Dear Mark,
Thanks for looking into it. I was wondering how much you want me to upload, I have first uploaded only the concattenated .bvars file and the matrix files which produces the error (ref number 954149). I'm not sure if this has enough information in it, I would be happy to upload the FIRST folders of each subject, just let me know.
Thanks again.
Best,
Jan-Mendelt
________________________________________
From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Mark Jenkinson [[log in to unmask]]
Sent: Monday, February 18, 2013 8:25 PM
To: [log in to unmask]
Subject: Re: [FSL] first_utils --useReconNative error?
Hi,
I'm surprised by this given that it works for me. Can you send us your data using the upload site (see out Support page).
All the best,
Mark
"Tillema, Jan-Mendelt, M.D." <[log in to unmask]> wrote:
Hi Mark,
Thanks. Yes, I'm using 5.0.2.
Command:
first_utils --vertexAnalysis --usebvars -i {$m}.bvars -d {$n}.mat -o vertex/{$o} --useReconNative --useRigidAlign
I attached the outputs... sorry for the clutter.
Thanks for your help.
Jan-Mendelt
exerpt output:
...
1.26394 0.000598381 -0.0284979 -16.9694
0.0231609 1.15963 0.241991 -81.3236
0.00607778 -0.29421 1.17908 -64.6887
0 0 0 1
1.26446 -0.0636186 0.10574 -30.3852
0.0727577 1.27623 0.057774 -57.9623
-0.129501 -0.144462 1.29205 -105.434
0 0 0 1
done recon
done recon and reg
new design matrix
1 0.714286
1 0.714286
1 0.714286
1 0.714286
1 0.714286
1 0.714286
1 0.714286
1 0.714286
1 0.714286
1 -1.28571
1 -1.28571
1 -1.28571
1 -1.28571
1 -1.28571
$ fslsize vertex/{$o}
dim1 1
dim2 1
dim3 1
dim4 14
pixdim1 1.0000000000
pixdim2 1.0000000000
pixdim3 1.0000000000
pixdim4 1.0000000000
On MNI template
first_utils --vertexAnalysis --usebvars -i {$m}.bvars -d {$n}.mat -o vertex/{$o} --useReconMNI
output:
Attempting to switch to: /usr/local/fsl/fsl5/data/first/models_336_bin/05mm/L_Thal_05mm.bmv
model loaded
done recon and reg
new design matrix
1 0.714286
1 0.714286
1 0.714286
1 0.714286
1 0.714286
1 0.714286
1 0.714286
1 0.714286
1 0.714286
1 -1.28571
1 -1.28571
1 -1.28571
1 -1.28571
1 -1.28571
$ fslsize vertex/{$o}
dim1 182
dim2 218
dim3 182
dim4 14
pixdim1 1.0000000000
pixdim2 1.0000000000
pixdim3 1.0000000000
pixdim4 1.0000000000
________________________________________
From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Mark Jenkinson [[log in to unmask]]
Sent: Friday, February 15, 2013 6:52 AM
To: [log in to unmask]
Subject: Re: [FSL] first_utils --useReconNative error?
Hi,
This doesn't happen to me when I try it here - both versions work fine and produce outputs of the same size.
Are you using the most recent version of FSL?
If so, then please tell us the exact command you are running.
All the best,
Mark
On 12 Feb 2013, at 15:50, Jan <[log in to unmask]> wrote:
> Dear FSL members,
>
> I was trying to run first_utils on a cohort of 34 patients. All went well until I used randomise, when an error popped up. If I use the --useReconMNI in fsl_utils, there is no problem and I get all the results needed. If I use the --useReconNative --useRigidAlign flags, there is no information in the created -o .nii.gz file and subsequently randomise crashes not surprisingly as the files have the following dimensions.
> -- using MNI:: Size = 182 x 218 x 182 x 34 : Dims = 1.0000000000 x 1.0000000000 x 1.0000000000
> -- using Native:: Size = 1 x 1 x 1 x 34 : Dims = 1.0000000000 x 1.0000000000 x 1.0000000000
>
> What is the user-error that I'm looking for?
> Thanks.
> Jan
