Hi,
What happens if you just use the data provided (not running FIRST
yourself) and do the concat_bvars on the provided .bvars files?
Does that work? It should.
What version of FSL are you using? You can check by doing:
cat $FSLDIR/etc/fslversion
The file naming when you just segment one structure is a bit
different. You should get something more like:
con0047_brain-L_Hipp_first.nii.gz
If you do not get something like this then you should check
the error logs by doing:
cat *.logs/*.e*
or similar, and seeing if something went wrong.
All the best,
Mark
On 30 Jun 2010, at 20:59, Fahima Dossa wrote:
> To generate the all.bvars file I used the command concat_bvars
> all.bvars *L_Hipp*.bvars
>
> I tried downloading the data again but this did not resolve the
> issue. I also noticed that when running the FIRST segmentation on
> con0047_brain using first_utils the *_all_fast_firstseg.nii.gz and
> *_all_fast_origsegs.nii.gz files are not generated although i do get
> the *_first.vtk and *_first.bvars files for each structure. Not sure
> if these issues are related.
>
>
>
> On Wed, Jun 30, 2010 at 1:10 PM, Mark Jenkinson
> <[log in to unmask]> wrote:
> Hi,
>
> I didn't realise that you were just trying to run the
> tutorial data. I can not replicate this problem here.
> It is quite odd as it seems to have got quite close.
> What did you do to create the all.bvars file?
> It might be worth downloading a fresh copy of the
> data and trying again using the commands in the
> tutorial. If you still have trouble please let us know.
>
> All the best,
> Mark
>
>
> On 30 Jun 2010, at 14:23, Fahima Dossa wrote:
>
> Hi Mark,
>
> I used the design matrix provided in the downloaded file set for the
> tutorial (design_con0_dis1.mat) The matrix is:
> /NumWaves 1
> /NumPoints 8
> /PPheights 1.000000e+00
>
> /Matrix
> 0.000000e+00
> 0.000000e+00
> 0.000000e+00
> 0.000000e+00
> 0.000000e+00
> 1.000000e+00
> 1.000000e+00
> 1.000000e+00
>
>
> 30, 2010 at 4:25 AM, Mark Jenkinson <[log in to unmask]> wrote:
> Hi,
>
> Did you set your design matrix up using the GLM GUI?
> If not, do that as it requires it to be setup that way.
> If so, what should it have been, how many subjects do
> you have, etc?
>
> All the best,
> Mark
>
>
>
> On 29 Jun 2010, at 18:27, Jeanine McAlpine wrote:
>
> Hi
>
> After downloading the practical files, I've been attempting to run a
> vertex analysis according to the tutorial steps but when I run the
> command first_utils --usebvars --vertexAnalysis -i all.bvars -o
> diff_con0_dis1_L_Hipp_mni -d design_con0_dis1.mat --useReconMNI I
> get the following message:
>
> read model
> done reading model
> setting up shape/appearance model
> The shape has 732 vertices.
> 336 modes of variation are retained.
> The model was constructed from 336 training subjects.
> model loaded
> done recon and reg
> new design matrix
> 1 -0.375
> 1 -0.375
> 1 -0.375
> 1 -0.375
> 1 -0.375
> 1 0.625
> 1 0.625
> 1 0.625
> 1 0
> terminate called after throwing an instance of
> 'NEWMAT::SingularException'
>
> any ideas as to what the problem might be?
>
> Thanks in advance.
>
>
>
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