looks ok. you should not need --outdir you can use mri_aparc2aseg to create a nifti file. This is what is used to create aparc+aseg.mgz from the aparc annotation and aseg.mgz. Look in the recon-all.log file for an example command line (just change the output name so you don't overwrite). The aseg.mgz is the volumetric labeling that includes cerebral WM and subcortical gray. It does not include lobes. doug

On 11/19/2013 04:06 PM, Mojdeh Zamyadi wrote:

Thanks a lot for the very quick reply!

does this look OK? mri_annotation2label --subject P2 --hemi rh --outdir freeSurfer_Results/P2/moj_labels/ --lobesStrict freeSurfer_Results/P2/moj_labels/freeSurfer_lobes

how can I convert the annotation file to nii.gz?!

also, could please explain a bit what the "aseg" file contains? because I though that file had the complete sub-cortical parcellation (including different parts of different lobes!)

sorry if my questions are rather basic, I'm very new to freeSurfer

-M On 11/19/2013 11:21 AM, Douglas N Greve wrote:

...

Try running mri_annotation2label with the --lobesStrict option doug

On 11/19/2013 11:15 AM, Mojdeh Zamyadi wrote:

...

Hi all,

I'm interested in getting a lobar segmentation of the cortex and I've already ran recon-all on my subjects. I'm now confused by the outputs and was wondering if someone could tell me which output file contains segmentation that can be merged to get a 4 lobe parcellation similar to: http://freesurfer.net/fswiki/CorticalParcellation?

Thanks a lot, -Mojdeh

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