 
wmparc to the surface? The wmparc will have segmentation boundaries 
right at the surface, so the actual value there will be unpredicatable.


On 09/30/2016 03:31 PM, Crawford, Anna wrote:
> Thank you everyone for your help! I do have a follow up question. I believe 
> this did what I wanted and is what I will want to do for PET data for 
> example. When I did the wmparc to the surface, I was expecting to  see the 
> different areas mapped out similar to the volume. I have attached a screen 
> capture of what it looks like. Can someone confirm that this seems to be 
> correct and I was just expecting the wrong thing? I suspect this is the case 
> since to see the different areas in the volume you use the look up table for 
> the color map and that is not an option for the surface overlay.
>
> Thank you all again for your feedback!
>
> Anna
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Friday, September 30, 2016 2:42 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Volume to Surface
>
> Anna, try removing --out_type paint and instead specify the output file
> as wmparcSlh.mgh
>
> Trisanna, thanks so much for chipping in!
>
>
>
> On 09/30/2016 01:14 PM, Trisanna Sprung-Much wrote:
>> Ok so this is where my knowledge might be limited because you did a
>> slightly different thing than me by specifying the output type as
>> "paint" - that is what the .w format is. This is a label, I believe
>> and needs to be loaded as such.
>>
>> What happens if you try to remove the "output_type" and try to load
>> the result as an overlay?
>>
>> --
>> Ph.D. Candidate
>> McGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Fri, Sep 30, 2016 at 1:00 PM, Crawford, Anna <crawf...@ccf.org
>> <mailto:crawf...@ccf.org>> wrote:
>>
>>  Thank you! So good news, that worked and created wmparcSlh.w
>>
>>  I'm not sure what the .w means. When I try to load it onto the
>>  surface, I get an error: "Failed to load Surface overlay."
>>
>>  Thank you,
>>  Anna
>>  
>>  *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>>  <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
>>  [freesurfer-boun...@nmr.mgh.harvard.edu
>>      <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of
>>  Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca
>>  <mailto:trisanna.sprung-m...@mail.mcgill.ca>]
>>  *Sent:* Friday, September 30, 2016 12:51 PM
>>
>>  *To:* Freesurfer support list
>>  *Subject:* Re: [Freesurfer] Volume to Surface
>>
>>  My apologies, I meant "--regheader subject"
>>
>>  --
>>  Ph.D. Candidate
>>  McGill University
>>  Integrated Program in Neuroscience
>>  Psychology
>>
>>
>>  On Fri, Sep 30, 2016 at 12:46 PM, Crawford, Anna <crawf...@ccf.org
>>  <mailto:crawf...@ccf.org>> wrote:
>>
>>  Yeah, I get Error: Option unknown for --regmethod
>>
>>  Anna
>>  
>> 
>>      *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>>  <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
>>  [freesurfer-boun...@nmr.mgh.harvard.edu
>>  <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of
>>  Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca
>>  <mailto:trisanna.sprung-m...@mail.mcgill.ca>]
>>  *Sent:* Friday, September 30, 2016 12:41 PM
>>
>>  *To:* Freesurfer support list
>>  *Subject:* Re: [Freesurfer] Volume to Surface
>>
>>  hmmm, yup not sure there. Did you try "--regmethod subject"
>>
>>  --
>>  Ph.D. Candidate
>>  McGill University
>>  Integrated Program in Neuroscience
>>  Psychology
>>
>>
>>  On Fri, Sep 30, 2016 at 12:14 PM, Crawford, Anna
>>  <crawf...@ccf.org <mailto:crawf...@ccf.org>> wrote:
>>
>>  Just to make sure I am actually doing what you are
>>  suggesting my input

Re: [Freesurfer] Volume to Surface

2016-09-30 Thread Bruce Fischl 
or better yet, use our naming conventions an dcall it lh.wmparcS.mgh (or 
.mgz)

On Fri, 30 Sep 2016, Douglas N Greve wrote:

> Anna, try removing --out_type paint and instead specify the output file
> as wmparcSlh.mgh
>
> Trisanna, thanks so much for chipping in!
>
>
>
> On 09/30/2016 01:14 PM, Trisanna Sprung-Much wrote:
>> Ok so this is where my knowledge might be limited because you did a
>> slightly different thing than me by specifying the output type as
>> "paint" - that is what the .w format is. This is a label, I believe
>> and needs to be loaded as such.
>>
>> What happens if you try to remove the "output_type" and try to load
>> the result as an overlay?
>>
>> --
>> Ph.D. Candidate
>> McGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Fri, Sep 30, 2016 at 1:00 PM, Crawford, Anna <crawf...@ccf.org
>> <mailto:crawf...@ccf.org>> wrote:
>>
>> Thank you! So good news, that worked and created wmparcSlh.w
>>
>> I'm not sure what the .w means. When I try to load it onto the
>> surface, I get an error: "Failed to load Surface overlay."
>>
>> Thank you,
>> Anna
>> 
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
>> [freesurfer-boun...@nmr.mgh.harvard.edu
>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of
>> Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca
>> <mailto:trisanna.sprung-m...@mail.mcgill.ca>]
>> *Sent:* Friday, September 30, 2016 12:51 PM
>>
>> *To:* Freesurfer support list
>> *Subject:* Re: [Freesurfer] Volume to Surface
>>
>> My apologies, I meant "--regheader subject"
>>
>> --
>> Ph.D. Candidate
>> McGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Fri, Sep 30, 2016 at 12:46 PM, Crawford, Anna <crawf...@ccf.org
>> <mailto:crawf...@ccf.org>> wrote:
>>
>> Yeah, I get Error: Option unknown for --regmethod
>>
>> Anna
>> 
>> 
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>>     <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
>> [freesurfer-boun...@nmr.mgh.harvard.edu
>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of
>> Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca
>> <mailto:trisanna.sprung-m...@mail.mcgill.ca>]
>> *Sent:* Friday, September 30, 2016 12:41 PM
>>
>> *To:* Freesurfer support list
>> *Subject:* Re: [Freesurfer] Volume to Surface
>>
>> hmmm, yup not sure there. Did you try "--regmethod subject"
>>
>> --
>> Ph.D. Candidate
>> McGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Fri, Sep 30, 2016 at 12:14 PM, Crawford, Anna
>> <crawf...@ccf.org <mailto:crawf...@ccf.org>> wrote:
>>
>> Just to make sure I am actually doing what you are
>> suggesting my input and output is below.
>>
>> Thanks,
>> Anna
>>
>> mri_vol2surf --src
>> 
>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz
>> --out
>> 
>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh
>> --reg
>> 
>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg
>> --hemi lh --surf white --out_type paint
>> INFO: output format is paint
>> srcvol =
>> 
>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz
>> srcreg =
>> 
>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg
>> srcregold = 0
>> srcwarp unspecified
>> surf = white
>> hemi = lh
>> reshape = 0
>> interp = nearest
>> float2int = round
>> GetProjMax = 0
>> INFO: float2int code = 0
>>

Re: [Freesurfer] Volume to Surface

2016-09-30 Thread Douglas N Greve 
Anna, try removing --out_type paint and instead specify the output file 
as wmparcSlh.mgh

Trisanna, thanks so much for chipping in!



On 09/30/2016 01:14 PM, Trisanna Sprung-Much wrote:
> Ok so this is where my knowledge might be limited because you did a 
> slightly different thing than me by specifying the output type as 
> "paint" - that is what the .w format is. This is a label, I believe 
> and needs to be loaded as such.
>
> What happens if you try to remove the "output_type" and try to load 
> the result as an overlay?
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Fri, Sep 30, 2016 at 1:00 PM, Crawford, Anna <crawf...@ccf.org 
> <mailto:crawf...@ccf.org>> wrote:
>
> Thank you! So good news, that worked and created wmparcSlh.w
>
> I'm not sure what the .w means. When I try to load it onto the
> surface, I get an error: "Failed to load Surface overlay."
>
> Thank you,
> Anna
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> [freesurfer-boun...@nmr.mgh.harvard.edu
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of
> Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca
> <mailto:trisanna.sprung-m...@mail.mcgill.ca>]
> *Sent:* Friday, September 30, 2016 12:51 PM
>
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Volume to Surface
>
> My apologies, I meant "--regheader subject"
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Fri, Sep 30, 2016 at 12:46 PM, Crawford, Anna <crawf...@ccf.org
> <mailto:crawf...@ccf.org>> wrote:
>
> Yeah, I get Error: Option unknown for --regmethod
>
> Anna
> 
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> [freesurfer-boun...@nmr.mgh.harvard.edu
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of
>     Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca
> <mailto:trisanna.sprung-m...@mail.mcgill.ca>]
> *Sent:* Friday, September 30, 2016 12:41 PM
>
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Volume to Surface
>
> hmmm, yup not sure there. Did you try "--regmethod subject"
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Fri, Sep 30, 2016 at 12:14 PM, Crawford, Anna
> <crawf...@ccf.org <mailto:crawf...@ccf.org>> wrote:
>
> Just to make sure I am actually doing what you are
> suggesting my input and output is below.
>
> Thanks,
> Anna
>
> mri_vol2surf --src
> 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz
> --out
> 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh
> --reg
> 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg
> --hemi lh --surf white --out_type paint
> INFO: output format is paint
> srcvol =
> 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz
> srcreg =
> 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg
> srcregold = 0
> srcwarp unspecified
> surf = white
> hemi = lh
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
> INFO: changing type to float
> Done loading volume
> regio_read_register(): Success
> Error reading inplaneres from
> 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg
> 
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>         <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> [freesurfer-boun...@nmr.mgh.harvard.edu
> <mailto:freesurfer-bou

Re: [Freesurfer] Volume to Surface

2016-09-30 Thread Bruce Fischl 
try including --out_type mgh and naming your output something like 
lh.wmparc.mgz


cheers
Bruce
On Fri, 30 Sep 2016, Crawford, Anna wrote:

> Thank you! So good news, that worked and created wmparcSlh.w
> 
> I'm not sure what the .w means. When I try to load it onto the surface, I
> get an error: "Failed to load Surface overlay."
> 
> Thank you,
> Anna
> 
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much
> [trisanna.sprung-m...@mail.mcgill.ca]
> Sent: Friday, September 30, 2016 12:51 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Volume to Surface
> 
> My apologies, I meant "--regheader subject"
> 
> --
> Ph.D. Candidate McGill University
> Integrated Program in Neuroscience
> Psychology
> 
> 
> On Fri, Sep 30, 2016 at 12:46 PM, Crawford, Anna <crawf...@ccf.org> wrote:
>   Yeah, I get Error: Option unknown for --regmethod
>
>   Anna
> 
> 
>   From: freesurfer-boun...@nmr.mgh.harvard.edu
>   [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna
>   Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca]
>   Sent: Friday, September 30, 2016 12:41 PM
>   To: Freesurfer support list
>   Subject: Re: [Freesurfer] Volume to Surface
> 
> hmmm, yup not sure there. Did you try "--regmethod subject"
> 
> --
> Ph.D. Candidate McGill University
> Integrated Program in Neuroscience
> Psychology
> 
> 
> On Fri, Sep 30, 2016 at 12:14 PM, Crawford, Anna <crawf...@ccf.org>
> wrote:
>   Just to make sure I am actually doing what you are
>   suggesting my input and output is below.
>
>   Thanks,
>   Anna
>
>   mri_vol2surf --src
>   
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz
>   --out
>   
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh
>   
> --reg/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.r
>   eg --hemi lh --surf white --out_type paint
>   INFO: output format is paint
>   srcvol =
>   
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz
>   srcreg 
> =/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.r
>   eg
>   srcregold = 0
>   srcwarp unspecified
>   surf = white
>   hemi = lh
>   reshape = 0
>   interp = nearest
>   float2int = round
>   GetProjMax = 0
>   INFO: float2int code = 0
>   INFO: changing type to float
>   Done loading volume
>   regio_read_register(): Success
>   Error reading inplaneres 
> from/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.r
>   eg
> 
> ________
>   From: freesurfer-boun...@nmr.mgh.harvard.edu
>   [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of
>   Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca]
>   Sent: Friday, September 30, 2016 12:08 PM
>   To: Freesurfer support list
>   Subject: Re: [Freesurfer] Volume to Surface
> 
> Did you try --regmethod subjid? or --reg sphere.reg ?
> 
> If that doesn't work then I'm not sure how to help - Bruce or
> Doug, any thoughts?
> 
> Trisanna
> 
> --
> Ph.D. Candidate McGill University
> Integrated Program in Neuroscience
> Psychology
> 
> 
> On Fri, Sep 30, 2016 at 11:22 AM, Crawford, Anna
> <crawf...@ccf.org> wrote:
>   I am still having problems. If I do --reg subject I
>   get an error back that it is a directory. If I pick
>   a specific file such as orig.mgz (default according
>   to help file), I get the same error as before.
>
>   Thanks,
>   Anna
> 
> ____
>   From: freesurfer-boun...@nmr.mgh.harvard.edu
>   [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf
>   of Trisanna Sprung-Much
>   [trisanna.sprung-m...@mail.mcgill.ca]
>   Sent: Friday, September 30, 2016 11:04 AM
>   To: Freesurfer support list
>   Subject: Re: [Freesurfer] Volume to Surface
> 
> Gotcha, so when I was trying to do something similar I
> used mri_vol2surf with --regmethod subjid since you don't
> actually want to perform a transformation.
> 
> Maybe try that?
> 
> Trisanna
> 
> --
> Ph.D. Candidate McGill University
> Integrated Pro

