Reply To: Cerebrum Labelling with custom atlas and label files

Forums Forums Cortical Surface Extraction Cerebrum Labelling with custom atlas and label files Reply To: Cerebrum Labelling with custom atlas and label files

#121
Rachel
Participant

Hi David, thanks for your reply.

I did as you said above and am now having this problem (also tried -c 3 and got the same result):

% cerebro -i e3834_OxM130_AP.nii –atlas /Applications/BrainSuite15b/atlas/inia19-t1-brain_16bit.img –atlaslabels /Applications/BrainSuite15b/atlas/inia19-struct.img -o e3834_OxM130_AP.cerebrum.mask.nii.gz -l e3834_OxM130_AP.hem.label.nii.gz -m e3834_OxM130_AP.mask.nii.gz -c 2 –air e3834_OxM130_AP.air –warp e3834_OxM130_AP.warp

Initializing brain volume
Performing linear alignment of atlas brain to subject brain
Performing warp alignment (order=5) of atlas brain to subject brain
alignwarp.c: 262: WARNING: Registration terminated due to a Hessian matrix that was not positive definite
Inspection of results is advised
alignwarp.c: 262: WARNING: Registration terminated due to a Hessian matrix that was not positive definite
Inspection of results is advised
Labeling brain regions
open_header.c: 232: cannot read 32 bit/pixel data from file /Applications/BrainSuite15b/atlas/inia19-struct.hdr
The image header indicates an unsupported number of bits per pixel. (AIR_INFO_BITS_ERROR)
reslice process failed.
error labeling lobes
unable to finish making label output.

The AIR documentation says:
“If you are having frequent problems with an error indicating the Hessian matrix is not positive definite, try using the -q option. The non-positive definite Hessian matrix is especially likely to arise when you try to register a file to a resliced version of itself (as people often do when they first try out the algorithm). In this particular situation, the problem is created by the fact that the two files only differ by interpolation and round-off errors which do not have well behaved second derivatives.”

What would you suggest? Is there a way perhaps to include this -q option from AIR?

Thanks for your help!