Hi Yerong

the indices and names are all in the FreeSurferColorLUT.txt file. The indices in [1000,2000) are for lh and in [2000,3000) are rh. For example, 2008 is ctx-rh-inferiorparietal.

cheers Bruce

On Tue, 8 Jan 2019, Yerong Li wrote:

   External Email - Use Caution

Dear Bruce:

Thank you.

So my question would be if aparc+aseg.mgz is from ?h.aparc.annot and aparc.a2009s+aseg.mgz is from ?h.aparc.a2009s.annot.

Then how I can find the mapping between labels in aparc+aseg.mgz to labels in ?h.aparc.annot?

The labels in ?h.aparc.annot are 0 6500 660700 1316060 1326300 1351760 2146559 2647065 3296035 3302420 3302560 3957880 3988500 3988540 4924360 6553700 6558940 7874740 8204875 9180240 9180300 9182740 9211105 9221140 9221340 9231540 10511485 10542100 11146310 11832480 13145750 14423100 14433500 14464220 14474380

they have naming:

{'unknown'                 }
{'bankssts'                }
{'caudalanteriorcingulate' }
{'caudalmiddlefrontal'     }
{'corpuscallosum'          }
{'cuneus'                  }
{'entorhinal'              }
{'fusiform'                }
{'inferiorparietal'        }
{'inferiortemporal'        }
{'isthmuscingulate'        }
{'lateraloccipital'        }
{'lateralorbitofrontal'    }
{'lingual'                 }
{'medialorbitofrontal'     }
{'middletemporal'          }
{'parahippocampal'         }
{'paracentral'             }
{'parsopercularis'         }
{'parsorbitalis'           }
{'parstriangularis'        }
{'pericalcarine'           }
{'postcentral'             }
{'posteriorcingulate'      }
{'precentral'              }
{'precuneus'               }
{'rostralanteriorcingulate'}
{'rostralmiddlefrontal'    }
{'superiorfrontal'         }
{'superiorparietal'        }
{'superiortemporal'        }
{'supramarginal'           }
{'frontalpole'             }
{'temporalpole'            }
{'transversetemporal'      }
{'insula'                  }

The labels in aparc+aseg.mgz are from 0-2035 and most of them are under 88.

And in lookup tables, labels in aparc+aseg.mgz have different naming.

Do you know how to do find relationship between volumtic labels and surface labels?

Yerong

Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:

...

Hi Yerong

the parcellations are done on the surface to generate the annot files. These are then sampled into the cortical ribbon to extend the aseg so that every voxel in the cortex is given a label from the corresponding annot file (aparc+aseg.mgz from aparc.annot and aparc.a2009s+aseg.mgz from aparc.a2009s.annot)

cheers Bruce

On Tue, 8 Jan 2019, Yerong Li wrote:

...

   External Email - Use Caution

Dear Freesurfer experts:

I am on ROI analysis tutorial: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROIV6.0

And I am trying to understand the relationship between:

/label/?h.aparc.annot and /mri/aparc+aseg.mgz /label/?h.aparc.a2009s.annot and /mri/aparc.a2009s+aseg.mgz

I understand /label/?h.aparc.annot corresponds to "Desikan-Killiany atlas" and its labels have 35 different labels (except unknown 0), while in several cases you mentioned that "/mri/aparc+aseg.mgz" corresponds to "Desikan-Killiany atlas", which I DO NOT understand. "/mri/aparc+aseg.mgz" to me are subcortical segmentations while "/label/?h.aparc.annot" are cortical(surface) parcellations. "Desikan-Killiany atlas" should mean "cortical (surface) parcellations". That's why I do not understand why "/mri/aparc+aseg.mgz" corresponds to "Desikan-Killiany atlas"?

Could anyone help me understand this?

Yerong

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