Dear Mark,
I have 2 groups, 11 subjects in each. This the design matrix that I used lately. I created it with design_ttest2 DES 11 11.
/NumWaves 2
/NumPoints 22
/PPheights 1 1
/Matrix
1 0
1 0
1 0
1 0
1 0
1 0
1 0
1 0
1 0
1 0
1 0
0 1
0 1
0 1
0 1
0 1
0 1
0 1
0 1
0 1
0 1
0 1
First off, I concatenated all L_Hipp.bvars with
concat_bvars all.bvars *L_Hipp*.bvars
and then I used the following command for vertex analysis:
first_utils --usebvars --vertexAnalysis -i all.bvars -o diff_c -d DES.mat --useReconMNI
After I updated the FSL now I need to put fsl4.1- as as prefix to every command I want to use. Does this have anything to do with fsl installation?
Thank you very much,
Arash
________________________________________
From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Mark Jenkinson [[log in to unmask]]
Sent: Thursday, June 09, 2011 4:05 AM
To: [log in to unmask]
Subject: Re: [FSL] Problem with FIRST vetex analysis
Dear Arash,
The conversion of the individual vtk files with the command you use
is absolutely fine and nothing to worry about. It does not affect the
accuracy or reliability of the results in any way, so do not worry about that.
It is purely a viewing issue.
The abort of your vertex analysis is a concern though. It is possible that
your matrix is badly formed. Can you please include a copy of the
design matrix and some more details on the analysis (number of subjects,
exact command you ran, etc.). With this information we should be able
to figure out what is wrong.
All the best,
Mark
On 9 Jun 2011, at 04:12, Arash Nazeri wrote:
> Dear all,
>
> We've been trying to run first_utils on our run_first_all results. But no matter what flag or GLM (either with design_ttest2 or GLM) we use, we end up with the following error:
> .
> .
> .
> set shape Mesh
> 1 0 0
> 0 0 1
> do mvglm
> terminate called after throwing an instance of 'NEWMAT::SingularException'
> Aborted
>
> Nevertheless, first_utils works perfectly fine with fsl course data. Also, fslview crashes while opening the original *.vtk files generated by our own run_first_all, unless we reformat the vtk files using the following command:
> run_mesh_utils --doConvert_Binary_To_ASCII -m original_file.vtk -o new_file.vtk
>
> Can anyone help us solve this issue?
>
> Cheers,
> Arash
>
>
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