[Freesurfer] Reorientation of raw images?

[chenchunhuichina]

Hello Bruce, and Freesurfers,

Sorry for asking an old question, but I really need more confirmation.

I am running recon-all to processing my structural data, but i am not sure do I 
have to reorient the data or not. The data were acquired in sagital view, and 
dicom data were converted into nift format using dcm2nii, the transformed nii 
file (called original image below) are in wrong orienation, in fslview, it's X 
axis is acturally from anterior to posterior, the Y, Z  axises were also wrong. 
dcm2nii also created a o*.nii image, which is in right orientation. I run 
recon-all using both images, and the results (volume for each region) are a 
little bit different, about 0.25%, for example, volume of a brain rigion got 
with original image is 2000 , but got with o*.nii image is 1995. It's not a big 
problem, but since they are exactly the same data, why the results are not 
exactly the same? is it better to use original image or even dicom files or to 
use reoriented data? the resolution of my data is 1*1*2 mm.

Another related quetion is, if data are left-right fliped, do I have to flip 
the raw data and run recon-all again or can I just flip left-right of results, 
i.e., consider volume got for a left region as that of the corresponding right 
region?

Thank you very much!

2010-02-02 



Chunhui Chen
_

Institute of Cognitive Neuroscience and Learning
Beijing Normal University
Beijing, China 100875



发件人： Bruce Fischl 
发送时间： 2010-01-22  12:38:11 
收件人： chenchunhuichina 
抄送： 
主题： Re: Re: [Freesurfer] Orientation of 001.mgz versus raw dicom data 
 
no, that shouldn't matter
On Fri, 22 Jan 2010, chenchunhuichina wrote:

> May I ask a related question?
>
> My structural data are acquired in sagital view, do I have to re-orient it 
> before I run recon-all? In fslview, it's X axis is acturally from anterior to 
> posterior.
>
> Thanks!
>
>
> 2010-01-22
>
>
>
> chenchunhuichina
>
>
>
> 发件人： Bruce Fischl
> 发送时间： 2010-01-22  07:06:58
> 收件人： yzha...@artsci.wustl.edu
> 抄送： freesurfer@nmr.mgh.harvard.edu
> 主题： Re: [Freesurfer] Orientation of 001.mgz versus raw dicom data
>
> How do you know? It should be in the same space.
> Bruce
>
>
>
> On Jan 21, 2010, at 5:01 PM, yzha...@artsci.wustl.edu wrote:
>
> > I have run the following command to create a 001.mgz file from raw
> > *.dcm
> > data:
> >
> > recon-all -s-i   
> >
> > The output 001.mgz file is not in the same native space as the
> > original
> > *.dcm data. Could anyone tell me what space the 001.mgz file is in?
> > Does
> > the above command change the orientation (i.e does it rotate/
> > translate)
> > besides simply converting from .dcm to 001.mgz
> >
> > thanks a lot
> >
> > yuning
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
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> >
> >
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Re: [Freesurfer] Reorientation of raw images?

[chenchunhuichina]

in some regions like left amygdata, the difference exceed 5%

2010-02-02 



Chunhui Chen
_

Institute of Cognitive Neuroscience and Learning
Beijing Normal University
Beijing, China 100875



发件人： Bruce Fischl 
发送时间： 2010-01-22  12:38:11 
收件人： chenchunhuichina 
抄送： 
主题： Re: Re: [Freesurfer] Orientation of 001.mgz versus raw dicom data 
no, that shouldn't matter
On Fri, 22 Jan 2010, chenchunhuichina wrote:

> May I ask a related question?
>
> My structural data are acquired in sagital view, do I have to re-orient it 
> before I run recon-all? In fslview, it's X axis is acturally from anterior to 
> posterior.
>
> Thanks!
>
>
> 2010-01-22
>
>
>
> chenchunhuichina
>
>
>
> 发件人： Bruce Fischl
> 发送时间： 2010-01-22  07:06:58
> 收件人： yzha...@artsci.wustl.edu
> 抄送： freesurfer@nmr.mgh.harvard.edu
> 主题： Re: [Freesurfer] Orientation of 001.mgz versus raw dicom data
>
> How do you know? It should be in the same space.
> Bruce
>
>
>
> On Jan 21, 2010, at 5:01 PM, yzha...@artsci.wustl.edu wrote:
>
> > I have run the following command to create a 001.mgz file from raw
> > *.dcm
> > data:
> >
> > recon-all -s-i   
> >
> > The output 001.mgz file is not in the same native space as the
> > original
> > *.dcm data. Could anyone tell me what space the 001.mgz file is in?
> > Does
> > the above command change the orientation (i.e does it rotate/
> > translate)
> > besides simply converting from .dcm to 001.mgz
> >
> > thanks a lot
> >
> > yuning
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
<>
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Re: [Freesurfer] GM volume and cortical thickness

[keepmoon]

 Dear all experters,

First I am appreciated for the help of Bruce.
 I tried to following his instruction, but I still have some problem and  I
can't show any result on the flated surface. I don't know whether my method
to calculate the volume is wrong or I display it wrongly. Expecting someone
gives me a struction again!
My method is: using *read_curv* function to read*
lh.thickness* and*lh.area
*. Then the matrix of thickness product the matrix of area getting a new
matrix. Then using *write_curv* function to write this new matrix into a
*.volume. I think this volume file should be the grey volume image. (I am
not sure about this process)
   And now I want to show this volume on a flated lh hemispere (using
tksurfer), But when I overlay this volume onto inflated surface, there is
not anything overlay on this surface? (this matrix is not all with 0. )

   Anywhere am I wrong?

