Thanks, Bruce. That was my assumption, but I thought it was worthwhile asking.
Related, for the hippocampal subfield segmentation, I understand the voxel values are the probabilities of belonging to a given subfield. Is there way to extract a list of voxels with their values for each region? I realize this would generate a very long stream of data. But then one could post-hoc adjust the number of voxels per region by setting some criteria (e.g., the probability of belonging to the fornix has to be >95%). Thanks, Wil |-----Original Message----- |From: Bruce Fischl [mailto:[email protected]] |Sent: Wednesday, August 24, 2011 12:28 PM |To: Irwin, William |Cc: [email protected] |Subject: Re: [Freesurfer] Procedure to get amygdalar sub-regions and |brainstem Brainstem consituents volumes | |Hi Wil | |sorry, we don't have anything for that yet, although we are actively working |on it. | |cheers |Bruce |On Wed, 24 Aug 2011, Irwin, William wrote: | |> |> Hello- |> |> |> |> In the FreeSurferColorLUT.txt,v 1.70.2.1 2011/05/02 file, there are labels for |sub-regions of interest. For example amygdala and brainstem. |> |> |> |> How does one go about extracting the volumes for these regions? |> |> |> |> Thank you in advance, |> |> Wil |> |> |> |> |> |> #No. Label Name: R G B A |> |> 7001 Lateral-nucleus 72 132 181 0 |> |> 7002 Basolateral-nucleus 243 243 243 0 |> |> 7003 Basal-nucleus 207 63 79 0 |> |> 7004 Centromedial-nucleus 121 20 135 0 |> |> 7005 Central-nucleus 197 60 248 0 |> |> 7006 Medial-nucleus 2 149 2 0 |> |> 7007 Cortical-nucleus 221 249 166 0 |> |> 7008 Accessory-Basal-nucleus 232 146 35 0 |> |> 7009 Corticoamygdaloid-transitio 20 60 120 0 |> |> 7010 Anterior-amygdaloid-area-AAA 250 250 0 0 |> |> 7011 Fusion-amygdala-HP-FAH 122 187 222 0 |> |> 7012 Hippocampal-amygdala-transition-HATA 237 12 177 0 |> |> 7013 Endopiriform-nucleus 10 49 255 0 |> |> 7014 Lateral-nucleus-olfactory-tract 205 184 144 0 |> |> 7015 Paralaminar-nucleus 45 205 165 0 |> |> 7016 Intercalated-nucleus 117 160 175 0 |> |> 7017 Prepiriform-cortex 221 217 21 0 |> |> 7018 Periamygdaloid-cortex 20 60 120 0 |> |> 7019 Envelope-Amygdala 141 21 100 0 |> |> 7020 Extranuclear-Amydala 225 140 141 0 |> |> |> |> |> |> # Label names and colors for Brainstem consituents |> |> # No. Label Name: R G B A |> |> 170 brainstem 119 159 176 0 |> |> 171 DCG 119 0 176 0 |> |> 172 Vermis 119 100 176 0 |> |> 173 Midbrain 119 200 176 0 |> |> 174 Pons 119 159 100 0 |> |> 175 Medulla 119 159 200 0 |> |> |> | | |The information in this e-mail is intended only for the person to whom it is |addressed. If you believe this e-mail was sent to you in error and the e-mail |contains patient information, please contact the Partners Compliance |HelpLine at http://www.partners.org/complianceline . If the e-mail was sent |to you in error but does not contain patient information, please contact the |sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