Re: [Freesurfer] Volume to Surface

2016-09-30 Thread Bruce Fischl 
yes, that's right. You will use mri_vol2surf with the identity matrix 
with the parcellation, but some bbregister-generated .dat file with PET 
data.

cheers
Bruce

On Fri, 30 Sep 2016, Crawford, Anna wrote:

> No problem. I'm not exactly sure, but I think I just want a surface overlay
> so mri_vol2surf would be what I want. Right now, I am just trying to get
> down the generic way of how to do it which is why I went with trying to
> overlay the parcellation onto the inflated surface. Later, I will have
> different modalities such as PET that I will want to overlay on the inflated
> surface that will already be registered to the MRI. So I just wanted to get
> the proper workflow of how to get a volume overlayed onto the surface if
> that makes sense.
> 
> Thank you,
> Anna
> 
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much
> [trisanna.sprung-m...@mail.mcgill.ca]
> Sent: Friday, September 30, 2016 10:48 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Volume to Surface
> 
> Sorry - always helps to read the whole question :D
> 
> So, you are trying to create an inflated white surface? As far as I know
> this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and
> inflated surfaces that are the pial pushed outwards.
> 
> Also, "mri_vol2surf" creates surface overlays on surfaces that already
> exist.
> 
> Trisanna
> 
> --
> Ph.D. Candidate McGill University
> Integrated Program in Neuroscience
> Psychology
> 
> 
> On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna <crawf...@ccf.org> wrote:
>   I already ran recall-all. I am trying to create a different
>   surface not created using recon-all.
>
>   Anna
> 
> 
>   From: freesurfer-boun...@nmr.mgh.harvard.edu
>   [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna
>       Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca]
>   Sent: Friday, September 30, 2016 10:40 AM
>   To: Freesurfer support list
>   Subject: Re: [Freesurfer] Volume to Surface
> 
> You have to run recon-all to get the surfaces of a volume.
> 
> Trisanna
> 
> --
> Ph.D. Candidate McGill University
> Integrated Program in Neuroscience
> Psychology
> 
> 
> On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna <crawf...@ccf.org>
> wrote:
>   Hello,
>
>   I am trying to take nay volume that is registered and
>   create an inflated surface. I am trying to use
>   mri_vol2surf. I am having problems with the registration
>   source. From the examples I could fine, it should be
>   --srcreg *.dat. The only *.dat file I have is segment.dat
>   which does not work. I also tried using the white matter
>   volume which also didn't work. My input and output is
>   below. Could you offer some guidance on the registration
>   file?
>
>   Thank you,
>   Anna
>
>   mri_vol2surf --src
>   
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz
>   --out
>   
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh
>   --srcreg
>   
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat
>   --hemi lh --surf white --out_type paint
>   INFO: output format is paint
>   srcvol =
>   
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz
>   srcreg =
>   
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat
>   srcregold = 0
>   srcwarp unspecified
>   surf = white
>   hemi = lh
>   reshape = 0
>   interp = nearest
>   float2int = round
>   GetProjMax = 0
>   INFO: float2int code = 0
>   INFO: changing type to float
>   Done loading volume
>   regio_read_register(): Success
>   Error reading betplaneres from
>   
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat
> 
> ===
> 
> Please consider the environment before printing this e-mail
> 
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> America by U.S.News & World Report (2015). Visit us online at
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> message is intended for use only by the individual or entity to
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> privileged, confidential, an

Re: [Freesurfer] Volume to Surface

2016-09-30 Thread Trisanna Sprung-Much 
Ok so this is where my knowledge might be limited because you did a
slightly different thing than me by specifying the output type as "paint" -
that is what the .w format is. This is a label, I believe and needs to be
loaded as such.

What happens if you try to remove the "output_type" and try to load the
result as an overlay?

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 1:00 PM, Crawford, Anna <crawf...@ccf.org> wrote:

> Thank you! So good news, that worked and created wmparcSlh.w
>
> I'm not sure what the .w means. When I try to load it onto the surface, I
> get an error: "Failed to load Surface overlay."
>
> Thank you,
> Anna
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much
> [trisanna.sprung-m...@mail.mcgill.ca]
> *Sent:* Friday, September 30, 2016 12:51 PM
>
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Volume to Surface
>
> My apologies, I meant "--regheader subject"
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Fri, Sep 30, 2016 at 12:46 PM, Crawford, Anna <crawf...@ccf.org> wrote:
>
>> Yeah, I get Error: Option unknown for --regmethod
>>
>> Anna
>> --
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
>> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna
>> Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca]
>> *Sent:* Friday, September 30, 2016 12:41 PM
>>
>> *To:* Freesurfer support list
>> *Subject:* Re: [Freesurfer] Volume to Surface
>>
>> hmmm, yup not sure there. Did you try "--regmethod subject"
>>
>> --
>> Ph.D. Candidate
>> McGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Fri, Sep 30, 2016 at 12:14 PM, Crawford, Anna <crawf...@ccf.org>
>> wrote:
>>
>>> Just to make sure I am actually doing what you are suggesting my input
>>> and output is below.
>>>
>>> Thanks,
>>> Anna
>>>
>>> mri_vol2surf --src /mnt/netScratch/crawforda/Brai
>>> nStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out
>>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh
>>> --reg 
>>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg
>>> --hemi lh --surf white --out_type paint
>>> INFO: output format is paint
>>> srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/m
>>> ri/wmparc.mgz
>>> srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/s
>>> urf/lh.sphere.reg
>>> srcregold = 0
>>> srcwarp unspecified
>>> surf = white
>>> hemi = lh
>>> reshape = 0
>>> interp = nearest
>>> float2int = round
>>> GetProjMax = 0
>>> INFO: float2int code = 0
>>> INFO: changing type to float
>>> Done loading volume
>>> regio_read_register(): Success
>>> Error reading inplaneres from /mnt/netScratch/crawforda/Brai
>>> nStem/study11074/S2sdt/segfs/surf/lh.sphere.reg
>>> --
>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
>>> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna
>>> Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca]
>>> *Sent:* Friday, September 30, 2016 12:08 PM
>>>
>>> *To:* Freesurfer support list
>>> *Subject:* Re: [Freesurfer] Volume to Surface
>>>
>>> Did you try --regmethod subjid? or --reg sphere.reg ?
>>>
>>> If that doesn't work then I'm not sure how to help - Bruce or Doug, any
>>> thoughts?
>>>
>>> Trisanna
>>>
>>> --
>>> Ph.D. Candidate
>>> McGill University
>>> Integrated Program in Neuroscience
>>> Psychology
>>>
>>>
>>> On Fri, Sep 30, 2016 at 11:22 AM, Crawford, Anna <crawf...@ccf.org>
>>> wrote:
>>>
>>>> I am still having problems. If I do --reg subject I get an error back
>>>> that it is a directory. If I pick a specific file such as orig.mgz (default
>>>> according to help file), I get the same error as before.
>>>>
>>>> Thanks,
>>>> Anna
>>>> --
>>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
>>>> freesurfer-boun...@nmr.mgh.har

Re: [Freesurfer] Volume to Surface

2016-09-30 Thread Crawford, Anna 
Thank you! So good news, that worked and created wmparcSlh.w

I'm not sure what the .w means. When I try to load it onto the surface, I get 
an error: "Failed to load Surface overlay."

Thank you,
Anna

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much 
[trisanna.sprung-m...@mail.mcgill.ca]
Sent: Friday, September 30, 2016 12:51 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Volume to Surface

My apologies, I meant "--regheader subject"

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 12:46 PM, Crawford, Anna 
<crawf...@ccf.org<mailto:crawf...@ccf.org>> wrote:
Yeah, I get Error: Option unknown for --regmethod

Anna

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Trisanna Sprung-Much 
[trisanna.sprung-m...@mail.mcgill.ca<mailto:trisanna.sprung-m...@mail.mcgill.ca>]
Sent: Friday, September 30, 2016 12:41 PM

To: Freesurfer support list
Subject: Re: [Freesurfer] Volume to Surface

hmmm, yup not sure there. Did you try "--regmethod subject"

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 12:14 PM, Crawford, Anna 
<crawf...@ccf.org<mailto:crawf...@ccf.org>> wrote:
Just to make sure I am actually doing what you are suggesting my input and 
output is below.

Thanks,
Anna

mri_vol2surf --src 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --reg 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg 
--hemi lh --surf white --out_type paint
INFO: output format is paint
srcvol = 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz
srcreg = 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
regio_read_register(): Success
Error reading inplaneres from 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Trisanna Sprung-Much 
[trisanna.sprung-m...@mail.mcgill.ca<mailto:trisanna.sprung-m...@mail.mcgill.ca>]
Sent: Friday, September 30, 2016 12:08 PM

To: Freesurfer support list
Subject: Re: [Freesurfer] Volume to Surface

Did you try --regmethod subjid? or --reg sphere.reg ?

If that doesn't work then I'm not sure how to help - Bruce or Doug, any 
thoughts?

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 11:22 AM, Crawford, Anna 
<crawf...@ccf.org<mailto:crawf...@ccf.org>> wrote:
I am still having problems. If I do --reg subject I get an error back that it 
is a directory. If I pick a specific file such as orig.mgz (default according 
to help file), I get the same error as before.

Thanks,
Anna

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Trisanna Sprung-Much 
[trisanna.sprung-m...@mail.mcgill.ca<mailto:trisanna.sprung-m...@mail.mcgill.ca>]
Sent: Friday, September 30, 2016 11:04 AM

To: Freesurfer support list
Subject: Re: [Freesurfer] Volume to Surface

Gotcha, so when I was trying to do something similar I used mri_vol2surf with 
--regmethod subjid since you don't actually want to perform a transformation.

Maybe try that?

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna 
<crawf...@ccf.org<mailto:crawf...@ccf.org>> wrote:
No problem. I'm not exactly sure, but I think I just want a surface overlay so 
mri_vol2surf would be what I want. Right now, I am just trying to get down the 
generic way of how to do it which is why I went with trying to overlay the 
parcellation onto the inflated surface. Later, I will have different modalities 
such as PET that I will want to overlay on the inflated surface that will 
already be registered to the MRI. So I just wanted to get the proper workflow 
of how to get a volume overlayed onto the surface if that makes sense.

Thank you,
Anna

Fr

Re: [Freesurfer] Volume to Surface

2016-09-30 Thread Trisanna Sprung-Much 
My apologies, I meant "--regheader subject"

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 12:46 PM, Crawford, Anna <crawf...@ccf.org> wrote:

> Yeah, I get Error: Option unknown for --regmethod
>
> Anna
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much
> [trisanna.sprung-m...@mail.mcgill.ca]
> *Sent:* Friday, September 30, 2016 12:41 PM
>
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Volume to Surface
>
> hmmm, yup not sure there. Did you try "--regmethod subject"
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Fri, Sep 30, 2016 at 12:14 PM, Crawford, Anna <crawf...@ccf.org> wrote:
>
>> Just to make sure I am actually doing what you are suggesting my input
>> and output is below.
>>
>> Thanks,
>> Anna
>>
>> mri_vol2surf --src /mnt/netScratch/crawforda/Brai
>> nStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out
>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh
>> --reg 
>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg
>> --hemi lh --surf white --out_type paint
>> INFO: output format is paint
>> srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/
>> mri/wmparc.mgz
>> srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/
>> surf/lh.sphere.reg
>> srcregold = 0
>> srcwarp unspecified
>> surf = white
>> hemi = lh
>> reshape = 0
>> interp = nearest
>> float2int = round
>> GetProjMax = 0
>> INFO: float2int code = 0
>> INFO: changing type to float
>> Done loading volume
>> regio_read_register(): Success
>> Error reading inplaneres from /mnt/netScratch/crawforda/Brai
>> nStem/study11074/S2sdt/segfs/surf/lh.sphere.reg
>> --------------
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
>> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna
>> Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca]
>> *Sent:* Friday, September 30, 2016 12:08 PM
>>
>> *To:* Freesurfer support list
>> *Subject:* Re: [Freesurfer] Volume to Surface
>>
>> Did you try --regmethod subjid? or --reg sphere.reg ?
>>
>> If that doesn't work then I'm not sure how to help - Bruce or Doug, any
>> thoughts?
>>
>> Trisanna
>>
>> --
>> Ph.D. Candidate
>> McGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Fri, Sep 30, 2016 at 11:22 AM, Crawford, Anna <crawf...@ccf.org>
>> wrote:
>>
>>> I am still having problems. If I do --reg subject I get an error back
>>> that it is a directory. If I pick a specific file such as orig.mgz (default
>>> according to help file), I get the same error as before.
>>>
>>> Thanks,
>>> Anna
>>> --
>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
>>> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna
>>> Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca]
>>> *Sent:* Friday, September 30, 2016 11:04 AM
>>>
>>> *To:* Freesurfer support list
>>> *Subject:* Re: [Freesurfer] Volume to Surface
>>>
>>> Gotcha, so when I was trying to do something similar I used mri_vol2surf
>>> with --regmethod subjid since you don't actually want to perform a
>>> transformation.
>>>
>>> Maybe try that?
>>>
>>> Trisanna
>>>
>>> --
>>> Ph.D. Candidate
>>> McGill University
>>> Integrated Program in Neuroscience
>>> Psychology
>>>
>>>
>>> On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna <crawf...@ccf.org>
>>> wrote:
>>>
>>>> No problem. I'm not exactly sure, but I think I just want a surface
>>>> overlay so mri_vol2surf would be what I want. Right now, I am just trying
>>>> to get down the generic way of how to do it which is why I went with trying
>>>> to overlay the parcellation onto the inflated surface. Later, I will have
>>>> different modalities such as PET that I will want to overlay on the
>>>> inflated surface that will already be registered to the MRI. So I just
>>>> wanted to get the proper workflow of how to get a volume overlayed onto the
>>>> surface if that makes sense.
>>

Re: [Freesurfer] Volume to Surface

2016-09-30 Thread Crawford, Anna 
Yeah, I get Error: Option unknown for --regmethod

Anna

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much 
[trisanna.sprung-m...@mail.mcgill.ca]
Sent: Friday, September 30, 2016 12:41 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Volume to Surface

hmmm, yup not sure there. Did you try "--regmethod subject"

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 12:14 PM, Crawford, Anna 
<crawf...@ccf.org<mailto:crawf...@ccf.org>> wrote:
Just to make sure I am actually doing what you are suggesting my input and 
output is below.

Thanks,
Anna

mri_vol2surf --src 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --reg 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg 
--hemi lh --surf white --out_type paint
INFO: output format is paint
srcvol = 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz
srcreg = 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
regio_read_register(): Success
Error reading inplaneres from 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Trisanna Sprung-Much 
[trisanna.sprung-m...@mail.mcgill.ca<mailto:trisanna.sprung-m...@mail.mcgill.ca>]
Sent: Friday, September 30, 2016 12:08 PM

To: Freesurfer support list
Subject: Re: [Freesurfer] Volume to Surface

Did you try --regmethod subjid? or --reg sphere.reg ?

If that doesn't work then I'm not sure how to help - Bruce or Doug, any 
thoughts?

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 11:22 AM, Crawford, Anna 
<crawf...@ccf.org<mailto:crawf...@ccf.org>> wrote:
I am still having problems. If I do --reg subject I get an error back that it 
is a directory. If I pick a specific file such as orig.mgz (default according 
to help file), I get the same error as before.

Thanks,
Anna

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Trisanna Sprung-Much 
[trisanna.sprung-m...@mail.mcgill.ca<mailto:trisanna.sprung-m...@mail.mcgill.ca>]
Sent: Friday, September 30, 2016 11:04 AM

To: Freesurfer support list
Subject: Re: [Freesurfer] Volume to Surface

Gotcha, so when I was trying to do something similar I used mri_vol2surf with 
--regmethod subjid since you don't actually want to perform a transformation.

Maybe try that?

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna 
<crawf...@ccf.org<mailto:crawf...@ccf.org>> wrote:
No problem. I'm not exactly sure, but I think I just want a surface overlay so 
mri_vol2surf would be what I want. Right now, I am just trying to get down the 
generic way of how to do it which is why I went with trying to overlay the 
parcellation onto the inflated surface. Later, I will have different modalities 
such as PET that I will want to overlay on the inflated surface that will 
already be registered to the MRI. So I just wanted to get the proper workflow 
of how to get a volume overlayed onto the surface if that makes sense.

Thank you,
Anna

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Trisanna Sprung-Much 
[trisanna.sprung-m...@mail.mcgill.ca<mailto:trisanna.sprung-m...@mail.mcgill.ca>]
Sent: Friday, September 30, 2016 10:48 AM

To: Freesurfer support list
Subject: Re: [Freesurfer] Volume to Surface

Sorry - always helps to read the whole question :D

So, you are trying to create an inflated white surface? As far as I know this 
doesn't exist. Freesurfer creates white surfaces, pial surfaces, and inflated 
surfaces that are the pial pushed outwards.

Also, "mri_vol2surf" creates surface overlays on surfaces that already exist.

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna 
<crawf...@ccf.org

Re: [Freesurfer] Volume to Surface

2016-09-30 Thread Trisanna Sprung-Much 
hmmm, yup not sure there. Did you try "--regmethod subject"

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 12:14 PM, Crawford, Anna <crawf...@ccf.org> wrote:

> Just to make sure I am actually doing what you are suggesting my input and
> output is below.
>
> Thanks,
> Anna
>
> mri_vol2surf --src 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz
> --out 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh
> --reg 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg
> --hemi lh --surf white --out_type paint
> INFO: output format is paint
> srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/
> segfs/mri/wmparc.mgz
> srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/
> segfs/surf/lh.sphere.reg
> srcregold = 0
> srcwarp unspecified
> surf = white
> hemi = lh
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
> INFO: changing type to float
> Done loading volume
> regio_read_register(): Success
> Error reading inplaneres from /mnt/netScratch/crawforda/
> BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much
> [trisanna.sprung-m...@mail.mcgill.ca]
> *Sent:* Friday, September 30, 2016 12:08 PM
>
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Volume to Surface
>
> Did you try --regmethod subjid? or --reg sphere.reg ?
>
> If that doesn't work then I'm not sure how to help - Bruce or Doug, any
> thoughts?
>
> Trisanna
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Fri, Sep 30, 2016 at 11:22 AM, Crawford, Anna <crawf...@ccf.org> wrote:
>
>> I am still having problems. If I do --reg subject I get an error back
>> that it is a directory. If I pick a specific file such as orig.mgz (default
>> according to help file), I get the same error as before.
>>
>> Thanks,
>> Anna
>> --
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
>> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna
>> Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca]
>> *Sent:* Friday, September 30, 2016 11:04 AM
>>
>> *To:* Freesurfer support list
>> *Subject:* Re: [Freesurfer] Volume to Surface
>>
>> Gotcha, so when I was trying to do something similar I used mri_vol2surf
>> with --regmethod subjid since you don't actually want to perform a
>> transformation.
>>
>> Maybe try that?
>>
>> Trisanna
>>
>> --
>> Ph.D. Candidate
>> McGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna <crawf...@ccf.org>
>> wrote:
>>
>>> No problem. I'm not exactly sure, but I think I just want a surface
>>> overlay so mri_vol2surf would be what I want. Right now, I am just trying
>>> to get down the generic way of how to do it which is why I went with trying
>>> to overlay the parcellation onto the inflated surface. Later, I will have
>>> different modalities such as PET that I will want to overlay on the
>>> inflated surface that will already be registered to the MRI. So I just
>>> wanted to get the proper workflow of how to get a volume overlayed onto the
>>> surface if that makes sense.
>>>
>>> Thank you,
>>> Anna
>>> --
>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
>>> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna
>>> Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca]
>>> *Sent:* Friday, September 30, 2016 10:48 AM
>>>
>>> *To:* Freesurfer support list
>>> *Subject:* Re: [Freesurfer] Volume to Surface
>>>
>>> Sorry - always helps to read the whole question :D
>>>
>>> So, you are trying to create an inflated white surface? As far as I know
>>> this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and
>>> inflated surfaces that are the pial pushed outwards.
>>>
>>> Also, "mri_vol2surf" creates surface overlays on surfaces that already
>>> exist.
>>>
>>> Trisanna
>>>
>>> --
>>> Ph.D. Candidate
>>> McGill University
>>> Integrated Program in Neuroscience
&

Re: [Freesurfer] Volume to Surface

2016-09-30 Thread Crawford, Anna 
Just to make sure I am actually doing what you are suggesting my input and 
output is below.

Thanks,
Anna

mri_vol2surf --src 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --reg 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg 
--hemi lh --surf white --out_type paint
INFO: output format is paint
srcvol = 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz
srcreg = 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
regio_read_register(): Success
Error reading inplaneres from 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much 
[trisanna.sprung-m...@mail.mcgill.ca]
Sent: Friday, September 30, 2016 12:08 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Volume to Surface

Did you try --regmethod subjid? or --reg sphere.reg ?

If that doesn't work then I'm not sure how to help - Bruce or Doug, any 
thoughts?

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 11:22 AM, Crawford, Anna 
<crawf...@ccf.org<mailto:crawf...@ccf.org>> wrote:
I am still having problems. If I do --reg subject I get an error back that it 
is a directory. If I pick a specific file such as orig.mgz (default according 
to help file), I get the same error as before.

Thanks,
Anna

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Trisanna Sprung-Much 
[trisanna.sprung-m...@mail.mcgill.ca<mailto:trisanna.sprung-m...@mail.mcgill.ca>]
Sent: Friday, September 30, 2016 11:04 AM

To: Freesurfer support list
Subject: Re: [Freesurfer] Volume to Surface

Gotcha, so when I was trying to do something similar I used mri_vol2surf with 
--regmethod subjid since you don't actually want to perform a transformation.

Maybe try that?

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna 
<crawf...@ccf.org<mailto:crawf...@ccf.org>> wrote:
No problem. I'm not exactly sure, but I think I just want a surface overlay so 
mri_vol2surf would be what I want. Right now, I am just trying to get down the 
generic way of how to do it which is why I went with trying to overlay the 
parcellation onto the inflated surface. Later, I will have different modalities 
such as PET that I will want to overlay on the inflated surface that will 
already be registered to the MRI. So I just wanted to get the proper workflow 
of how to get a volume overlayed onto the surface if that makes sense.

Thank you,
Anna

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Trisanna Sprung-Much 
[trisanna.sprung-m...@mail.mcgill.ca<mailto:trisanna.sprung-m...@mail.mcgill.ca>]
Sent: Friday, September 30, 2016 10:48 AM

To: Freesurfer support list
Subject: Re: [Freesurfer] Volume to Surface

Sorry - always helps to read the whole question :D

So, you are trying to create an inflated white surface? As far as I know this 
doesn't exist. Freesurfer creates white surfaces, pial surfaces, and inflated 
surfaces that are the pial pushed outwards.

Also, "mri_vol2surf" creates surface overlays on surfaces that already exist.

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna 
<crawf...@ccf.org<mailto:crawf...@ccf.org>> wrote:
I already ran recall-all. I am trying to create a different surface not created 
using recon-all.

Anna

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Trisanna Sprung-Much 
[trisanna.sprung-m...@mail.mcgill.ca<mailto:trisanna.sprung-m...@mail.mcgill.ca>]
Sent: Friday, September 30, 2016 10:40 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Volume to Surface

You have to run recon-all to get the surfaces of a volume.

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 201

Re: [Freesurfer] Volume to Surface

2016-09-30 Thread Trisanna Sprung-Much 
Did you try --regmethod subjid? or --reg sphere.reg ?

