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 keepmoon1224@googlemail.com:

...

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

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 fischl@nmr.mgh.harvard.edu:

...

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 keepmoon1224@googlemail.com:

...

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

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 keepmoon1224@googlemail.com:

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 fischl@nmr.mgh.harvard.edu:

...

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 fischl@nmr.mgh.harvard.edu:

...

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 keepmoon1224@googlemail.com:

...

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

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 fischl@nmr.mgh.harvard.edu

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 fischl@nmr.mgh.harvard.edu:

...

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 fischl@nmr.mgh.harvard.edu:

...

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 keepmoon1224@googlemail.com:

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 > > > >