On Tue, Apr 19, 2011 at 12:33 PM, Allie Rosen <rosen.allie@gmail.com> wrote:

Hi Doug,

It worked with +1 -1 0. But I also have an agediff.mat file (0 0 +1 -1) that I'd like to look at. Therefore I'd be looking at age differences and also sex differences. Can I do this using DODS? I'm not sure if I'd be able to do that with 3 regressors.

So honestly I'm not even sure whether I should use DOSS or DODS. My groups are male and female and I'm not sure if there are differences between them. I thought that the first 2 regressors were male and female, and the 3rd and 4th were age. Am I correct?

Thanks,
Allie

On Tue, Apr 19, 2011 at 12:26 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Hi Alli,e you are running it with DOSS which will create 4 regressors (MaleOffset, FemaleOff, AgeSlope). Your contrast has 4 columns. So change to DODS or change the number of column in your contrast. If you go with DODS, make sure to test for an interaction (ie, a contrast of 0 0 +1 -1). If you have substantial interaction, then testing the offsets is tricky. If you don't have an interaction, then change to DOSS and use (+1 -1 0).

doug

Allie Rosen wrote:

Update: ran on a different computer in the lab and progressed a little, but got the following error: "dimension mismatch between X and contrast sexdiff.mat X has 3 cols, C has 4 cols"

I am not positive what X is, but here is my FSGD file (abbreviated):

GroupDescriptorFile 1
Class Male
Class Female
Variables Age

Input C1 Female 27
Input C2 Female 53
Input C3 Male 22
Input C4 Female 62
Input C5 Male 27

And here is my contrast file:

1 -1 0 0

Any ideas?

Thank you,
Allie

On Tue, Apr 19, 2011 at 11:51 AM, Allie Rosen <rosen.allie@gmail.com <mailto:rosen.allie@gmail.com>> wrote:

Hi All,

I am running mri_glmfit and get the following error:

mri_glmfit --y lh.insula.thickness.6.mgz --fsgd fsgd2.txt doss
--glmdir lh.insula.thickness.6.glmdir --surf fsaverage lh --C
sexdiff.mat
gdfReadHeader: reading fsgd2.txt
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age 37.9483
Class Means of each Continuous Variable
1 Male 34.5417
2 Female 40.3529
INFO: gd2mtx_method is doss
Reading source surface
/media/AMMONIS/fsSubjects/AR_normals/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces 327680
Total area 65416.648438
AvgVtxArea 0.399267
AvgVtxDist 0.721953
StdVtxDist 0.195470

$Id: mri_glmfit.c,v 1.187.2.1 2010/07/26 15:54:39 greve Exp $
cwd /media/AMMONIS/fsSubjects/AR_normals
cmdline mri_glmfit --y lh.insula.thickness.6.mgz --fsgd fsgd2.txt
doss --glmdir lh.insula.thickness.6.glmdir --surf fsaverage lh --C
sexdiff.mat
sysname Linux
hostname Caduceus
machine x86_64
user arosen
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y /media/AMMONIS/fsSubjects/AR_normals/lh.insula.thickness.6.mgz
logyflag 0
usedti 0
FSGD fsgd2.txt
labelmask /media/AMMONIS/fsSubjects/AR_normals/fsaverage/label/lh.cortex.label
maskinv 0
glmdir lh.insula.thickness.6.glmdir
IllCondOK 0
DoFFx 0
Creating output directory lh.insula.thickness.6.glmdir
Segmentation fault

The directory IS created, but contains only "mri_glmfit.log". Here
are the contents:

$Id: mri_glmfit.c,v 1.187.2.1 2010/07/26 15:54:39 greve Exp $
cwd /media/AMMONIS/fsSubjects/AR_normals
cmdline mri_glmfit --y lh.insula.thickness.6.mgz --fsgd fsgd2.txt
doss --glmdir lh.insula.thickness.6.glmdir --surf fsaverage lh --C
sexdiff.mat
sysname Linux
hostname Caduceus
machine x86_64
user arosen
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y /media/AMMONIS/fsSubjects/AR_normals/lh.insula.thickness.6.mgz
logyflag 0
usedti 0
FSGD fsgd2.txt
labelmask /media/AMMONIS/fsSubjects/AR_normals/fsaverage/label/lh.cortex.label
maskinv 0
glmdir lh.insula.thickness.6.glmdir
IllCondOK 0
DoFFx 0

If this all sounds familiar, I realize that I've submitted this
problem back in January and haven't managed to work it out. Any
help would be appreciated!

Thank you,
Allie Rosen, MSc Candidate
Graduate Student, Department of Neurosurgery
Toronto Western Hospital 14-327
399 Bathurst St.
University of Toronto

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