If that doesn't work then I'm not sure how to help - Bruce or Doug, any
thoughts?

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 11:22 AM, Crawford, Anna <crawf...@ccf.org> wrote:

> I am still having problems. If I do --reg subject I get an error back that
> it is a directory. If I pick a specific file such as orig.mgz (default
> according to help file), I get the same error as before.
>
> Thanks,
> Anna
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much
> [trisanna.sprung-m...@mail.mcgill.ca]
> *Sent:* Friday, September 30, 2016 11:04 AM
>
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Volume to Surface
>
> Gotcha, so when I was trying to do something similar I used mri_vol2surf
> with --regmethod subjid since you don't actually want to perform a
> transformation.
>
> Maybe try that?
>
> Trisanna
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna <crawf...@ccf.org> wrote:
>
>> No problem. I'm not exactly sure, but I think I just want a surface
>> overlay so mri_vol2surf would be what I want. Right now, I am just trying
>> to get down the generic way of how to do it which is why I went with trying
>> to overlay the parcellation onto the inflated surface. Later, I will have
>> different modalities such as PET that I will want to overlay on the
>> inflated surface that will already be registered to the MRI. So I just
>> wanted to get the proper workflow of how to get a volume overlayed onto the
>> surface if that makes sense.
>>
>> Thank you,
>> Anna
>> --
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
>> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna
>> Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca]
>> *Sent:* Friday, September 30, 2016 10:48 AM
>>
>> *To:* Freesurfer support list
>> *Subject:* Re: [Freesurfer] Volume to Surface
>>
>> Sorry - always helps to read the whole question :D
>>
>> So, you are trying to create an inflated white surface? As far as I know
>> this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and
>> inflated surfaces that are the pial pushed outwards.
>>
>> Also, "mri_vol2surf" creates surface overlays on surfaces that already
>> exist.
>>
>> Trisanna
>>
>> --
>> Ph.D. Candidate
>> McGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna <crawf...@ccf.org>
>> wrote:
>>
>>> I already ran recall-all. I am trying to create a different surface not
>>> created using recon-all.
>>>
>>> Anna
>>> --
>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
>>> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna
>>> Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca]
>>> *Sent:* Friday, September 30, 2016 10:40 AM
>>> *To:* Freesurfer support list
>>> *Subject:* Re: [Freesurfer] Volume to Surface
>>>
>>> You have to run recon-all to get the surfaces of a volume.
>>>
>>> Trisanna
>>>
>>> --
>>> Ph.D. Candidate
>>> McGill University
>>> Integrated Program in Neuroscience
>>> Psychology
>>>
>>>
>>> On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna <crawf...@ccf.org>
>>> wrote:
>>>
>>>> Hello,
>>>>
>>>> I am trying to take nay volume that is registered and create an
>>>> inflated surface. I am trying to use mri_vol2surf. I am having problems
>>>> with the registration source. From the examples I could fine, it should be
>>>> --srcreg *.dat. The only *.dat file I have is segment.dat which does not
>>>> work. I also tried using the white matter volume which also didn't work. My
>>>> input and output is below. Could you offer some guidance on the
>>>> registration file?
>>>>
>>>> Thank you,
>>>> Anna
>>>>
>>>> mri_vol2surf --src /mnt/netScratch/crawforda/Brai
>>>> nStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out
>>>> /mnt/netScratch/crawforda/BrainStem

Re: [Freesurfer] Volume to Surface

2016-09-30 Thread Crawford, Anna 
I am still having problems. If I do --reg subject I get an error back that it 
is a directory. If I pick a specific file such as orig.mgz (default according 
to help file), I get the same error as before.

Thanks,
Anna

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much 
[trisanna.sprung-m...@mail.mcgill.ca]
Sent: Friday, September 30, 2016 11:04 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Volume to Surface

Gotcha, so when I was trying to do something similar I used mri_vol2surf with 
--regmethod subjid since you don't actually want to perform a transformation.

Maybe try that?

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna 
<crawf...@ccf.org<mailto:crawf...@ccf.org>> wrote:
No problem. I'm not exactly sure, but I think I just want a surface overlay so 
mri_vol2surf would be what I want. Right now, I am just trying to get down the 
generic way of how to do it which is why I went with trying to overlay the 
parcellation onto the inflated surface. Later, I will have different modalities 
such as PET that I will want to overlay on the inflated surface that will 
already be registered to the MRI. So I just wanted to get the proper workflow 
of how to get a volume overlayed onto the surface if that makes sense.

Thank you,
Anna

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Trisanna Sprung-Much 
[trisanna.sprung-m...@mail.mcgill.ca<mailto:trisanna.sprung-m...@mail.mcgill.ca>]
Sent: Friday, September 30, 2016 10:48 AM

To: Freesurfer support list
Subject: Re: [Freesurfer] Volume to Surface

Sorry - always helps to read the whole question :D

So, you are trying to create an inflated white surface? As far as I know this 
doesn't exist. Freesurfer creates white surfaces, pial surfaces, and inflated 
surfaces that are the pial pushed outwards.

Also, "mri_vol2surf" creates surface overlays on surfaces that already exist.

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna 
<crawf...@ccf.org<mailto:crawf...@ccf.org>> wrote:
I already ran recall-all. I am trying to create a different surface not created 
using recon-all.

Anna

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Trisanna Sprung-Much 
[trisanna.sprung-m...@mail.mcgill.ca<mailto:trisanna.sprung-m...@mail.mcgill.ca>]
Sent: Friday, September 30, 2016 10:40 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Volume to Surface

You have to run recon-all to get the surfaces of a volume.

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna 
<crawf...@ccf.org<mailto:crawf...@ccf.org>> wrote:
Hello,

I am trying to take nay volume that is registered and create an inflated 
surface. I am trying to use mri_vol2surf. I am having problems with the 
registration source. From the examples I could fine, it should be --srcreg 
*.dat. The only *.dat file I have is segment.dat which does not work. I also 
tried using the white matter volume which also didn't work. My input and output 
is below. Could you offer some guidance on the registration file?

Thank you,
Anna

mri_vol2surf --src 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh 
--srcreg 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat 
--hemi lh --surf white --out_type paint
INFO: output format is paint
srcvol = 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz
srcreg = 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
regio_read_register(): Success
Error reading betplaneres from 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat

===
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & 
World Report (2015). Visit us online at http://www.clevelandclinic.org for a 
complete listing of our services, staff and locations. Confidentiality Note: 
This message is inten

Re: [Freesurfer] Volume to Surface

2016-09-30 Thread Trisanna Sprung-Much 
Gotcha, so when I was trying to do something similar I used mri_vol2surf
with --regmethod subjid since you don't actually want to perform a
transformation.

Maybe try that?

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna <crawf...@ccf.org> wrote:

> No problem. I'm not exactly sure, but I think I just want a surface
> overlay so mri_vol2surf would be what I want. Right now, I am just trying
> to get down the generic way of how to do it which is why I went with trying
> to overlay the parcellation onto the inflated surface. Later, I will have
> different modalities such as PET that I will want to overlay on the
> inflated surface that will already be registered to the MRI. So I just
> wanted to get the proper workflow of how to get a volume overlayed onto the
> surface if that makes sense.
>
> Thank you,
> Anna
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much
> [trisanna.sprung-m...@mail.mcgill.ca]
> *Sent:* Friday, September 30, 2016 10:48 AM
>
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Volume to Surface
>
> Sorry - always helps to read the whole question :D
>
> So, you are trying to create an inflated white surface? As far as I know
> this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and
> inflated surfaces that are the pial pushed outwards.
>
> Also, "mri_vol2surf" creates surface overlays on surfaces that already
> exist.
>
> Trisanna
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna <crawf...@ccf.org> wrote:
>
>> I already ran recall-all. I am trying to create a different surface not
>> created using recon-all.
>>
>> Anna
>> --
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
>> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna
>> Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca]
>> *Sent:* Friday, September 30, 2016 10:40 AM
>> *To:* Freesurfer support list
>> *Subject:* Re: [Freesurfer] Volume to Surface
>>
>> You have to run recon-all to get the surfaces of a volume.
>>
>> Trisanna
>>
>> --
>> Ph.D. Candidate
>> McGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna <crawf...@ccf.org> wrote:
>>
>>> Hello,
>>>
>>> I am trying to take nay volume that is registered and create an inflated
>>> surface. I am trying to use mri_vol2surf. I am having problems with the
>>> registration source. From the examples I could fine, it should be --srcreg
>>> *.dat. The only *.dat file I have is segment.dat which does not work. I
>>> also tried using the white matter volume which also didn't work. My input
>>> and output is below. Could you offer some guidance on the registration file?
>>>
>>> Thank you,
>>> Anna
>>>
>>> mri_vol2surf --src /mnt/netScratch/crawforda/Brai
>>> nStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out
>>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh
>>> --srcreg 
>>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat
>>> --hemi lh --surf white --out_type paint
>>> INFO: output format is paint
>>> srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/m
>>> ri/wmparc.mgz
>>> srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/m
>>> ri/segment.dat
>>> srcregold = 0
>>> srcwarp unspecified
>>> surf = white
>>> hemi = lh
>>> reshape = 0
>>> interp = nearest
>>> float2int = round
>>> GetProjMax = 0
>>> INFO: float2int code = 0
>>> INFO: changing type to float
>>> Done loading volume
>>> regio_read_register(): Success
>>> Error reading betplaneres from /mnt/netScratch/crawforda/Brai
>>> nStem/study11074/S2sdt/segfs/mri/segment.dat
>>>
>>> ===
>>>
>>> Please consider the environment before printing this e-mail
>>> Cleveland Clinic is ranked as one of the top hospitals in America by
>>> U.S.News & World Report (2015). Visit us online at
>>> http://www.clevelandclinic.org for a complete listing of our services,
>>> staff and locat

Re: [Freesurfer] Volume to Surface

2016-09-30 Thread Crawford, Anna 
No problem. I'm not exactly sure, but I think I just want a surface overlay so 
mri_vol2surf would be what I want. Right now, I am just trying to get down the 
generic way of how to do it which is why I went with trying to overlay the 
parcellation onto the inflated surface. Later, I will have different modalities 
such as PET that I will want to overlay on the inflated surface that will 
already be registered to the MRI. So I just wanted to get the proper workflow 
of how to get a volume overlayed onto the surface if that makes sense.

Thank you,
Anna

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much 
[trisanna.sprung-m...@mail.mcgill.ca]
Sent: Friday, September 30, 2016 10:48 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Volume to Surface

Sorry - always helps to read the whole question :D

So, you are trying to create an inflated white surface? As far as I know this 
doesn't exist. Freesurfer creates white surfaces, pial surfaces, and inflated 
surfaces that are the pial pushed outwards.

Also, "mri_vol2surf" creates surface overlays on surfaces that already exist.

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna 
<crawf...@ccf.org<mailto:crawf...@ccf.org>> wrote:
I already ran recall-all. I am trying to create a different surface not created 
using recon-all.

Anna

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Trisanna Sprung-Much 
[trisanna.sprung-m...@mail.mcgill.ca<mailto:trisanna.sprung-m...@mail.mcgill.ca>]
Sent: Friday, September 30, 2016 10:40 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Volume to Surface

You have to run recon-all to get the surfaces of a volume.

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna 
<crawf...@ccf.org<mailto:crawf...@ccf.org>> wrote:
Hello,

I am trying to take nay volume that is registered and create an inflated 
surface. I am trying to use mri_vol2surf. I am having problems with the 
registration source. From the examples I could fine, it should be --srcreg 
*.dat. The only *.dat file I have is segment.dat which does not work. I also 
tried using the white matter volume which also didn't work. My input and output 
is below. Could you offer some guidance on the registration file?

Thank you,
Anna

mri_vol2surf --src 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh 
--srcreg 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat 
--hemi lh --surf white --out_type paint
INFO: output format is paint
srcvol = 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz
srcreg = 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
regio_read_register(): Success
Error reading betplaneres from 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat

===
Please consider the environment before printing this e-mail
Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & 
World Report (2015). Visit us online at http://www.clevelandclinic.org for a 
complete listing of our services, staff and locations. Confidentiality Note: 
This message is intended for use only by the individual or entity to which it 
is addressed and may contain information that is privileged, confidential, and 
exempt from disclosure under applicable law. If the reader of this message is 
not the intended recipient or the employee or agent responsible for delivering 
the message to the intended recipient, you are hereby notified that any 
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Re: [Freesurfer] Volume to Surface

2016-09-30 Thread Trisanna Sprung-Much 
Sorry - always helps to read the whole question :D

So, you are trying to create an inflated white surface? As far as I know
this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and
inflated surfaces that are the pial pushed outwards.

