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 toshow 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! Joe2010/2/2, 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!
Joe2010/2/1, 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 regardsJoe