Re: [Freesurfer] Interactions for continuous variables

2008-04-11 Thread Jerry Yeou-Wei Chen 
That was the problem!
Thanks!
- Jerry

On Thu, Apr 10, 2008 at 5:55 PM, Doug Greve <[EMAIL PROTECTED]>
wrote:

>  I think the problem is that the last line is a blank line. Remove that
> and retry.
>
> doug
>
> Jerry Yeou-Wei Chen wrote:
>
> I am getting the following error when I run mri_glmfit with my custom
> design matrix:
>
> WARNING: matlab elment type is 940126218, which is not a matrix.
> could not allocate 822685706 x 805908489 matrix
>
> Cannot allocate memory
> unsupported matlab format -849662976 (unknown)
>
> Cannot allocate memory
>
> Below is the full output, and I have attached my custom design matrix
> (orig is my original matrix, the other is formatted like Xg.dat)
>
> Thanks,
> - Jerry
>
> -
> Full output:
> -
> *% mri_glmfit --y rh.vbmDesign.thickness.10.mgh --X vbmDesign.mat --glmdir
> rh.vbmDesign.glmdir --surf fsaverage rh --C N_FvsM.mat
> Reading source surface
> /scratch/freesurfer/subjects/adina/descic39_allSubjects_readyForStats/fsaverage/surf/rh.white
> reading group avg surface area 822 cm^2 from file
> Reading in average area
> /scratch/freesurfer/subjects/adina/descic39_allSubjects_readyForStats/fsaverage/surf/rh.white.avg.area.mgh
> Number of vertices 163842
> Number of faces327680
> Total area 65020.765625
> AvgVtxArea   0.396850
> AvgVtxDist   0.717994
> StdVtxDist   0.193566
>
> $Id: mri_glmfit.c,v MailScanner has detected a possible fraud attempt from
> "1.138.2.1" claiming to be MailScanner has detected a possible fraud
> attempt from "1.138.2.1" claiming to be MailScanner warning: numerical
> links are often malicious: 1.138.2.1  2007/09/12
> 15:38:19 nicks Exp $
>
> cwd
> /scratch/freesurfer/subjects/adina/descic39_allSubjects_readyForStats/oldStats_vbmDesign
> cmdline mri_glmfit --y rh.vbmDesign.thickness.10.mgh --X vbmDesign.mat
> --glmdir rh.vbmDesign.glmdir --surf fsaverage rh --C N_FvsM.mat
> sysname  Linux
> hostname kdavis8-efef.uhnres.utoronto.ca
> machine  i686
> user jerryc
> FixVertexAreaFlag = 1
> UseMaskWithSmoothing 1
> OneSampleGroupMean 0
> y
> /scratch/freesurfer/subjects/adina/descic39_allSubjects_readyForStats/oldStats_vbmDesign/rh.vbmDesign.thickness.10.mgh
> logyflag 0
> XvbmDesign.mat
> usedti  0
> glmdir rh.vbmDesign.glmdir
> DoFFx 0
> Creating output directory rh.vbmDesign.glmdir
> Loading y from
> /scratch/freesurfer/subjects/adina/descic39_allSubjects_readyForStats/oldStats_vbmDesign/rh.vbmDesign.thickness.10.mgh
> MatrixReadTxT: could not scan value [36][1]
>
> WARNING: matlab elment type is 940126218, which is not a matrix.
> could not allocate 822685706 x 805908489 matrix
>
> Cannot allocate memory
> unsupported matlab format -849662976 (unknown)
>
> Cannot allocate memory
> *
>
>
>
> On Thu, Apr 10, 2008 at 11:02 AM, Jerry Yeou-Wei Chen <
> [EMAIL PROTECTED]> wrote:
>
> > Thanks for the clarification, Doug.
> > The Wiki page for mri_glmfit says to "Specify the design matrix in
> > matlab4 format."
> >
> > - Jerry
> >
> > On Wed, Apr 9, 2008 at 5:19 PM, Doug Greve <[EMAIL PROTECTED]>
> > wrote:
> >
> > >
> > > >From mri_glmflit --help :
> > >
> > > --X design matrix file
> > >
> > > Explicitly specify the design matrix. Can be in simple text or in
> > > matlab4
> > > format. If matlab4, you can save a matrix with
> > > save('X.mat','X','-v4');
> > >
> > > It does not need/expect any extension.
> > >
> > > doug
> > >
> > >
> > > Jerry Yeou-Wei Chen wrote:
> > >
> > > Regarding custom design matrices, does the --X flag require a design
> > > matrix in matlab format? If so, can I simply create it in a text editor 
> > > and
> > > name it with the suffix ".mat"?
> > > Also, if I use the --X to specify a design matrix, am I still supposed
> > > to specify the fsgd file?
> > > Thanks,
> > > - Jerry
> > >
> > > On Wed, Apr 9, 2008 at 4:58 PM, Jerry Yeou-Wei Chen <
> > > [EMAIL PROTECTED]> wrote:
> > >
> > > > Great! Thanks!
> > > > - Jerry
> > > >
> > > > On Wed, Apr 9, 2008 at 3:50 PM, Doug Greve <
> > > > [EMAIL PROTECTED]> wrote:
> > > >
> > > > >
> > > > > You can pass custom design and contrast matrices to mri_glmfit, so
> > > > > you can pass the same matrices to mri_glmfit that you would use with 
> > > > > spm.
> > > > > Alternatively, you can set up an fsgd file with a 3rd continuous 
> > > > > variable
> > > > > that is the produce of the first two.
> > > > >
> > > > > doug
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > Jerry Yeou-Wei Chen wrote:
> > > > >
> > > > >  Hello,
> > > > > I would like to know how to examine an interaction between
> > > > > continuous variables.
> > > > > In SPM, my understanding is that a new interaction regressor,
> > > > > comprised of the product of the two continuous variables of interest, 
> > > > > can be
> > > > > coded and entered into the model.
> > > > > Would this be appropriate for CTA group analysis in Fre

[Freesurfer] tksurfer buttons grayed out

2008-04-11 Thread hranilovich 
We're taking a look at using FreeSurfer for our lab's analysis of  
cortical thickness...just ran a fully automated recon-all on one of  
our lab's brains that generated no error messages and looks good in  
the "Inspection of Freesurfer Output" exercise from your tutorial.   
However, I noticed while moving through this exercise that the  
curvature file button, pial surface button, and the thickness map  
button are grayed out (not available for use) in the tksurfer toolbox.  
 If this means there was some subtle error in the output - any ideas  
where to begin troubleshooting?  Perhaps automatic topology defect  
correction? Not sure how obvious the topology defects you refer to  
would be on inspection; there were no holes or handles that I could  
see in the inflated surface, though ours was more lumpy than the  
tutorial's...Some dura was left in and was designated cortex, lying  
outside of the pial surface generated.  Could this be the issue?  If  
so, would the solution be an adjustment of the watershed parameters  
fix it, or is that really intended for large over-inclusions of skull?


Thanks - Jennifer

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Re: [Freesurfer] tksurfer buttons grayed out

2008-04-11 Thread Bruce Fischl 

 Hi Jennifer,

did you try loading them with file->... (curvature for thickness and 
surface configuration for pial). You can also ctrl-right click on either 
one to bring up the appropriate file menu. We don't load them by default I 
don't think.


Bruce


On Fri, 11 Apr 2008 
[EMAIL PROTECTED] wrote:


We're taking a look at using FreeSurfer for our lab's analysis of cortical 
thickness...just ran a fully automated recon-all on one of our lab's brains 
that generated no error messages and looks good in the "Inspection of 
Freesurfer Output" exercise from your tutorial.  However, I noticed while 
moving through this exercise that the curvature file button, pial surface 
button, and the thickness map button are grayed out (not available for use) 
in the tksurfer toolbox.  If this means there was some subtle error in the 
output - any ideas where to begin troubleshooting?  Perhaps automatic 
topology defect correction? Not sure how obvious the topology defects you 
refer to would be on inspection; there were no holes or handles that I could 
see in the inflated surface, though ours was more lumpy than the 
tutorial's...Some dura was left in and was designated cortex, lying outside 
of the pial surface generated.  Could this be the issue?  If so, would the 
solution be an adjustment of the watershed parameters fix it, or is that 
really intended for large over-inclusions of skull?


Thanks - Jennifer

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[Freesurfer] converting a region defined by a surface to a label file

2008-04-11 Thread Michael Harms 

Hello,

We have some white matter surfaces created using non-FS software in
which we have subsequently "cut-out" via hand contouring specific gyri
and sulci of interest (e.g., cingulate).  I would like to be able to use
these extracted surfaces to create a label file in FS corresponding to
the matching surface region within FS.  Is there a way to accomplish
this using existing Freesurfer binary or matlab functions?

More specifically, we can define these extracted surfaces in the native
scan space, and get them into a vtk format (which should be readable by
mris_convert).  Do you have any suggestions for the easiest way to then
"translate" the region defined by this surface into a corresponding
region on the FS white matter surface?  Ideally, since our in-house
surface defines an enclosed set of vertices, the ensuing label file in
FS would represent an enclosed set of vertices as well.

thanks for your suggestions,
Mike H.


-- 
Michael Harms, Ph.D.

Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
Renard Hospital, Room 6615   Tel: 314-747-6173
660 South Euclid Ave.Fax: 314-747-2182
St. Louis, MO 63110  Email: [EMAIL PROTECTED]



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