Also, "mri_vol2surf" creates surface overlays on surfaces that already
exist.

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna <crawf...@ccf.org> wrote:

> I already ran recall-all. I am trying to create a different surface not
> created using recon-all.
>
> Anna
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much
> [trisanna.sprung-m...@mail.mcgill.ca]
> *Sent:* Friday, September 30, 2016 10:40 AM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Volume to Surface
>
> You have to run recon-all to get the surfaces of a volume.
>
> Trisanna
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna <crawf...@ccf.org> wrote:
>
>> Hello,
>>
>> I am trying to take nay volume that is registered and create an inflated
>> surface. I am trying to use mri_vol2surf. I am having problems with the
>> registration source. From the examples I could fine, it should be --srcreg
>> *.dat. The only *.dat file I have is segment.dat which does not work. I
>> also tried using the white matter volume which also didn't work. My input
>> and output is below. Could you offer some guidance on the registration file?
>>
>> Thank you,
>> Anna
>>
>> mri_vol2surf --src /mnt/netScratch/crawforda/Brai
>> nStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out
>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh
>> --srcreg 
>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat
>> --hemi lh --surf white --out_type paint
>> INFO: output format is paint
>> srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/
>> mri/wmparc.mgz
>> srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/
>> mri/segment.dat
>> srcregold = 0
>> srcwarp unspecified
>> surf = white
>> hemi = lh
>> reshape = 0
>> interp = nearest
>> float2int = round
>> GetProjMax = 0
>> INFO: float2int code = 0
>> INFO: changing type to float
>> Done loading volume
>> regio_read_register(): Success
>> Error reading betplaneres from /mnt/netScratch/crawforda/Brai
>> nStem/study11074/S2sdt/segfs/mri/segment.dat
>>
>> ===
>>
>> Please consider the environment before printing this e-mail
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>> only by the individual or entity to which it is addressed and may contain
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>> under applicable law. If the reader of this message is not the intended
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>> to the intended recipient, you are hereby notified that any dissemination,
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>> you have received this communication in error, please contact the sender
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Re: [Freesurfer] Volume to Surface

2016-09-30 Thread Bruce Fischl 
Hi Anna
I think you are trying to project an overlay on a surface, not create a 
surface, right?
Bruce

> On Sep 30, 2016, at 10:44 AM, Crawford, Anna <crawf...@ccf.org> wrote:
> 
> I already ran recall-all. I am trying to create a different surface not 
> created using recon-all.
> 
> Anna
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much 
> [trisanna.sprung-m...@mail.mcgill.ca]
> Sent: Friday, September 30, 2016 10:40 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Volume to Surface
> 
> You have to run recon-all to get the surfaces of a volume.
> 
> Trisanna
> 
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
> 
> 
>> On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna <crawf...@ccf.org> wrote:
>> Hello,
>> 
>> I am trying to take nay volume that is registered and create an inflated 
>> surface. I am trying to use mri_vol2surf. I am having problems with the 
>> registration source. From the examples I could fine, it should be --srcreg 
>> *.dat. The only *.dat file I have is segment.dat which does not work. I also 
>> tried using the white matter volume which also didn't work. My input and 
>> output is below. Could you offer some guidance on the registration file?
>> 
>> Thank you,
>> Anna
>> 
>> mri_vol2surf --src 
>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz 
>> --out 
>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh 
>> --srcreg 
>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat 
>> --hemi lh --surf white --out_type paint
>> INFO: output format is paint
>> srcvol = 
>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz
>> srcreg = 
>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat
>> srcregold = 0
>> srcwarp unspecified
>> surf = white
>> hemi = lh
>> reshape = 0
>> interp = nearest
>> float2int = round
>> GetProjMax = 0
>> INFO: float2int code = 0
>> INFO: changing type to float
>> Done loading volume
>> regio_read_register(): Success
>> Error reading betplaneres from 
>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat
>> === 
>> Please consider the environment before printing this e-mail
>> 
>> Cleveland Clinic is ranked as one of the top hospitals in America by 
>> U.S.News & World Report (2015). Visit us online at 
>> http://www.clevelandclinic.org for a complete listing of our services, staff 
>> and locations. Confidentiality Note: This message is intended for use only 
>> by the individual or entity to which it is addressed and may contain 
>> information that is privileged, confidential, and exempt from disclosure 
>> under applicable law. If the reader of this message is not the intended 
>> recipient or the employee or agent responsible for delivering the message to 
>> the intended recipient, you are hereby notified that any dissemination, 
>> distribution or copying of this communication is strictly prohibited. If you 
>> have received this communication in error, please contact the sender 
>> immediately and destroy the material in its entirety, whether electronic or 
>> hard copy. Thank you.
>> 
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>> 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
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> 
> === 
> 
> Please consider the environment before printing this e-mail
> 
> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News 
> & World Report (2015). Visit us online at http://www.clevelandclinic.org for 
> a complete listing of our services, staff and locations. Confidentiality 
> Note: This message is intended for use only by the individual or entity to 
> which it is addressed and may contain inf

Re: [Freesurfer] Volume to Surface

2016-09-30 Thread Crawford, Anna 
I already ran recall-all. I am trying to create a different surface not created 
using recon-all.

Anna

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much 
[trisanna.sprung-m...@mail.mcgill.ca]
Sent: Friday, September 30, 2016 10:40 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Volume to Surface

You have to run recon-all to get the surfaces of a volume.

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna 
<crawf...@ccf.org<mailto:crawf...@ccf.org>> wrote:
Hello,

I am trying to take nay volume that is registered and create an inflated 
surface. I am trying to use mri_vol2surf. I am having problems with the 
registration source. From the examples I could fine, it should be --srcreg 
*.dat. The only *.dat file I have is segment.dat which does not work. I also 
tried using the white matter volume which also didn't work. My input and output 
is below. Could you offer some guidance on the registration file?

Thank you,
Anna

mri_vol2surf --src 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh 
--srcreg 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat 
--hemi lh --surf white --out_type paint
INFO: output format is paint
srcvol = 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz
srcreg = 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
regio_read_register(): Success
Error reading betplaneres from 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat

===
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Visit us online at http://www.clevelandclinic.org for a complete listing of our 
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Re: [Freesurfer] Volume to Surface

2016-09-30 Thread Trisanna Sprung-Much 
You have to run recon-all to get the surfaces of a volume.

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna  wrote:

> Hello,
>
> I am trying to take nay volume that is registered and create an inflated
> surface. I am trying to use mri_vol2surf. I am having problems with the
> registration source. From the examples I could fine, it should be --srcreg
> *.dat. The only *.dat file I have is segment.dat which does not work. I
> also tried using the white matter volume which also didn't work. My input
> and output is below. Could you offer some guidance on the registration file?
>
> Thank you,
> Anna
>
> mri_vol2surf --src 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz
> --out 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh
> --srcreg 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat
> --hemi lh --surf white --out_type paint
> INFO: output format is paint
> srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/
> segfs/mri/wmparc.mgz
> srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/
> segfs/mri/segment.dat
> srcregold = 0
> srcwarp unspecified
> surf = white
> hemi = lh
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
> INFO: changing type to float
> Done loading volume
> regio_read_register(): Success
> Error reading betplaneres from /mnt/netScratch/crawforda/
> BrainStem/study11074/S2sdt/segfs/mri/segment.dat
>
> ===
>
> Please consider the environment before printing this e-mail
> Cleveland Clinic is ranked as one of the top hospitals in America by
> U.S.News & World Report (2015). Visit us online at
> http://www.clevelandclinic.org for a complete listing of our services,
> staff and locations. Confidentiality Note: This message is intended for use
> only by the individual or entity to which it is addressed and may contain
> information that is privileged, confidential, and exempt from disclosure
> under applicable law. If the reader of this message is not the intended
> recipient or the employee or agent responsible for delivering the message
> to the intended recipient, you are hereby notified that any dissemination,
> distribution or copying of this communication is strictly prohibited. If
> you have received this communication in error, please contact the sender
> immediately and destroy the material in its entirety, whether electronic or
> hard copy. Thank you.
>
>
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Re: [Freesurfer] volume to surface - average across normal

2015-05-06 Thread Bruce Fischl 
you can try running the commands with --help and see what they tell you 
(or sometimes -h). That's where this came from

cheers
Bruce


On Wed, 6 May 2015, Andersson, Jonas Patrik wrote:

 Hi Bruce,

 Thanks a lot for your answer! This is exactly what I was looking for.
 I looked at the https://surfer.nmr.mgh.harvard.edu/fswiki/mri_vol2surf 
 website that did not specify these options.

 Thanks again!
 Patrik
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Re: [Freesurfer] volume to surface - average across normal

2015-05-06 Thread Bruce Fischl 
Hi Patrik

vol2surf is very flexible about this. If you look at the help you will see:

  Options for projecting along the surface normal:
--projfrac frac : (0-1)fractional projection along normal
--projfrac-avg min max del : average along normal
--projfrac-max min max del : max along normal
--projdist mmdist : distance projection along normal
--projdist-avg min max del : average along normal
--projopt fraction stem : use optimal linear estimation and previously
computed volume fractions (see mri_compute_volume_fractions)


cheers
Bruce


On Wed, 6 May 2015, Andersson, Jonas Patrik wrote:

 Dear all,

 I would like to project a volume of statistical values (ang.nii) to the 
 surface. At the moment I do it as in this example:

 mri_vol2surf --src ang.nii --srcreg register.dat --hemi lh --projfrac 0.5  
 --out ./ang-lh.w --out_type paint

 However, what I would like to get is the average value along the surface 
 normal (say between white and pial or so), not just the single value at a 
 certain distance (--projfrac).
 Is this somehow possible?

 Best,
 Patrik
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Re: [Freesurfer] volume to surface registration problem

2014-10-16 Thread Douglas N Greve 

The problem is probabably that the fsl flirt registration failed and 
that caused bbr to fail. If you have spm and matlab installed, running 
it with

cd /misc/data41/yuex/humanfMRI/human_curvature/subjdata/field090514
bbregister --s field --init-spm --6 --bold --mov bold/template.nii --reg 
bold/register.dof6.dat --init-reg-out bold/init.register.dof6.dat




On 10/16/2014 11:14 AM, Xiaomin Yue wrote:
 Hi,

 When I used preproc-sess processing my data, the registration output 
 is off a great of deal.  The functional data was collected using 7T, 
 and the surface was reconstructed successfully from 3T data and was 
 checked visually multiple times.   I am using fs5.3 installed on a 
 linux system. Attached is the registration log file.

 Any suggestions will be appreciated.

 Xiaomin Yue


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-- 
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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] volume to surface registration problem

2014-10-16 Thread Xiaomin Yue 
Hi Doug,
Thanks for the promptly response.   I do have spm8 and spm12b installed.  Which 
version should I use?  Also, how to change the spm as the inital registration 
method in the preproc-sess?  
Xiaomin

 Date: Thu, 16 Oct 2014 12:00:04 -0400
 From: gr...@nmr.mgh.harvard.edu
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] volume to surface registration problem
 
 
 The problem is probabably that the fsl flirt registration failed and 
 that caused bbr to fail. If you have spm and matlab installed, running 
 it with
 
 cd /misc/data41/yuex/humanfMRI/human_curvature/subjdata/field090514
 bbregister --s field --init-spm --6 --bold --mov bold/template.nii --reg 
 bold/register.dof6.dat --init-reg-out bold/init.register.dof6.dat
 
 
 
 
 On 10/16/2014 11:14 AM, Xiaomin Yue wrote:
  Hi,
 
  When I used preproc-sess processing my data, the registration output 
  is off a great of deal.  The functional data was collected using 7T, 
  and the surface was reconstructed successfully from 3T data and was 
  checked visually multiple times.   I am using fs5.3 installed on a 
  linux system. Attached is the registration log file.
 
  Any suggestions will be appreciated.
 
  Xiaomin Yue
 
 
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 -- 
 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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 addressed. If you believe this e-mail was sent to you in error and the e-mail
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 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] volume to surface registration problem

2014-10-16 Thread Douglas N Greve 

I have not tested it with spm12, so use spm8. There is not currently a 
way to run the spm init from preproc-sess, so you'll have to run it from 
register-sess.