  Any instruction will be appriciated!

   Joe





2010/2/1, keepmoon :
>
> Dear developer,
>
>  I want to compare the grey matter volume by VBM to cortical thickness
> by freesurfer. But in this process, I meet a problem: how to change the
> points number of grey matter into the same with the vertex of thickness by
> freesurfer?
>
>   Any help will be appreciated!
>
>   Best regards
>
> Joe
>
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Re: [Freesurfer] GM volume and cortical thickness

[Bruce Fischl]

have you tried changing the threshold in configure->functional overlay? 
What kind of values do you see?
On Tue, 2 Feb 2010, keepmoon wrote:

> Dear all experters,
>
>First I am appreciated for the help of Bruce.
> I tried to following his instruction, but I still have some problem and  I
> can't show any result on the flated surface. I don't know whether my method
> to calculate the volume is wrong or I display it wrongly. Expecting someone
> gives me a struction again!
>My method is: using *read_curv* function to read*
> lh.thickness* and*lh.area
> *. Then the matrix of thickness product the matrix of area getting a new
> matrix. Then using *write_curv* function to write this new matrix into a
> *.volume. I think this volume file should be the grey volume image. (I am
> not sure about this process)
>   And now I want to show this volume on a flated lh hemispere (using
> tksurfer), But when I overlay this volume onto inflated surface, there is
> not anything overlay on this surface? (this matrix is not all with 0. )
>
>   Anywhere am I wrong?
>
>  Any instruction will be appriciated!
>
>   Joe
>
>
>
>
>
> 2010/2/1, keepmoon :
>>
>> Dear developer,
>>
>>  I want to compare the grey matter volume by VBM to cortical thickness
>> by freesurfer. But in this process, I meet a problem: how to change the
>> points number of grey matter into the same with the vertex of thickness by
>> freesurfer?
>>
>>   Any help will be appreciated!
>>
>>   Best regards
>>
>> Joe
>>
>
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Re: [Freesurfer] Reorientation of raw images?

[Bruce Fischl]

Hi Chunhui
you should not need to reorient your data. What version are you using?
cheers,
Bruce


On Tue, 2 Feb 2010, 
chenchunhuichina wrote:



Hello Bruce, and Freesurfers,

Sorry for asking an old question, but I really need more confirmation.

I am running recon-all to processing my structural data, but i am not sure do I 
have to reorient the data or not. The data were acquired in sagital view, and 
dicom data were converted into nift format using dcm2nii, the transformed nii 
file (called original image below) are in wrong orienation, in fslview, it's X 
axis is acturally from anterior to posterior, the Y, Z  axises were also wrong. 
dcm2nii also created a o*.nii image, which is in right orientation. I run 
recon-all using both images, and the results (volume for each region) are a 
little bit different, about 0.25%, for example, volume of a brain rigion got 
with original image is 2000 , but got with o*.nii image is 1995. It's not a big 
problem, but since they are exactly the same data, why the results are not 
exactly the same? is it better to use original image or even dicom files or to 
use reoriented data? the resolution of my data is 1*1*2 mm.

 Another related quetion is, if data are left-right fliped, do I have to 
flip the raw data and run recon-all again or can I just flip left-right of 
results, i.e., consider volume got for a left region as that of the 
corresponding right region?>

Thank you very much!

2010-02-02



Chunhui Chen
_

Institute of Cognitive Neuroscience and Learning
Beijing Normal University
Beijing, China 100875



·¢¼þÈË£º Bruce Fischl
·¢ËÍʱ¼ä£º 2010-01-22  12:38:11
ÊÕ¼þÈË£º chenchunhuichina
³­ËÍ£º
Ö÷Ì⣺ Re: Re: [Freesurfer] Orientation of 001.mgz versus raw dicom data

no, that shouldn't matter
On Fri, 22 Jan 2010, chenchunhuichina wrote:


May I ask a related question?

My structural data are acquired in sagital view, do I have to re-orient it 
before I run recon-all? In fslview, it's X axis is acturally from anterior to 
posterior.

Thanks!


2010-01-22



chenchunhuichina



·¢¼þÈË£º Bruce Fischl
·¢ËÍʱ¼ä£º 2010-01-22  07:06:58
ÊÕ¼þÈË£º yzha...@artsci.wustl.edu
³­ËÍ£º freesurfer@nmr.mgh.harvard.edu
Ö÷Ì⣺ Re: [Freesurfer] Orientation of 001.mgz versus raw dicom data

How do you know? It should be in the same space.
Bruce



On Jan 21, 2010, at 5:01 PM, yzha...@artsci.wustl.edu wrote:


I have run the following command to create a 001.mgz file from raw
*.dcm
data:

recon-all -s-i   

The output 001.mgz file is not in the same native space as the
original
*.dcm data. Could anyone tell me what space the 001.mgz file is in?
Does
the above command change the orientation (i.e does it rotate/
translate)
besides simply converting from .dcm to 001.mgz

thanks a lot

yuning


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[Freesurfer] Postdoctoral position in multimodal imaging (autism) available

[Herbert, Martha R.,M.D.,Ph.D.]

