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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