On Thu, Apr 10, 2008 at 5:55 PM, Doug Greve <greve@nmr.mgh.harvard.edu> 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 faces    327680
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 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
X    vbmDesign.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 <jyw.chen@utoronto.ca> 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 <greve@nmr.mgh.harvard.edu> 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 <jyw.chen@utoronto.ca> wrote:

Great! Thanks!
- Jerry

On Wed, Apr 9, 2008 at 3:50 PM, Doug Greve <greve@nmr.mgh.harvard.edu> 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 FreeSurfer? Is there any difference if I use the old command line method or the QDEC GUI?
Thanks,
- Jerry

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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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