Postdoctoral position in multimodal imaging (autism) available


 

I would like to make known the availability of a two year postdoctoral position
in my laboratory.  Strong MRI/DTI/Spectroscopy signal processing analysis skills
plus experience with and commitment to multimodal imaging are required; EEG or
MEG experience is an advantage.  The TRANSCEND Research Program
(http://www.nmr.mgh.harvard.edu/transcend/ and
www.mghneuro.transcendresearch.org 
) performs multimodal imaging and biomaterial collection with a central focus on
neurodevelopmental disorders in general, and autism in particular.  Our main
location is at the Martinos Center for Biomedical Imaging in Charlestown, MA
(www.martinos.org  ) which is affiliated with
Massachusetts General Hospital, Harvard Medical School and MIT.  We have a
second location at a clinical site, the Lurie Family Center for Autism where we
have a 128 lead EGI EEG in a shielded room as well as a photogrammetry machine.

 

This position will involve analysis of multimodal imaging data, integrating EEG
data with multimodal MRI and behavioral data, and collection of new data.  Our
research projects include MRI (volumetrics, diffusion, MRS, etc.) and MEG
(usually on the same subjects allowing coregistration) as well as EEG from early
infancy through mid-childhood; the subjects are all carefully phenotyped.  We
additionally analyze clinical EEG and imaging data.  An additional interest in
metabolic, toxicological or molecular measures and imaging will be welcomed.
The Martinos Center provides ample opportunities for interacting with
outstanding colleagues.

 

Please direct any interested members of your lab or anyone else amongst your
colleagues or colleagues' labs to write to me at mherbe...@partners.org and
please cc transc...@partners.org. 

 

Please forward to any potentially interested colleagues.

 

Thank you.

Yours truly,

Martha R. Herbert, MD, PhD 

 

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Re: [Freesurfer] GM volume and cortical thickness

[keepmoon]

Dear Bruce and All,

   In my *View--Configure*there are three button which are activated
(*Light, caption and phase Encoded Dat Display*), without "*functional
overlay*" option.
   And in these activated buttons: light(light 0,...,light 3, with the
value, 0.4, 0.0, 0.6, 0.2. and brightness: 0.35). In the option of *phase
Encoded Dat Display *(*Angle Cycles:1.0; Angle offset: 0.0*)

   I just use *File--load overlay*  then choose that **.volume* file to
show that volume. And in the terminal there are error information:Couldn't
load *.volume, Vset_read_vertex_set:MRISreadVertexposition failed.

  Thanks a lot for your help!

  Joe






2010/2/2, Bruce Fischl :
>
> have you tried changing the threshold in configure->functional overlay?
> What kind of values do you see?
> On Tue, 2 Feb 2010, keepmoon wrote:
>
>  Dear all experters,
>>
>>   First I am appreciated for the help of Bruce.
>> I tried to following his instruction, but I still have some problem and  I
>> can't show any result on the flated surface. I don't know whether my
>> method
>> to calculate the volume is wrong or I display it wrongly. Expecting
>> someone
>> gives me a struction again!
>>   My method is: using *read_curv* function to read*
>> lh.thickness* and*lh.area
>> *. Then the matrix of thickness product the matrix of area getting a new
>> matrix. Then using *write_curv* function to write this new matrix into a
>> *.volume. I think this volume file should be the grey volume image. (I am
>> not sure about this process)
>>  And now I want to show this volume on a flated lh hemispere (using
>> tksurfer), But when I overlay this volume onto inflated surface, there is
>> not anything overlay on this surface? (this matrix is not all with 0. )
>>
>>  Anywhere am I wrong?
>>
>> Any instruction will be appriciated!
>>
>>  Joe
>>
>>
>>
>>
>>
>> 2010/2/1, keepmoon :
>>
>>>
>>> Dear developer,
>>>
>>> I want to compare the grey matter volume by VBM to cortical thickness
>>> by freesurfer. But in this process, I meet a problem: how to change the
>>> points number of grey matter into the same with the vertex of thickness
>>> by
>>> freesurfer?
>>>
>>>  Any help will be appreciated!
>>>
>>>  Best regards
>>>
>>> Joe
>>>
>>>
>>
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[Freesurfer] why FreeSurfer Surface Atlas does not contain subcortical region

[Guang Zeng]

Hi, there,

Kind of wondering,  why FreeSurfer Surface Atlas does not contain subcortical 
region?

Thanks!

Guang
  
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Re: [Freesurfer] why FreeSurfer Surface Atlas does not contain subcortical region

[Bruce Fischl]

we keep the subcortical information in a different atlas. The 
surface-based one contains info about cortical geometry, which doesn't 
apply for non-cortical structures
On Tue, 2 Feb 2010, Guang Zeng wrote:

>
> Hi, there,
>
> Kind of wondering,  why FreeSurfer Surface Atlas does not contain subcortical 
> region?
>
> Thanks!
>
> Guang
>
> _
> Hotmail: Free, trusted and rich email service.
> http://clk.atdmt.com/GBL/go/201469228/direct/01/
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Re: [Freesurfer] GM volume and cortical thickness

[Bruce Fischl]

can you send us the complete output in the tcl window (the one with the % 
prompt)
On Tue, 2 Feb 2010, keepmoon wrote:

