Re: [Freesurfer] Procedure to get amygdalar sub-regions and brainstem Brainstem consituents volumes

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:fischl@nmr.mgh.harvard.edu] |Sent: Wednesday, August 24, 2011 12:28 PM |To: Irwin, William |Cc: freesurfer@nmr.mgh.harvard.edu |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.