Nurunisa,

For mri_ca_normalize, the flags must be the first args, like this:

mri_ca_normalize -noatlas -noxform -mask ...

otherwise the flags will be ignored if they are at the end of the command (which is bad, but thats the way this works for this bin).

Nick

On Tue, 2008-11-04 at 15:58 -0500, Nurunisa Neyzi wrote:

Hi, I am getting an error with the command:

mri_ca_normalize -mask /Users/Nurunisa/Documents/MLS_STUDY/cma_segs/10281/mri/brain.mgz -seg /Users/Nurunisa/Documents/MLS_STUDY/cma_segs/10281/mri/cma_seg_noAA.mgz /Users/Nurunisa/Documents/MLS_STUDY/cma_segs/10281/mri/nu.mgz -noatlas -noxform /Users/Nurunisa/Documents/MLS_STUDY/cma_segs/10281/mri/norm_trn1.mgz

using MR volume /Users/Nurunisa/Documents/MLS_STUDY/cma_segs/10281/mri/brain.mgz to mask input volume... using segmentation volume /Users/Nurunisa/Documents/MLS_STUDY/cma_segs/10281/mri/cma_seg_noAA.mgz to generate control points... reading 9 input volumess reading atlas from '8'... reading input volume from /Users/Nurunisa/Documents/MLS_STUDY/cma_segs/10281/mri/nu.mgz... reading input volume from -noatlas... mri_read(): couldn't determine type of file /Users/Nurunisa/Documents/MLS_STUDY/-noatlas mri_ca_normalize: could not read input MR volume from -noatlas end

Is the flag -noatlas not valid? Or am I doing something wrong here? _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer