There is already a label called ?h.cortex.label for all of cortex. For lobes, you can use mris_annotation2label to break up the annotation into its constituent labels, then use mri_mergelabels to combine subsets into a lobe, then use mris_label2annot to combine the lobes into a new annotation. Search through the mail archives because this has been asked/answered before

On 08/21/2016 01:43 PM, Adil Javed wrote:

Thanks,

any thoughts about Q#2: 2-Also, Is there a way to segment the cortices as a whole, like left and right frontal cx, parietal cx, temporal cx, occipital cx?

Thanks

aj

On Saturday, August 20, 2016 9:21 PM, "shahin@nmr.mgh.harvard.edu" shahin@nmr.mgh.harvard.edu wrote:

Hi Adil, My understanding is that, you can always change the location of SUBJECTS_DIR. Just use this command: setenv SUBJECTS_DIR <Your location of interest>

You do not need to mention this new address in your recon-all command.

Good luck

...

HI,1-I'm working with FreeSurfer that is on a server. I don't have permission to create files under the $SUBJECTS_DIR. Is there any

way I

...

can specify -subject to be in a directory for which I do have

permission?

...

for example: recon-all -subject /location of the file or my own subject_dir location -all 2-Also, Is there a way to segment the cortices as a whole, like left and right frontal cx, parietal cx, temporal cx, occipital cx?

Thanks, AJ_______________________________________________

...

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