> Dear Bruce and All,
>
>   In my *View--Configure*there are three button which are activated
> (*Light, caption and phase Encoded Dat Display*), without "*functional
> overlay*" option.
>   And in these activated buttons: light(light 0,...,light 3, with the
> value, 0.4, 0.0, 0.6, 0.2. and brightness: 0.35). In the option of *phase
> Encoded Dat Display *(*Angle Cycles:1.0; Angle offset: 0.0*)
>
>   I just use *File--load overlay*  then choose that **.volume* file to
> show that volume. And in the terminal there are error information:Couldn't
> load *.volume, Vset_read_vertex_set:MRISreadVertexposition failed.
>
>  Thanks a lot for your help!
>
>  Joe
>
>
>
>
>
>
> 2010/2/2, Bruce Fischl :
>>
>> have you tried changing the threshold in configure->functional overlay?
>> What kind of values do you see?
>> On Tue, 2 Feb 2010, keepmoon wrote:
>>
>>  Dear all experters,
>>>
>>>   First I am appreciated for the help of Bruce.
>>> I tried to following his instruction, but I still have some problem and  I
>>> can't show any result on the flated surface. I don't know whether my
>>> method
>>> to calculate the volume is wrong or I display it wrongly. Expecting
>>> someone
>>> gives me a struction again!
>>>   My method is: using *read_curv* function to read*
>>> lh.thickness* and*lh.area
>>> *. Then the matrix of thickness product the matrix of area getting a new
>>> matrix. Then using *write_curv* function to write this new matrix into a
>>> *.volume. I think this volume file should be the grey volume image. (I am
>>> not sure about this process)
>>>  And now I want to show this volume on a flated lh hemispere (using
>>> tksurfer), But when I overlay this volume onto inflated surface, there is
>>> not anything overlay on this surface? (this matrix is not all with 0. )
>>>
>>>  Anywhere am I wrong?
>>>
>>> Any instruction will be appriciated!
>>>
>>>  Joe
>>>
>>>
>>>
>>>
>>>
>>> 2010/2/1, keepmoon :
>>>

 Dear developer,

 I want to compare the grey matter volume by VBM to cortical thickness
 by freesurfer. But in this process, I meet a problem: how to change the
 points number of grey matter into the same with the vertex of thickness
 by
 freesurfer?

  Any help will be appreciated!

  Best regards

 Joe


>>>
>
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[Freesurfer] unpacksdcm/mri_convert question

[Sebastian Moeller]

Dear List,

 I got a question/problem regarding unpacksdcmdir and mri_convert (of version 
4.5.0 centos4_x86_64). When I unpack the siemens DICOMs (syngo B17, from a 
recent tim trio) as bshorts, mri_info reports the proper FOV of 96; when I 
unpack them as nii, I get a wrong FOV of 64 (also the xstart, ystart and zstart 
are wrong for nii as unpack target). In both cases does the unpack log give 96 
as FOV. Is this something to be alarmed about? Should I send example DICOMS? 

Best Regards & many thanks for the great tools
Sebastian



-- 
Sebastian Moeller

telephone: 626-395-6713
fax: 626-395-8826
German GSM:  0 15 77 - 1 90 31 41
moel...@caltech.edu

Division of Biology
MC 114-96
California Institute of Technology
1200 East California Boulevard
CA 91125, Pasadena
USA

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Re: [Freesurfer] GM volume and cortical thickness

[keepmoon]

 Dear Bruce,

This is the all information in tci:

%

 $  tksurfer xalbertM lh inflated
surfer: current subjects dir: /home/Joe/study
surfer: not in "scripts" dir ==> using cwd for session root

surfer: session root data dir ($session) set to:

surfer: /home/Joe/study
surfer: Reading header info from /home/Joe/study/xalbertM/mri/T1.mgz

surfer: vertices=119274, faces=238544




WARNING: No colortable found!


surfer: single buffered window
surfer: tkoInitWindow(xalbertM)

surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl

Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl
Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl

Reading /usr/local/freesurfer/lib/tcl/fsgdfPlo
t.tcl

Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl


Successfully parsed tksurfer.tcl

reading white matter vertex locations...

% MRISreadVertexPositions(/home/Joe/study/xalbertM/surf/lh_compute.volume):
surfaces differ. Main: 119274 verts 238544 faces,
/home/Joe/study/xalbertM/surf/lh_compute.volume: 465 verts 30670850 faces


surfer: Couldn't load *.volume, Vset_read_vertex_set:MRISreadVertexposition
failed.



%





 I am appreciated for your instruction!

Best regards

Joe














2010/2/2, keepmoon :
>
>
>
> Dear Bruce,
>
> This is the all information in tci:
>
> %
>
>  $  tksurfer xalbertM lh inflated
> surfer: current subjects dir: /home/Joe/study
> surfer: not in "scripts" dir ==> using cwd for session root
>
> surfer: session root data dir ($session) set to:
>
> surfer: /home/Joe/study
> surfer: Reading header info from /home/Joe/study/xalbertM/mri/T1.mgz
>
> surfer: vertices=119274, faces=238544
>
>
>
>
> WARNING: No colortable found!
>
>
> surfer: single buffered window
> surfer: tkoInitWindow(xalbertM)
>
> surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl
>
> Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl
> Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl
>
> Reading /usr/local/freesurfer/lib/tcl/fsgdfPlo
> t.tcl
>
> Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl
>
>
> Successfully parsed tksurfer.tcl
>
> reading white matter vertex locations...
>
> % MRISreadVertexPositions(/home/Joe/study/xalbertM/surf/lh_compute.volume):
> surfaces differ. Main: 119274 verts 238544 faces,
> /home/Joe/study/xalbertM/surf/lh_compute.volume: 465 verts 30670850 faces
>
>
> surfer: Couldn't load *.volume, Vset_read_vertex_set:MRISreadVertexposition
> failed.
>
>
>
> %
>
>  And I put the volume file I calculate in the attach.
>
>
>
>  I am appreciated for your instruction!
>
> Best regards
>
> Joe
>
>
>
>
>
> 2010/2/2, Bruce Fischl :
>>
>> can you send us the complete output in the tcl window (the one with the %
>> prompt)
>>
>> On Tue, 2 Feb 2010, keepmoon wrote:
>>
>> Dear Bruce and All,
>>>
>>>  In my *View--Configure*there are three button which are
>>> activated
>>> (*Light, caption and phase Encoded Dat Display*), without "*functional
>>> overlay*" option.
>>>  And in these activated buttons: light(light 0,...,light 3, with the
>>> value, 0.4, 0.0, 0.6, 0.2. and brightness: 0.35). In the option of *phase
>>> Encoded Dat Display *(*Angle Cycles:1.0; Angle offset: 0.0*)
>>>
>>>  I just use *File--load overlay*  then choose that **.volume* file to
>>> show that volume. And in the terminal there are error
>>> information:Couldn't
>>> load *.volume, Vset_read_vertex_set:MRISreadVertexposition failed.
>>>
>>> Thanks a lot for your help!
>>>
>>> Joe
>>>
>>>
>>>
>>>
>>>
>>>
>>> 2010/2/2, Bruce Fischl :
>>>

 have you tried changing the threshold in configure->functional overlay?
 What kind of values do you see?
 On Tue, 2 Feb 2010, keepmoon wrote:

  Dear all experters,

>
>  First I am appreciated for the help of Bruce.
> I tried to following his instruction, but I still have some problem and
>  I
> can't show any result on the flated surface. I don't know whether my
> method
> to calculate the volume is wrong or I display it wrongly. Expecting
> someone
> gives me a struction again!
>  My method is: using *read_curv* function to read*
> lh.thickness* and*lh.area
> *. Then the matrix of thickness product the matrix of area getting a
> new
> matrix. Then using *write_curv* function to write this new matrix into
> a
> *.volume. I think this volume file should be the grey volume image. (I
> am
> not sure about this process)
> And now I want to show this volume on a flated lh hemispere (using
> tksurfer), But when I overlay this volume onto inflated surface, there
> is
> not anything overlay on this surface? (this matrix is not all with 0. )
>
> Anywhere am I wrong?
>
>Any instruction will be appriciated!
>
> Joe
>
>
>
>
>
> 2010/2/1, keepmoon :
>
>
>> Dear developer,
>>
>>I want to compare the grey matter volume by

[Freesurfer] segmentation without conform

[magnet scanner]

Hi,

Please excuse me if this is an old question. I was wondering if there is a
way of not doing conform when segmentation on the whole brain since I am
dealing with spectroscopy data and need affine matrix. So I have to make
sure the matrix is the same.

Thanks,

Mag
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Re: [Freesurfer] segmentation without conform

[Bruce Fischl]

Hi Mag,

no, the conform is a necessary step, but it wouldn't be applied to your 
spectroscopy data in any case. You would register that to the anatomicals 
(that were conformed). Is that what you mean?
Bruce
On Tue, 2 Feb 2010, magnet 
scanner wrote:

> Hi,
>
> Please excuse me if this is an old question. I was wondering if there is a
> way of not doing conform when segmentation on the whole brain since I am
> dealing with spectroscopy data and need affine matrix. So I have to make
> sure the matrix is the same.
>
> Thanks,
>
> Mag
>
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[Freesurfer] Freesurfer , wfu pick atlas

[Sharmili 57]

Hey,

I want to do Cortical thickness analysis for regions defined by the wfu atlas 
in a MEG study. How can I define these areas in Freesurfer? It is imprecise to 
use the atlases implemented in Freesurfer, isn't it?

Thanks for your help

Sharmili
  
_
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Re: [Freesurfer] segmentation without conform

[magnet scanner]

Hi, Bruce,

Thanks for your quick response. here is what I am going to do with my
spectroscopy data;
1. mri_convert to convert all my T1 and T2 images to nifti format
mri_convert -it dicom {T1 filename} -ot nii {T1.nii} --out_orientation
RPS
mri_convert -it dicom{T2 filename} -ot nii {T2.nii}
2. obtain affine matrix from T1.nii and T2.nii hdr.
3. register T1 to T2 and align with my spectroscopic data.
4. do segmentation
5. assign my spectroscopic data to segmented images

I used FSL bet command for segmentation before, and it does not change
anything. However, I need to obtain the information about subcortical
structure like Hippo, Thal, etc. Therefore, I used freesurfer segmentation
tool. But since conform is the necessary step, the volsizes for the
segmented region are changed, the coordinates are changed.  So my affine
matrix is different. My questions are here again:

1. In that case, do I need to conform T1.nii and T2.nii as well?
2. I did conform and T2.nii looks weird to me.

Thanks,

Jun





On Tue, Feb 2, 2010 at 12:31 PM, Bruce Fischl wrote:

> Hi Mag,
>
> no, the conform is a necessary step, but it wouldn't be applied to your
> spectroscopy data in any case. You would register that to the anatomicals
> (that were conformed). Is that what you mean?
> Bruce
>
> On Tue, 2 Feb 2010, magnet scanner wrote:
>
> Hi,
>>
>> Please excuse me if this is an old question. I was wondering if there is a
>> way of not doing conform when segmentation on the whole brain since I am
>> dealing with spectroscopy data and need affine matrix. So I have to make
>> sure the matrix is the same.
>>
>> Thanks,
>>
>> Mag
>>
>>
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Re: [Freesurfer] segmentation without conform

[Bruce Fischl]

you need to run recon-all on your T1.nii, then register your spectroscopy 
images to the recons (we use bbregister for this). Then you can use our 
segmentations to analyze the spectroscopy data.

cheers,
Bruce
On Tue, 2 Feb 2010, magnet 
scanner wrote:

> Hi, Bruce,
>
> Thanks for your quick response. here is what I am going to do with my
> spectroscopy data;
> 1. mri_convert to convert all my T1 and T2 images to nifti format
>mri_convert -it dicom {T1 filename} -ot nii {T1.nii} --out_orientation
> RPS
>mri_convert -it dicom{T2 filename} -ot nii {T2.nii}
> 2. obtain affine matrix from T1.nii and T2.nii hdr.
> 3. register T1 to T2 and align with my spectroscopic data.
> 4. do segmentation
> 5. assign my spectroscopic data to segmented images
>
> I used FSL bet command for segmentation before, and it does not change
> anything. However, I need to obtain the information about subcortical
> structure like Hippo, Thal, etc. Therefore, I used freesurfer segmentation
> tool. But since conform is the necessary step, the volsizes for the
> segmented region are changed, the coordinates are changed.  So my affine
> matrix is different. My questions are here again:
>
> 1. In that case, do I need to conform T1.nii and T2.nii as well?
> 2. I did conform and T2.nii looks weird to me.
>
> Thanks,
>
> Jun
>
>
>
>
>
> On Tue, Feb 2, 2010 at 12:31 PM, Bruce Fischl 
> wrote:
>
>> Hi Mag,
>>
>> no, the conform is a necessary step, but it wouldn't be applied to your
>> spectroscopy data in any case. You would register that to the anatomicals
>> (that were conformed). Is that what you mean?
>> Bruce
>>
>> On Tue, 2 Feb 2010, magnet scanner wrote:
>>
>> Hi,
>>>
>>> Please excuse me if this is an old question. I was wondering if there is a
>>> way of not doing conform when segmentation on the whole brain since I am
>>> dealing with spectroscopy data and need affine matrix. So I have to make
>>> sure the matrix is the same.
>>>
>>> Thanks,
>>>
>>> Mag
>>>
>>>
>
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Re: [Freesurfer] GM volume and cortical thickness

[Bruce Fischl]

it looks like you are trying to load the volume measures as a surface, not 
as an overlay. Use file->load overlay. Note that you can also use mris_calc 
to generate the volume 
measures.

cheers
Bruce
On Tue, 2 Feb 2010, keepmoon wrote:

> Dear Bruce,
>
>This is the all information in tci:
>
> %
>
> $  tksurfer xalbertM lh inflated
> surfer: current subjects dir: /home/Joe/study
> surfer: not in "scripts" dir ==> using cwd for session root
>
> surfer: session root data dir ($session) set to:
>
> surfer: /home/Joe/study
> surfer: Reading header info from /home/Joe/study/xalbertM/mri/T1.mgz
>
> surfer: vertices=119274, faces=238544
>
>
>
>
> WARNING: No colortable found!
>
>
> surfer: single buffered window
> surfer: tkoInitWindow(xalbertM)
>
> surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl
>
> Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl
> Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl
>
> Reading /usr/local/freesurfer/lib/tcl/fsgdfPlo
> t.tcl
>
> Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl
>
>
> Successfully parsed tksurfer.tcl
>
> reading white matter vertex locations...
>
> % MRISreadVertexPositions(/home/Joe/study/xalbertM/surf/lh_compute.volume):
> surfaces differ. Main: 119274 verts 238544 faces,
> /home/Joe/study/xalbertM/surf/lh_compute.volume: 465 verts 30670850 faces
>
>
> surfer: Couldn't load *.volume, Vset_read_vertex_set:MRISreadVertexposition
> failed.
>
>
>
> %
>
> And I put the volume file I calculate in the attach.
>
>
>
> I am appreciated for your instruction!
>
> Best regards
>
> Joe
>
>
>
>
>
> 2010/2/2, Bruce Fischl :
>>
>> can you send us the complete output in the tcl window (the one with the %
>> prompt)
>>
>> On Tue, 2 Feb 2010, keepmoon wrote:
>>
>> Dear Bruce and All,
>>>
>>>  In my *View--Configure*there are three button which are activated
>>> (*Light, caption and phase Encoded Dat Display*), without "*functional
>>> overlay*" option.
>>>  And in these activated buttons: light(light 0,...,light 3, with the
>>> value, 0.4, 0.0, 0.6, 0.2. and brightness: 0.35). In the option of *phase
>>> Encoded Dat Display *(*Angle Cycles:1.0; Angle offset: 0.0*)
>>>
>>>  I just use *File--load overlay*  then choose that **.volume* file to
>>> show that volume. And in the terminal there are error information:Couldn't
>>> load *.volume, Vset_read_vertex_set:MRISreadVertexposition failed.
>>>
>>> Thanks a lot for your help!
>>>
>>> Joe
>>>
>>>
>>>
>>>
>>>
>>>
>>> 2010/2/2, Bruce Fischl :
>>>

 have you tried changing the threshold in configure->functional overlay?
 What kind of values do you see?
 On Tue, 2 Feb 2010, keepmoon wrote:

