Re: [Freesurfer] question about painting SPM results onto Freesurfer

2012-09-06 Thread keepmoon
Hi Doug, As Bruce suggested, you may give me some help. My question is: I paint SPM results onto Freesurfer surface, is it possible to get the size and name of clusters on the surface? Thanks Karry On Mon, Sep 3, 2012 at 10:16 PM, keepmoon wrote: > > Hi Bruce, > > Thanks for

Re: [Freesurfer] question about painting SPM results onto Freesurfer

2012-09-03 Thread keepmoon
do that, but > you'll need to wait for Doug's return for the details > > cheers > Bruce > > On Mon, 3 Sep 2012, keepmoon wrote: > > Hi Bruce, >> >> Thanks for your detailed explaination! >> I have one more question about it! >> Is it possibl

Re: [Freesurfer] question about painting SPM results onto Freesurfer

2012-09-03 Thread keepmoon
t to the surface so if there are significant > cluster that aren't intersected by the sampling band you specify they will > not appear on the surface. > > cheers > Bruce > > > On Sun, 2 Sep 2012, keepmoon wrote: > > Hello everyone, >> >> I just read the in

[Freesurfer] question about painting SPM results onto Freesurfer

2012-09-02 Thread keepmoon
Hello everyone, I just read the information about "paintig SPM results onto Freesurfer" ( http://surfer.nmr.mgh.harvard.edu/fswiki/SpmPainting). It shows how to painting SPM results from statistic step (ex. spmT.img) to surface space. I tested the procedure and it worked. But I don't understand w

Re: [Freesurfer] load multiple overlays with different colors

2012-05-05 Thread keepmoon
://github.com/nipy/PySurfer/zipball/master > > then do from the folder: > > python setup.py install > > HTH > > Alex > > On Sat, May 5, 2012 at 10:09 PM, keepmoon > wrote: > > Hi Michael and Alex, > > > > Thanks for your suggestion about my question!

Re: [Freesurfer] load multiple overlays with different colors

2012-05-05 Thread keepmoon
y 2, 2012 at 6:32 PM, Michael Waskom wrote: > Hi, > > If you're somewhat handy with Python, you can use PySurfer for this. > See this example: > http://pysurfer.github.com/auto_examples/plot_fmri_conjunction.html > > Best, > Michael > > On Wed, May 2, 2012 at 7:51 AM,

Re: [Freesurfer] load multiple overlays with different colors

2012-05-04 Thread keepmoon
Hi Kathy, > > subprocess.check_output > > was introduced in python 2.7. You use 2.6 > > I recommend to upgrade if possible. > > Otherwise we need to fix this > > Alex > > On Fri, May 4, 2012 at 3:44 PM, keepmoon > wrote: > > Dear Michael, > > > &g

Re: [Freesurfer] load multiple overlays with different colors

2012-05-04 Thread keepmoon
Hi, > > If you're somewhat handy with Python, you can use PySurfer for this. > See this example: > http://pysurfer.github.com/auto_examples/plot_fmri_conjunction.html > > Best, > Michael > > On Wed, May 2, 2012 at 7:51 AM, keepmoon > wrote: > > Dear all, > >

Re: [Freesurfer] load multiple overlays with different colors

2012-05-02 Thread keepmoon
chael Waskom wrote: > Hi, > > If you're somewhat handy with Python, you can use PySurfer for this. > See this example: > http://pysurfer.github.com/auto_examples/plot_fmri_conjunction.html > > Best, > Michael > > On Wed, May 2, 2012 at 7:51 AM, keepmoon &g

Re: [Freesurfer] load multiple overlays with different colors

2012-05-02 Thread keepmoon
ate an annotation with those 3 colors based on > the thresholded sig maps. Let me know if you want instructions to do this. > doug > > On 05/02/2012 10:51 AM, keepmoon wrote: > > Dear all, > > > > I search my question before I post it. I did find similar questions, > >

[Freesurfer] load multiple overlays with different colors

2012-05-02 Thread keepmoon
Dear all, I search my question before I post it. I did find similar questions, but didn't find answer. I want to overlay two files with different colors. For example, one is sig1.mgh from cortical thickness, the other is sig2.mgh from area. I want to use tksurfer overlaying them with three colors:

[Freesurfer] how to overlap two signicant regions together

2010-11-26 Thread keepmoon
Dear everyone, Anyone knows how to display overlap regions of two significant changes in one image ? For example, I got the significantly different regions of thickness and curv between patients and controls. Normally we can display them seperately, but now I want to display them toget

[Freesurfer] FSDG problem

2010-09-01 Thread keepmoon
Dear all, I am using Freesurfer longitudinal analysis to detect the relationship between the change of thickness in patients and a clinical test (ex: MMSE). I just have MRI of patients at two time points (baseline and followup) without normal control subjects. I have already completed longitu

Re: [Freesurfer] GM volume and cortical thickness

2010-02-02 Thread keepmoon
ad 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 th

Re: [Freesurfer] GM volume and cortical thickness

2010-02-02 Thread keepmoon
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&q

Re: [Freesurfer] GM volume and cortical thickness

2010-02-02 Thread keepmoon
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 a

Re: [Freesurfer] GM volume and cortical thickness

2010-02-02 Thread keepmoon
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 th

[Freesurfer] GM volume and cortical thickness

2010-02-01 Thread 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