On 10/16/2014 12:04 PM, Xiaomin Yue wrote:
 Hi Doug,

 Thanks for the promptly response.   I do have spm8 and spm12b 
 installed.  Which version should I use?  Also, how to change the spm 
 as the inital registration method in the preproc-sess?

 Xiaomin

  Date: Thu, 16 Oct 2014 12:00:04 -0400
  From: gr...@nmr.mgh.harvard.edu
  To: freesurfer@nmr.mgh.harvard.edu
  Subject: Re: [Freesurfer] volume to surface registration problem
 
 
  The problem is probabably that the fsl flirt registration failed and
  that caused bbr to fail. If you have spm and matlab installed, running
  it with
 
  cd /misc/data41/yuex/humanfMRI/human_curvature/subjdata/field090514
  bbregister --s field --init-spm --6 --bold --mov bold/template.nii 
 --reg bold/register.dof6.dat --init-reg-out bold/init.register.dof6.dat
 
 
 
 
  On 10/16/2014 11:14 AM, Xiaomin Yue wrote:
   Hi,
  
   When I used preproc-sess processing my data, the registration output
   is off a great of deal. The functional data was collected using 7T,
   and the surface was reconstructed successfully from 3T data and was
   checked visually multiple times. I am using fs5.3 installed on a
   linux system. Attached is the registration log file.
  
   Any suggestions will be appreciated.
  
   Xiaomin Yue
  
  
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  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
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 whom it is
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 HelpLine at
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] volume to surface registration problem

2014-10-16 Thread Xiaomin Yue 
Is it right that the prep roc-sess includes the following steps: 1) 
mktemplate-sess; 2) mkbrainmask-sess; 3)register-sess; 4) mc-sess; 5) 
rawfunc2surf-sess.  So, I need to rerun step3, 4, and 5 manually, is that 
right? 
Thanks,Xiaomin

 Date: Thu, 16 Oct 2014 12:12:23 -0400
 From: gr...@nmr.mgh.harvard.edu
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] volume to surface registration problem
 
 
 I have not tested it with spm12, so use spm8. There is not currently a 
 way to run the spm init from preproc-sess, so you'll have to run it from 
 register-sess.
 
 On 10/16/2014 12:04 PM, Xiaomin Yue wrote:
  Hi Doug,
 
  Thanks for the promptly response.   I do have spm8 and spm12b 
  installed.  Which version should I use?  Also, how to change the spm 
  as the inital registration method in the preproc-sess?
 
  Xiaomin
 
   Date: Thu, 16 Oct 2014 12:00:04 -0400
   From: gr...@nmr.mgh.harvard.edu
   To: freesurfer@nmr.mgh.harvard.edu
   Subject: Re: [Freesurfer] volume to surface registration problem
  
  
   The problem is probabably that the fsl flirt registration failed and
   that caused bbr to fail. If you have spm and matlab installed, running
   it with
  
   cd /misc/data41/yuex/humanfMRI/human_curvature/subjdata/field090514
   bbregister --s field --init-spm --6 --bold --mov bold/template.nii 
  --reg bold/register.dof6.dat --init-reg-out bold/init.register.dof6.dat
  
  
  
  
   On 10/16/2014 11:14 AM, Xiaomin Yue wrote:
Hi,
   
When I used preproc-sess processing my data, the registration output
is off a great of deal. The functional data was collected using 7T,
and the surface was reconstructed successfully from 3T data and was
checked visually multiple times. I am using fs5.3 installed on a
linux system. Attached is the registration log file.
   
Any suggestions will be appreciated.
   
Xiaomin Yue
   
   
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   --
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   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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   The information in this e-mail is intended only for the person to 
  whom it is
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  the e-mail
   contains patient information, please contact the Partners Compliance 
  HelpLine at
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  you in error
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  and properly
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 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
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Re: [Freesurfer] volume to surface registration problem

2014-10-16 Thread Douglas N Greve 

It does include those steps, but you won't need to re-run them manually. 
Just run register-sess, then run preproc-sess as you normally would. It 
should see that the most recent files are the registration files and 
then perform all the steps afterwards. You should double check that it 
does not rerun the registration, but it should not.
doug

On 10/16/2014 12:54 PM, Xiaomin Yue wrote:
 Is it right that the prep roc-sess includes the following steps: 1) 
 mktemplate-sess; 2) mkbrainmask-sess; 3)register-sess; 4) mc-sess; 5) 
 rawfunc2surf-sess.  So, I need to rerun step3, 4, and 5 manually, is 
 that right?

 Thanks,
 Xiaomin

  Date: Thu, 16 Oct 2014 12:12:23 -0400
  From: gr...@nmr.mgh.harvard.edu
  To: freesurfer@nmr.mgh.harvard.edu
  Subject: Re: [Freesurfer] volume to surface registration problem
 
 
  I have not tested it with spm12, so use spm8. There is not currently a
  way to run the spm init from preproc-sess, so you'll have to run it 
 from
  register-sess.
 
  On 10/16/2014 12:04 PM, Xiaomin Yue wrote:
   Hi Doug,
  
   Thanks for the promptly response. I do have spm8 and spm12b
   installed. Which version should I use? Also, how to change the spm
   as the inital registration method in the preproc-sess?
  
   Xiaomin
  
Date: Thu, 16 Oct 2014 12:00:04 -0400
From: gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] volume to surface registration problem
   
   
The problem is probabably that the fsl flirt registration failed and
that caused bbr to fail. If you have spm and matlab installed, 
 running
it with
   
cd /misc/data41/yuex/humanfMRI/human_curvature/subjdata/field090514
bbregister --s field --init-spm --6 --bold --mov bold/template.nii
   --reg bold/register.dof6.dat --init-reg-out 
 bold/init.register.dof6.dat
   
   
   
   
On 10/16/2014 11:14 AM, Xiaomin Yue wrote:
 Hi,

 When I used preproc-sess processing my data, the registration 
 output
 is off a great of deal. The functional data was collected 
 using 7T,
 and the surface was reconstructed successfully from 3T data 
 and was
 checked visually multiple times. I am using fs5.3 installed on a
 linux system. Attached is the registration log file.

 Any suggestions will be appreciated.

 Xiaomin Yue


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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
   
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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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 Compliance
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  gr...@nmr.mgh.harvard.edu
  Phone Number: 617-724-2358
  Fax: 617-726-7422
 
  Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Volume to surface coordinates

2014-09-24 Thread Douglas N Greve 

See if this page gives you the answer you need

http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems


On 09/23/2014 10:39 AM, Michael WOODMAN wrote:
 Hello freesurfers,

 I would like to identify, in surface/vertex coordinates, certain points
 in a volume. Is there a straightforward way to obtain relevant transform?

 Thank you,
 Marmaduke Woodman

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Re: [Freesurfer] volume to surface

2013-12-19 Thread Bruce Fischl 

Hi Yue

you can use bbregister to generate the registration.

cheers
Bruce
On Thu, 19 Dec 2013, 
赵越 wrote:



Hi All,
I would like to use mri_vol2surf to overlay a volume onto a surface. The
synopsis is mri_vol2surf [options] --src inputfile --out outpufile
--srcreg registrationfile --hemi hemisphere.
But I don't know how to generate the registrationfile. Could someone help me
with that?

Thanks a lot!


Yue

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Re: [Freesurfer] Volume to surface

2012-05-08 Thread Gabriel Gonzalez Escamilla 
Thank you Anderson,It looks like do just what I want to do, but I'm having a problem, I've give the permissions to make the file an executable as follows chmod +x /root/freesurfer/bin/aseg2surf but when I call it  always say that bash: aseg2surf: command not found. My FS v5.1 is working properly and Actually as you can see I'd put the script you sent me into the bin folder on the $FREESURFER_HOME directoryRegards,GabrielEl 07/05/12, Anderson Winkler  andersonwink...@hotmail.com escribió:
  

  
  
Hi Gabriel,

Attached is a script that probably does what you need. Just make it
executable and call it without arguments to get usage information.
The label indices you can get from the aseg.stats file or from
FreeSurferColorLUT.txt.

The surfaces will be saved in a subdirectory called ascii inside
each subject's directory, and have extension .srf. They are
internally the same as the .asc surfaces, just with a different
extension.

Note that the idea of the script is to generate surfaces for
visualization purposes only. If you'd like to do statistical
analysis (e.g., compare shapes between patients and controls), these
surfaces may not be appropriate.

Hope it helps!

All the best,

Anderson


On 07/05/12 12:15, Gabriel Gonzalez Escamilla wrote:

  
Hello all FS users and experts,


I'm wanting to get the sub cortical segmentation as ASCII
  files, so I'm trying convert the aseg.mgz into a surface file,
  to finally get an ASCII file,
For this I'm using the next commands:


First: mri_convert -rl rawavg.mgz -rt nearest aseg.mgz
  aseg2raw.nii
To preserve  the aseg volume in native space 


Second: mri_vol2surf --mov aseg2raw.nii --regheader
  mysubject --hemi lh --o ./lg.aseg2raw.mgh
  
  
  
  And last: mris_convert lh.aseg2raw.mgh lh.aseg2raw.asc
  
  
  I'm Not sure if I should do this for the whole aseg or if
should I try to separate the segmented structures first...
  
  
  Many Thanks in advanced,
  Gabriel
  
  
  
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-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/
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Re: [Freesurfer] Volume to surface

2012-05-08 Thread Gabriel Gonzalez Escamilla 
Well now the aseg2srf script is working perfectly, it was a thing of the shell (changed to: #!/bin/sh -f) and the format of the script when I'd downloaded it.Now I'm wanting to use the srf2obj script, and something similar happens, but since it is for gawk I have no idea how to change it or fix it to make it run, it gave me the same error as the last time:[root@localhost] srf2obj aseg_004.srf  aseg_4.objgawk: /root/freesurfer/bin/srf2obj:2:' invalid on the expressionrfer/bin/srf2obj:2: ^ character ' Regards,GabrielEl 07/05/12, Anderson Winkler  andersonwink...@hotmail.com escribió:
  

  
  
Hi Gabriel,

Attached is a script that probably does what you need. Just make it
executable and call it without arguments to get usage information.
The label indices you can get from the aseg.stats file or from
FreeSurferColorLUT.txt.

The surfaces will be saved in a subdirectory called ascii inside
each subject's directory, and have extension .srf. They are
internally the same as the .asc surfaces, just with a different
extension.

Note that the idea of the script is to generate surfaces for
visualization purposes only. If you'd like to do statistical
analysis (e.g., compare shapes between patients and controls), these
surfaces may not be appropriate.

Hope it helps!

All the best,

Anderson


On 07/05/12 12:15, Gabriel Gonzalez Escamilla wrote:

  
Hello all FS users and experts,


I'm wanting to get the sub cortical segmentation as ASCII
  files, so I'm trying convert the aseg.mgz into a surface file,
  to finally get an ASCII file,
For this I'm using the next commands:


First: mri_convert -rl rawavg.mgz -rt nearest aseg.mgz
  aseg2raw.nii
To preserve  the aseg volume in native space 


Second: mri_vol2surf --mov aseg2raw.nii --regheader
  mysubject --hemi lh --o ./lg.aseg2raw.mgh
  
  
  
  And last: mris_convert lh.aseg2raw.mgh lh.aseg2raw.asc
  
  
  I'm Not sure if I should do this for the whole aseg or if
should I try to separate the segmented structures first...
  
  
  Many Thanks in advanced,
  Gabriel
  
  
  
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-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/
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Re: [Freesurfer] Volume to surface

2012-05-08 Thread Anderson Winkler 

Hi Gabriel,

This sounds like a problem with downloading. Are you copying and pasting 
the content of the scripts rather than downloading? Are you copying from 
a Windows computer? Gawk is just a replacement for awk with a more 
permissive license and more features. It is the default in Linux and its 
explicit use only makes a difference for Mac users, who have to get it 
from MacPorts or Fink.


Also, the first script should work with bash. The sh can be ash, dash or 
even other depending on the system, being all with less features than 
bash itself. Ubuntu uses dash as sh for instance. Perhaps this one may 
work with any, but this isn't always the case.


All the best!

