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 <fis...@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 <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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