  Dear all experters,

>
>  First I am appreciated for the help of Bruce.
> I tried to following his instruction, but I still have some problem and
>  I
> can't show any result on the flated surface. I don't know whether my
> method
> to calculate the volume is wrong or I display it wrongly. Expecting
> someone
> gives me a struction again!
>  My method is: using *read_curv* function to read*
> lh.thickness* and*lh.area
> *. Then the matrix of thickness product the matrix of area getting a new
> matrix. Then using *write_curv* function to write this new matrix into a
> *.volume. I think this volume file should be the grey volume image. (I
> am
> not sure about this process)
> And now I want to show this volume on a flated lh hemispere (using
> tksurfer), But when I overlay this volume onto inflated surface, there
> is
> not anything overlay on this surface? (this matrix is not all with 0. )
>
> Anywhere am I wrong?
>
>Any instruction will be appriciated!
>
> Joe
>
>
>
>
>
> 2010/2/1, keepmoon :
>
>
>> Dear developer,
>>
>>I want to compare the grey matter volume by VBM to cortical
>> thickness
>> by freesurfer. But in this process, I meet a problem: how to change the
>> points number of grey matter into the same with the vertex of thickness
>> by
>> freesurfer?
>>
>> Any help will be appreciated!
>>
>> Best regards
>>
>> Joe
>>
>>
>>
>
>>>
>
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Re: [Freesurfer] Freesurfer , wfu pick atlas

[Bruce Fischl]

sorry, what is the WFU atlas?

On Tue, 2 Feb 2010, Sharmili 57 wrote:

>
> Hey,
>
> I want to do Cortical thickness analysis for regions defined by the wfu atlas 
> in a MEG study. How can I define these areas in Freesurfer? It is imprecise 
> to use the atlases implemented in Freesurfer, isn't it?
>
> Thanks for your help
>
> Sharmili
>
> _
> http://redirect.gimas.net/?n=M1001xIMFb2
> Was machst Du grad bei Facebook? So erfahren es alle im Messenger
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Re: [Freesurfer] Painting two contrasts simultaneously

[Bruce Fischl]

sorry, I don't think we do, although doing it in matlab would be easy 
enough
On Wed, 27 Jan 2010, John Gelburg wrote:

> Dear all,
>
> I am using tksurfer to paint in single subject contrast (step 6 here:
> http://surfer.nmr.mgh.harvard.edu/fswiki/SpmPainting). However,  I would
> like to see two contrasts simultaneously, like here:
> http://web.mit.edu/mcgovern/images/News_and_Publications/0512_kanwisher.gif
> In other words I want to see let's say face selective regions and scene
> selective regions at the same time. There are many papers, which show it
> this way, though I suspect they do it BrainVoyager. What is the way to do it
> FreeSurfer?
>
> Thanks for help,
> John
>
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Re: [Freesurfer] Freesurfer , wfu pick atlas

[Douglas N Greve]

yes, the pick atlas is just an atlas in standard space, so you lose all 
the subject-specific info

doug

Sharmili 57 wrote:
> Hey,
>
> I want to do Cortical thickness analysis for regions defined by the 
> wfu atlas in a MEG study. How can I define these areas in Freesurfer? 
> It is imprecise to use the atlases implemented in Freesurfer, isn't it?
>
> Thanks for your help
>
> Sharmili
>
> 
> Was machst Du grad bei Facebook? So erfahren es alle im Messenger 
> 
> 
>
> ___
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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] GM volume and cortical thickness

[keepmoon]

Dear Bruce,

   Thank you very much for your patient instruction!  In fact, I
used *"file--load
overlay*", then with below error information. Maybe I can try mris_calc.
Thanks again!

   Best regards!

  Joe





2010/2/2 Bruce Fischl 

> it looks like you are trying to load the volume measures as a surface, not
> as an overlay. Use file->load overlay. Note that you can also use mris_calc
> to generate the volume measures.
>
> cheers
> Bruce
>
> On Tue, 2 Feb 2010, keepmoon wrote:
>
> Dear Bruce,
>>
>>   This is the all information in tci:
>>
>> %
>>
>> $  tksurfer xalbertM lh inflated
>> surfer: current subjects dir: /home/Joe/study
>> surfer: not in "scripts" dir ==> using cwd for session root
>>
>> surfer: session root data dir ($session) set to:
>>
>> surfer: /home/Joe/study
>> surfer: Reading header info from /home/Joe/study/xalbertM/mri/T1.mgz
>>
>> surfer: vertices=119274, faces=238544
>>
>>
>>
>>
>> WARNING: No colortable found!
>>
>>
>> surfer: single buffered window
>> surfer: tkoInitWindow(xalbertM)
>>
>> surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl
>>
>> Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl
>> Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl
>>
>> Reading /usr/local/freesurfer/lib/tcl/fsgdfPlo
>> t.tcl
>>
>> Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl
>>
>>
>> Successfully parsed tksurfer.tcl
>>
>> reading white matter vertex locations...
>>
>> %
>> MRISreadVertexPositions(/home/Joe/study/xalbertM/surf/lh_compute.volume):
>> surfaces differ. Main: 119274 verts 238544 faces,
>> /home/Joe/study/xalbertM/surf/lh_compute.volume: 465 verts 30670850 faces
>>
>>
>> surfer: Couldn't load *.volume,
>> Vset_read_vertex_set:MRISreadVertexposition
>> failed.
>>
>>
>>
>> %
>>
>> And I put the volume file I calculate in the attach.
>>
>>
>>
>> I am appreciated for your instruction!
>>
>> Best regards
>>
>> Joe
>>
>>
>>
>>
>>
>> 2010/2/2, Bruce Fischl :
>>
>>>
>>> can you send us the complete output in the tcl window (the one with the %
>>> prompt)
>>>
>>> On Tue, 2 Feb 2010, keepmoon wrote:
>>>
>>> Dear Bruce and All,
>>>

 In my *View--Configure*there are three button which are
 activated
 (*Light, caption and phase Encoded Dat Display*), without "*functional
 overlay*" option.
 And in these activated buttons: light(light 0,...,light 3, with the
 value, 0.4, 0.0, 0.6, 0.2. and brightness: 0.35). In the option of
 *phase
 Encoded Dat Display *(*Angle Cycles:1.0; Angle offset: 0.0*)

 I just use *File--load overlay*  then choose that **.volume* file to
 show that volume. And in the terminal there are error
 information:Couldn't
 load *.volume, Vset_read_vertex_set:MRISreadVertexposition failed.

Thanks a lot for your help!

Joe






 2010/2/2, Bruce Fischl :


> have you tried changing the threshold in configure->functional overlay?
> What kind of values do you see?
> On Tue, 2 Feb 2010, keepmoon wrote:
>
>  Dear all experters,
>
>
>> First I am appreciated for the help of Bruce.
>> I tried to following his instruction, but I still have some problem
>> and
>>  I
>> can't show any result on the flated surface. I don't know whether my
>> method
>> to calculate the volume is wrong or I display it wrongly. Expecting
>> someone
>> gives me a struction again!
>> My method is: using *read_curv* function to read*
>> lh.thickness* and*lh.area
>> *. Then the matrix of thickness product the matrix of area getting a
>> new
>> matrix. Then using *write_curv* function to write this new matrix into
>> a
>> *.volume. I think this volume file should be the grey volume image. (I
>> am
>> not sure about this process)
>>And now I want to show this volume on a flated lh hemispere (using
>> tksurfer), But when I overlay this volume onto inflated surface, there
>> is
>> not anything overlay on this surface? (this matrix is not all with 0.
>> )
>>
>>Anywhere am I wrong?
>>
>>   Any instruction will be appriciated!
>>
>>Joe
>>
>>
>>
>>
>>
>> 2010/2/1, keepmoon :
>>
>>
>> Dear developer,
>>>
>>>   I want to compare the grey matter volume by VBM to cortical
>>> thickness
>>> by freesurfer. But in this process, I meet a problem: how to change
>>> the
>>> points number of grey matter into the same with the vertex of
>>> thickness
>>> by
>>> freesurfer?
>>>
>>>Any help will be appreciated!
>>>
>>>Best regards
>>>
>>> Joe
>>>
>>>
>>>
>>>
>>

>>
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[Freesurfer] scrambled boundaries

[Brendan Robert Ansell]

Hi, I have a set of fairly old MRIs which have been run on freesurfer.
Occasionally scans have scrambled pial or white matter boundaries - a
knot-like appearance especially in sulci. I am wondering how freesurfer
estimates cortical thickness in these regions. For example, does it take
the pial boundary closest to the white boundary i.e. the outer surface of
the 'pial knot'? Are the encapsulated GM voxels included in the overall
cortical thickness measurement?

Thanks-

Brendan Ansell
MNC

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Re: [Freesurfer] scrambled boundaries

[Bruce Fischl]

Hi Brendan
if you send us the sample we can take a look, but in general the 
thickness is the average of the distance from the white to the pial with 
the distance from the pial to the white. Sometimes things can seem like a 
knot or tangle, but really it's just that the surface is almost parallel 
to a viewing plane (so it crosses back and forth over it lots of times in 
a short distance). Try looking at it in a different orientation and see 
if it loooks better.

Bruce
On Wed, 3 Feb 2010, Brendan Robert Ansell wrote:

> Hi, I have a set of fairly old MRIs which have been run on freesurfer.
> Occasionally scans have scrambled pial or white matter boundaries - a
> knot-like appearance especially in sulci. I am wondering how freesurfer
> estimates cortical thickness in these regions. For example, does it take
> the pial boundary closest to the white boundary i.e. the outer surface of
> the 'pial knot'? Are the encapsulated GM voxels included in the overall
> cortical thickness measurement?
>
> Thanks-
>
> Brendan Ansell
> MNC
>
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>
>
>
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