Anderson


On 08/05/12 11:23, Gabriel Gonzalez Escamilla wrote:
Well now the aseg2srf script is working perfectly, it was a thing of 
the shell (changed to: #!/bin/sh -f) and the format of the script when 
I'd downloaded it.
Now I'm wanting to use the srf2obj script, and something similar 
happens, but since it is for gawk I have no idea how to change it or 
fix it to make it run, it gave me the same error as the last time:

[root@localhost] srf2obj aseg_004.srf  aseg_4.obj
gawk: /root/freesurfer/bin/srf2obj:2:
' invalid on the expressionrfer/bin/srf2obj:2: ^ character '

Regards,
Gabriel



El 07/05/12, *Anderson Winkler * andersonwink...@hotmail.com escribió:


Hi Gabriel,

Attached is a script that probably does what you need. Just make it 
executable and call it without arguments to get usage information. 
The label indices you can get from the aseg.stats file or from 
FreeSurferColorLUT.txt.


The surfaces will be saved in a subdirectory called ascii inside 
each subject's directory, and have extension .srf. They are 
internally the same as the .asc surfaces, just with a different 
extension.


Note that the idea of the script is to generate surfaces for 
visualization purposes only. If you'd like to do statistical analysis 
(e.g., compare shapes between patients and controls), these surfaces 
may not be appropriate.


Hope it helps!

All the best,

Anderson


On 07/05/12 12:15, Gabriel Gonzalez Escamilla wrote:


Hello all FS users and experts,

I'm wanting to get the sub cortical segmentation as ASCII files, so 
I'm trying convert the aseg.mgz into a surface file, to finally get 
an ASCII file,

For this I'm using the next commands:

First: mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg2raw.nii
To preserve  the aseg volume in native space

Second: mri_vol2surf --mov aseg2raw.nii --regheader mysubject --hemi 
lh --o ./lg.aseg2raw.mgh


And last: mris_convert lh.aseg2raw.mgh lh.aseg2raw.asc

I'm Not sure if I should do this for the whole aseg or if should I 
try to separate the segmented structures first...


Many Thanks in advanced,
Gabriel


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--
--
PhD. student Gabriel González-Escamilla
Laboratory of Functional Neuroscience
Department of Physiology, Anatomy, and Cell Biology
University Pablo de Olavide
Ctra. de Utrera, Km.1
41013 - Seville
- Spain -

Email: ggon...@upo.es
http://www.upo.es/neuroaging/es/


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Re: [Freesurfer] Volume to surface

2012-05-08 Thread Gabriel Gonzalez Escamilla 
Anderson, I'm downloading using a windows computer (but I always do like that with every single script), which automatically recognizes the scripts as txt files and add the extension, could you send me a link to the downloading page? That way I can try again and see what happens. I did check in my Linux distribution and is just as you said, the gawk is the default, so I have no any other idea for this.Regards,GabrielEl 08/05/12, Anderson Winkler  andersonwink...@hotmail.com escribió:
  

  
  
Hi Gabriel,

This sounds like a problem with downloading. Are you copying and
pasting the content of the scripts rather than downloading? Are you
copying from a Windows computer? Gawk is just a replacement for awk
with a more permissive license and more features. It is the default
in Linux and its explicit use only makes a difference for Mac users,
who have to get it from MacPorts or Fink.

Also, the first script should work with bash. The sh can be ash,
dash or even other depending on the system, being all with less
features than bash itself. Ubuntu uses dash as sh for instance.
Perhaps this one may work with any, but this isn't always the case.

All the best!

Anderson


On 08/05/12 11:23, Gabriel Gonzalez Escamilla wrote:

  
Well now the aseg2srf script is working perfectly, it was a
  thing of the shell (changed to: #!/bin/sh -f) and the format
  of the script when I'd downloaded it.
Now I'm wanting to use the srf2obj script, and something
  similar happens, but since it is for gawk I have no idea how
  to change it or fix it to make it run, it gave me the same
  error as the last time:
[root@localhost] srf2obj aseg_004.srf  aseg_4.obj
gawk: /root/freesurfer/bin/srf2obj:2:
' invalid on the expressionrfer/bin/srf2obj:2: ^ character
  ' 


Regards,
Gabriel






El 07/05/12, Anderson Winkler 
  andersonwink...@hotmail.com andersonwink...@hotmail.com escribió:

  
  

  
   Hi Gabriel,

Attached is a script that probably does what you need.
Just make it executable and call it without arguments to
get usage information. The label indices you can get
from the aseg.stats file or from FreeSurferColorLUT.txt.

The surfaces will be saved in a subdirectory called
ascii inside each subject's directory, and have
extension .srf. They are internally the same as the .asc
surfaces, just with a different extension.

Note that the idea of the script is to generate surfaces
for visualization purposes only. If you'd like to do
statistical analysis (e.g., compare shapes between
patients and controls), these surfaces may not be
appropriate.

Hope it helps!

All the best,

Anderson


On 07/05/12 12:15, Gabriel Gonzalez Escamilla wrote: 
  

  Hello all FS users and experts,
  
  
  I'm wanting to get the sub cortical segmentation
as ASCII files, so I'm trying convert the aseg.mgz
into a surface file, to finally get an ASCII file,
  For this I'm using the next commands:
  
  
  First: mri_convert -rl rawavg.mgz -rt nearest
aseg.mgz aseg2raw.nii
  To preserve  the aseg volume in native space 
  
  
  Second: mri_vol2surf --mov aseg2raw.nii
--regheader mysubject --hemi lh --o
./lg.aseg2raw.mgh



And last: mris_convert lh.aseg2raw.mgh
  lh.aseg2raw.asc


I'm Not sure if I should do this for the whole aseg
  or if should I try to separate the segmented
  structures first...


Many Thanks in advanced,
Gabriel



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Re: [Freesurfer] Volume to surface

2012-05-08 Thread Anderson Winkler 

Hi Gabriel,

Please, try downloading from here:
http://dl.dropbox.com/u/2785709/aseg2srf
http://dl.dropbox.com/u/2785709/srf2obj

Right-click and click Save As, to avoid Windows opening it up and 
messing up with character encoding. I'll write up a page about the 
aseg2srf and send the link later...


All the best,

Anderson


On 08/05/12 14:31, Gabriel Gonzalez Escamilla wrote:

Anderson,
I'm downloading using a windows computer (but I always do like that 
with every single script), which automatically recognizes the scripts 
as txt files and add the extension, could you send me a link to the 
downloading page? That way I can try again and see what happens. I did 
check in my Linux distribution and is just as you said, the gawk is 
the default, so I have no any other idea for this.


Regards,
Gabriel

El 08/05/12, *Anderson Winkler * andersonwink...@hotmail.com escribió:


Hi Gabriel,

This sounds like a problem with downloading. Are you copying and 
pasting the content of the scripts rather than downloading? Are you 
copying from a Windows computer? Gawk is just a replacement for awk 
with a more permissive license and more features. It is the default 
in Linux and its explicit use only makes a difference for Mac users, 
who have to get it from MacPorts or Fink.


Also, the first script should work with bash. The sh can be ash, dash 
or even other depending on the system, being all with less features 
than bash itself. Ubuntu uses dash as sh for instance. Perhaps this 
one may work with any, but this isn't always the case.


All the best!

Anderson


On 08/05/12 11:23, Gabriel Gonzalez Escamilla wrote:

Well now the aseg2srf script is working perfectly, it was a thing of 
the shell (changed to: #!/bin/sh -f) and the format of the script 
when I'd downloaded it.
Now I'm wanting to use the srf2obj script, and something similar 
happens, but since it is for gawk I have no idea how to change it or 
fix it to make it run, it gave me the same error as the last time:

[root@localhost] srf2obj aseg_004.srf  aseg_4.obj
gawk: /root/freesurfer/bin/srf2obj:2:
' invalid on the expressionrfer/bin/srf2obj:2: ^ character '

Regards,
Gabriel



El 07/05/12, *Anderson Winkler * andersonwink...@hotmail.com 
andersonwink...@hotmail.com escribió:


Hi Gabriel,

Attached is a script that probably does what you need. Just make it 
executable and call it without arguments to get usage information. 
The label indices you can get from the aseg.stats file or from 
FreeSurferColorLUT.txt.


The surfaces will be saved in a subdirectory called ascii inside 
each subject's directory, and have extension .srf. They are 
internally the same as the .asc surfaces, just with a different 
extension.


Note that the idea of the script is to generate surfaces for 
visualization purposes only. If you'd like to do statistical 
analysis (e.g., compare shapes between patients and controls), 
these surfaces may not be appropriate.


Hope it helps!

All the best,

Anderson


On 07/05/12 12:15, Gabriel Gonzalez Escamilla wrote:


Hello all FS users and experts,

I'm wanting to get the sub cortical segmentation as ASCII files, 
so I'm trying convert the aseg.mgz into a surface file, to finally 
get an ASCII file,

For this I'm using the next commands:

First: mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg2raw.nii
To preserve  the aseg volume in native space

Second: mri_vol2surf --mov aseg2raw.nii --regheader mysubject 
--hemi lh --o ./lg.aseg2raw.mgh


And last: mris_convert lh.aseg2raw.mgh lh.aseg2raw.asc

I'm Not sure if I should do this for the whole aseg or if should I 
try to separate the segmented structures first...


Many Thanks in advanced,
Gabriel


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The information in this e-mail is intended only for the person to whom it is
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--
--
PhD. student Gabriel González-Escamilla
Laboratory of Functional Neuroscience
Department of Physiology, Anatomy, and Cell Biology
University Pablo de Olavide
Ctra. de Utrera, Km.1
41013 - Seville
- Spain -

Email: ggon...@upo.es ggon...@upo.es
http://www.upo.es/neuroaging/es/


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Re: [Freesurfer] Volume to surface

2012-05-08 Thread Anderson Winkler 

ok, just posted... please, see here: http://brainder.org


On 08/05/12 15:51, Anderson Winkler wrote:

Hi Gabriel,

Please, try downloading from here:
http://dl.dropbox.com/u/2785709/aseg2srf
http://dl.dropbox.com/u/2785709/srf2obj

Right-click and click Save As, to avoid Windows opening it up and 
messing up with character encoding. I'll write up a page about the 
aseg2srf and send the link later...


All the best,

Anderson


On 08/05/12 14:31, Gabriel Gonzalez Escamilla wrote:

Anderson,
I'm downloading using a windows computer (but I always do like that 
with every single script), which automatically recognizes the scripts 
as txt files and add the extension, could you send me a link to the 
downloading page? That way I can try again and see what happens. I 
did check in my Linux distribution and is just as you said, the gawk 
is the default, so I have no any other idea for this.


Regards,
Gabriel

El 08/05/12, *Anderson Winkler * andersonwink...@hotmail.com escribió:


Hi Gabriel,

This sounds like a problem with downloading. Are you copying and 
pasting the content of the scripts rather than downloading? Are you 
copying from a Windows computer? Gawk is just a replacement for awk 
with a more permissive license and more features. It is the default 
in Linux and its explicit use only makes a difference for Mac users, 
who have to get it from MacPorts or Fink.


Also, the first script should work with bash. The sh can be ash, 
dash or even other depending on the system, being all with less 
features than bash itself. Ubuntu uses dash as sh for instance. 
Perhaps this one may work with any, but this isn't always the case.


All the best!

Anderson


On 08/05/12 11:23, Gabriel Gonzalez Escamilla wrote:

Well now the aseg2srf script is working perfectly, it was a thing 
of the shell (changed to: #!/bin/sh -f) and the format of the 
script when I'd downloaded it.
Now I'm wanting to use the srf2obj script, and something similar 
happens, but since it is for gawk I have no idea how to change it 
or fix it to make it run, it gave me the same error as the last time:

[root@localhost] srf2obj aseg_004.srf  aseg_4.obj
gawk: /root/freesurfer/bin/srf2obj:2:
' invalid on the expressionrfer/bin/srf2obj:2: ^ character '

Regards,
Gabriel



El 07/05/12, *Anderson Winkler * andersonwink...@hotmail.com 
andersonwink...@hotmail.com escribió:


Hi Gabriel,

Attached is a script that probably does what you need. Just make 
it executable and call it without arguments to get usage 
information. The label indices you can get from the aseg.stats 
file or from FreeSurferColorLUT.txt.


The surfaces will be saved in a subdirectory called ascii inside 
each subject's directory, and have extension .srf. They are 
internally the same as the .asc surfaces, just with a different 
extension.


Note that the idea of the script is to generate surfaces for 
visualization purposes only. If you'd like to do statistical 
analysis (e.g., compare shapes between patients and controls), 
these surfaces may not be appropriate.


Hope it helps!

