You will have to merge the labels into an annotation (mris_label2annot), then the annotation to a segmentation volume (mri_aparc2aseg), then apply mri_label2vol to the segmentation. doug

On 02/19/2013 10:45 AM, Vincent Koppelmans wrote:

Hi all,

I am trying to convert Brodmann area 4a and 4p to .nii file format in native space. I have used to following syntax:

tkregister2 --mov ${SUBJECTS_DIR}/mri/rawavg.mgz --noedit --s [SUBJECT_ID] --regheader --reg ./register.dat

mri_label2vol --label [PATH-TO-LABEL-FILE] --temp ${SUBJECTS_DIR}/mri/rawavg.mgz --subject [SUBJECT_ID] --hemi lh --o [OUTPUT-FILE-NAME] --proj frac 0 1 .1 --fillthresh .0 --reg [PATH-TO-register.dat-FILE]

This is the result: https://dl.dropbox.com/u/6747155/BA4a.png

As you can see, there are 'missing' voxels in the volume: it is not one smooth shape. However, when I convert aseg or aparc structures to volumes, I don't have this problem. Is it possible to get a a smooth, fully filled shape from a Brodmann label?

Thanks in advance,

Vincent

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