Hi Danny

yes, you can specify up to 100 labels. Make sure that the label name is exactly as it appears in the parcellation though

cheers Bruce On Wed, 27 May 2020, Danny Kim wrote:

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Hi FreeSurfer experts,

I'm currently working on a brain with a bit of atypical morphology and was wanting to parcellate through the DKT labels, but by using manually drawn labels as guides. The intent here is to fix specific labels to be where they are on the surface by drawing them manually and then automatically classify other labels around them (e.g. fix precentral and superiortemporal using manual labels).

However, it seems like during the mris_register step, I'm able to use one of my manual label to guide the registration to the sphere, but not more than one.

e.g. mris_register -L label/manual_precentral.label DKTatlas40.gcs precentral -curv sphere folding.atlas.acfb40.noaparc.tif surf/sphere.reg (WORKS, after mris_ca_label, precentral is where the manual label was. Superior temporal label is not where the manual label is)

e.g. mris_register -L label/manual_precentral.label DKTatlas40.gcs precentral -L label/manual_superiortemporal.label DKTatlas40.gcs superiortemporal -curv sphere folding.atlas.acfb40.noaparc.tif surf/sphere.reg (Runs but output looks exactly the same as before, i.e. superiortemporal label is not where the manual label was specified)

Is there a trick to specifying multiple manual labels in guiding mris_register? I am not sure if the -L flag can be specified multiple times and there's no information on that on the mris_register manual.

I'm using the following FreeSurfer on my MAC: freesurfer-i386-apple-darwin11.4.2-stable6-20170119

Thanks for your time in this experts!

Danny Kim