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 <keepmoon1...@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 <fis...@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 <fis...@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 <keepmoon1...@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
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>
>
>
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