All the best,

Anderson


On 07/05/12 12:15, Gabriel Gonzalez Escamilla wrote:


Hello all FS users and experts,

I'm wanting to get the sub cortical segmentation as ASCII files, 
so I'm trying convert the aseg.mgz into a surface file, to 
finally get an ASCII file,

For this I'm using the next commands:

First: mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg2raw.nii
To preserve  the aseg volume in native space

Second: mri_vol2surf --mov aseg2raw.nii --regheader mysubject 
--hemi lh --o ./lg.aseg2raw.mgh


And last: mris_convert lh.aseg2raw.mgh lh.aseg2raw.asc

I'm Not sure if I should do this for the whole aseg or if should 
I try to separate the segmented structures first...


Many Thanks in advanced,
Gabriel


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--
--
PhD. student Gabriel González-Escamilla
Laboratory of Functional Neuroscience
Department of Physiology, Anatomy, and Cell Biology
University Pablo de Olavide
Ctra. de Utrera, Km.1
41013 - Seville
- Spain -

Email: ggon...@upo.es ggon...@upo.es
http://www.upo.es/neuroaging/es/


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The

Re: [Freesurfer] Volume to surface

2012-05-08 Thread Gabriel Gonzalez Escamilla 
Hi Anderson,Now everything works perfectly, thank you so much!!!Best Regards,Gabriel
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] Volume to surface

2012-05-07 Thread Anderson Winkler 

Hi Gabriel,

Attached is a script that probably does what you need. Just make it 
executable and call it without arguments to get usage information. The 
label indices you can get from the aseg.stats file or from 
FreeSurferColorLUT.txt.


The surfaces will be saved in a subdirectory called ascii inside each 
subject's directory, and have extension .srf. They are internally the 
same as the .asc surfaces, just with a different extension.


Note that the idea of the script is to generate surfaces for 
visualization purposes only. If you'd like to do statistical analysis 
(e.g., compare shapes between patients and controls), these surfaces may 
not be appropriate.


Hope it helps!

All the best,

Anderson


On 07/05/12 12:15, Gabriel Gonzalez Escamilla wrote:

Hello all FS users and experts,

I'm wanting to get the sub cortical segmentation as ASCII files, so 
I'm trying convert the aseg.mgz into a surface file, to finally get an 
ASCII file,

For this I'm using the next commands:

First: mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg2raw.nii
To preserve  the aseg volume in native space

Second: mri_vol2surf --mov aseg2raw.nii --regheader mysubject --hemi 
lh --o ./lg.aseg2raw.mgh


And last: mris_convert lh.aseg2raw.mgh lh.aseg2raw.asc

I'm Not sure if I should do this for the whole aseg or if should I try 
to separate the segmented structures first...


Many Thanks in advanced,
Gabriel


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#!/bin/bash

# Print usage if no argument is given
if [ -z $1 ]; then
cat EOU
Generate surfaces for the subcortical structures
segmented with FreeSurfer.

Usage:
sub2srf -s list of subjects [-l list of labels] [-d]

Options:
-s list : Specify a list of subjects between quotes,
e.g. -s john bill mary mark or a text file
containing one subject per line.
-l list : Specify a list of labels between quotes,
e.g. 10 11 14 52 253, or a text file
containing one label per line, or ignore
this option to convert all labels.
-d  Debug mode. Leave all temporary files.

Requirements:
FreeSurfer must have been configured and the variables
FREESURFER_HOME and SUBJECTS_DIR must have been correctly set.

_
Anderson M. Winkler
Institute of Living / Yale University
Jul/2009
EOU
exit
fi

# List of labels to be converted  if no list is specified
LABLIST=4 5 7 8 10 11 12 13 14 15 16 17 18 26 28 43 44 46 47 49 50 51 52 53 54 
58 60 251 252 253 254 255

# Check and accept arguments
SBJLIST=
DEBUG=N
while getopts 's:l:d' OPTION
do
  case ${OPTION} in
s) SBJLIST=$( [[ -f ${OPTARG} ]]  cat ${OPTARG} || echo ${OPTARG} ) ;;
l) LABLIST=$( [[ -f ${OPTARG} ]]  cat ${OPTARG} || echo ${OPTARG} ) ;;
d) DEBUG=Y ;;
  esac
done

# Prepare a random string to save temporary files
RND0=$(head -n 1 /dev/random | md5sum)
RNDSTR=${RND0:0:12}

# Define a function for Ctrl+C as soon as the RNDSTR is defined
trap bashtrap INT
bashtrap()
{
  break ; break
  [[ ${s} !=  ]]  rm -rf ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR} # try to 
delete temp files
  exit 1
}

# For each subject
for s in ${SBJLIST} ; do

  # Create directories for temp files and results
  mkdir -p ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}
  mkdir -p ${SUBJECTS_DIR}/${s}/ascii

  # For each label
  for lab in ${LABLIST} ; do

# Label string
lab0=$(printf %03d ${lab})

# Pre-tessellate
echo == Pre-tessellating: ${s}, ${lab0}
${FREESURFER_HOME}/bin/mri_pretess \
   ${SUBJECTS_DIR}/${s}/mri/aseg.mgz ${lab} \
   ${SUBJECTS_DIR}/${s}/mri/norm.mgz \
   ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}_filled.mgz

# Tessellate
echo == Tessellating: ${s}, ${lab0}
${FREESURFER_HOME}/bin/mri_tessellate \
   ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}_filled.mgz \
   ${lab} ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}_notsmooth

# Smooth
echo == Smoothing: ${s}, ${lab0}
${FREESURFER_HOME}/bin/mris_smooth -nw \
   ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}_notsmooth \
   ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}

# Convert to ASCII
echo == Converting to ASCII: ${s}, ${lab0}
${FREESURFER_HOME}/bin/mris_convert \
   ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0} \
   ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}.asc
mv ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}.asc \

Re: [Freesurfer] Volume to surface dimension mismatch

2010-08-20 Thread Douglas N Greve 
You'll have to sample that mask onto the surface using mri_vol2surf with 
the --interp nearest option. You will also have to have a registration 
matrix, which will depend on where the volume came from.

doug

Lena Palaniyappan wrote:
 I have a mask file which I need to overlay on the individual images of 
 a group of subjects to extract thickness values within ht mask. But 
 the mask is of dimension 2X2X2, will this be an issue?

 Thanks
 Lena
 ___
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 *Clinical Lecturer  Honorary StR | Division of Psychiatry ( 
 University of Nottingham)
 South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH


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-- 
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] Volume to surface dimension mismatch

2010-08-20 Thread Lena Palaniyappan 
Doug, thanks
So, is this a correct sequence:

Im extracting thickness measures from VBM contrasts generated by FSL VBM
analysis (this is 2X2X2):
 
1. To convert VBM contrast file to a binary mask:
 
mri_binarize --i vbmcontrast.nii.gz --o vbmmask.nii --min 0.95 --max 1 (for
fsl vbm generated corrp maps, where values are stored as 1-p, min 0.95
identifies all voxels with p less than 0.05)
 
2. to check if this mask lies in appropriate place on fsaverage image:
 
tkmedit -f fsaverage/mri/T1.mgz -overlay vbmmask.nii -fthresh 0.5
 
3. to register groupaverage  with fsaverage
fslregister --s fsaverage --mov groupaverage/mri/T1.mgz --reg threshreg.dat
 
4. to view it on the fsaverage  volume
 
tkmedit fsaverage T1.mgz -overlay vbmmask.nii  -overlay-reg threshreg.dat
fthresh 0.5 -surface lh.white -aux-surface rh.white
 
5. to map it on the fsaverage SURFACE
 
mri_vol2surf  --mov $SUBJECTS_DIR/vbmmask.nii --reg
$SUBJECTS_DIR/threshreg.dat --projdist-max 0 1 0.1 --interp nearest --hemi
lh --out lh.fsaverage.masked.mgh  --reshape
 
6. to view it  on the surface

tksurfer fsaverage lh inflated -overlay lh.fsaverage.masked.mgh  -fthresh 1
 


But I am seeing the surface projections on completely different regions than
when using FSL templates to view the VBM contrast

Cheers
Lena

On 20/08/2010 20:41, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:

 You'll have to sample that mask onto the surface using mri_vol2surf with
 the --interp nearest option. You will also have to have a registration
 matrix, which will depend on where the volume came from.
 
 doug
 
 Lena Palaniyappan wrote:
 I have a mask file which I need to overlay on the individual images of
 a group of subjects to extract thickness values within ht mask. But
 the mask is of dimension 2X2X2, will this be an issue?
 
 Thanks
 Lena
 ___
 *Lena Palaniyappan
 *Clinical Lecturer  Honorary StR | Division of Psychiatry (
 University of Nottingham)
 South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
 
 
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Nottingham) 
South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH


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Re: [Freesurfer] Volume to surface dimension mismatch

2010-08-20 Thread Douglas N Greve 
If the source is the FSL standard brain, then use 
$FREESURFER_HOME/average/mni152.register.dat as the registration. See if 
that works at stage 4.

Lena Palaniyappan wrote:
 Doug, thanks
 So, is this a correct sequence:

 Im extracting thickness measures from VBM contrasts generated by FSL 
 VBM analysis (this is 2X2X2):
  
 1. To convert VBM contrast file to a binary mask:
  
 mri_binarize --i vbmcontrast.nii.gz --o vbmmask.nii --min 0.95 --max 1 
 (for fsl vbm generated corrp maps, where values are stored as 1-p, min 
 0.95 identifies all voxels with p less than 0.05)
  
 2. to check if this mask lies in appropriate place on fsaverage image:
  
 tkmedit -f fsaverage/mri/T1.mgz -overlay vbmmask.nii -fthresh 0.5
  
 3. to register groupaverage  with fsaverage
 fslregister --s fsaverage --mov groupaverage/mri/T1.mgz --reg 
 threshreg.dat
  
 4. to view it on the fsaverage  volume
  
 tkmedit fsaverage T1.mgz -overlay vbmmask.nii  -overlay-reg 
 threshreg.dat fthresh 0.5 -surface lh.white -aux-surface rh.white
  
 5. to map it on the fsaverage SURFACE
  
 mri_vol2surf  --mov $SUBJECTS_DIR/vbmmask.nii --reg 
 $SUBJECTS_DIR/threshreg.dat --projdist-max 0 1 0.1 --interp nearest 
 --hemi lh --out lh.fsaverage.masked.mgh  --reshape
  
 6. to view it  on the surface

 tksurfer fsaverage lh inflated -overlay lh.fsaverage.masked.mgh 
  -fthresh 1
  


 But I am seeing the surface projections on completely different 
 regions than when using FSL templates to view the VBM contrast

 Cheers
 Lena

 On 20/08/2010 20:41, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:

  You'll have to sample that mask onto the surface using mri_vol2surf with
  the --interp nearest option. You will also have to have a registration
  matrix, which will depend on where the volume came from.
 
  doug
 
  Lena Palaniyappan wrote:
  I have a mask file which I need to overlay on the individual images of
  a group of subjects to extract thickness values within ht mask. But
  the mask is of dimension 2X2X2, will this be an issue?
 
  Thanks
  Lena
  ___
  *Lena Palaniyappan
  *Clinical Lecturer  Honorary StR | Division of Psychiatry (
  University of Nottingham)
  South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
 
 
  This message and any attachment are intended solely for the addressee
  and may contain confidential information. If you have received this
  message in error, please send it back to me, and immediately delete
  it. Please do not use, copy or disclose the information contained in
  this message or in any attachment. Any views or opinions expressed by
  the author of this email do not necessarily reflect the views of the
  University of Nottingham.
 
  This message has been checked for viruses but the contents of an
  attachment may still contain software viruses which could damage your
  computer system: you are advised to perform your own checks. Email
  communications with the University of Nottingham may be monitored as
  permitted by UK legislation.
 
  
 
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 ___
 *Lena Palaniyappan
 *Clinical Lecturer  Honorary StR | Division of Psychiatry ( 
 University of Nottingham)
 South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH


 This message and any attachment are intended solely for the addressee 
 and may contain confidential information. If you have received this 
 message in error, please send it back to me, and immediately delete 
 it. Please do not use, copy or disclose the information contained in 
 this message or in any attachment. Any views or opinions expressed by 
 the author of this email do not necessarily reflect the views of the 
 University of Nottingham.

 This message has been checked for viruses but the contents of an 
 attachment may still contain software viruses which could damage your 
 computer system: you are advised to perform your own checks. Email 
 communications with the University of Nottingham may be monitored as 
 permitted by UK legislation.


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

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