Hi,
Have you tried running it without the -fnirt options?
Or possibly just the fnirt command on its own?
The fnirt command would be:
${FSLDIR}/bin/fnirt --in=${c}_brain --aff=${c}_template_brain.mat --cout=${c}_template_brain_warp --config=T1_2_MNI152_2mm --ref=template_final
Hopefully this will help debug the problem.
All the best,
Mark
On 5 Aug 2011, at 12:44, Signe Jeppesen wrote:
> Hi.
>
> I am using the following command
>
> fsl_reg ${c}_brain template_final ${c}_template_brain -fnirt "--aff=${c}_to_template_final.mat --cout=${c}_output --config=T1_2_MNI152_2mm.cnf"
>
> However, after it has set
>
> Setting subsampling
> Setting reg mode
> Setting lambda
>
> the loop stops with the error
>
>
> ** ERROR (nifti_image_read): failed to find header file for 'CON_001_template_brain_warp'
> ** ERROR: nifti_image_open(CON_001_template_brain_warp): bad header info
> Error: failed to open file CON_001_template_brain_warp
> ERROR: Could not open image CON_001_template_brain_warp
> Image Exception : #22 :: Failed to read volume CON_001_template_brain_warp
> An error occured while reading file: CON_001_template_brain_warp
> ** ERROR (nifti_image_read): failed to find header file for 'CON_001_template_brain_warp'
>
> The loop creates the CON_001_template_brain_warp.mfs file, but not the nifti file. What should I do?
> I have read somewhere in the archieves that it may be due to memory that the error comes, but I am only running a small script and my computer is usually very fast, and can handle both several VBM´s running at the same time.
>
> The --aff= input is maybe not as perfect as possible (just a simple fnirt) but could that be the reason?
> I am interested in cout for the jacobian. Can I remove the --config input. Would that be better?
>
> Thank you
> Signe, Glostrup Hospital
> Denmark
>
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