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| see https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011 for example | |
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| intro here, | {{attachment:flatpconl2inflated2014.jpg}} ''Author: Jean Augustinack'' Perirhinal cortex (area 35) is located in the parahippocampal gyrus. Perirhinal area 35 usually sits on the medial bank of the collateral sulcus but also on the lateral bank of the rhinal sulcus anteriorly, if the rhinal sulcus is present. Using high-resolution ex vivo imaging, we mapped perirhinal cortex (area 35) onto a surface template. Two different resolutions were collected 1) a "standard" 1 mm isotropic scan and 2) a high resolution 100 um isotropic scan. The high resolution scan showed architectural features (lamina and boundaries) while the standard 1mm scan provided the surface template that works with FreeSurfer. This perirhinal label was validated with histological staining and thus cytoarchitecturally-defined for perirhinal cortex (Brodmann's area 35). Reference for Perirhinal cortex, Cytoarchitecturally-defined labels: Augustinack JC et al, Predicting the location of human perirhinal cortex, Brodmann's area 35, from MRI, Neuroimage 2013 Jan 1;64:32-42. |
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| == Where to find the perirhinal (cytoarchitectural-defined) labels in FreeSurfer == Right and left labels for perirhinal are available in freesurfer 5.3 and 6.0+. |
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| you have three options for using these labels: | The labels are in freesurfer surface space and located in subjects dir: {{{ subj/label/?h.perirhinal_exvivo.label }}} |
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| labels in freesurfer surface space are in subjects dir subj/label/?h.perirhinal.label | They are generated by default by: {{{ recon-all -all }}} but can be regenerated with: {{{ recon-all -ba-labels }}} |
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| instructions on how to view in freeview | In freeview, after loading a surface, the label can be viewed either by loading the Annotation file: {{{ subj/label/?h.BA_exvivo.annot }}} or by loading the Label file: {{{ subj/label/?h.perirhinal_exvivo.label }}} (which allows selection of 'Heat Scale' viewing mode to display the probability mapping), or by loading the Label file: {{{ subj/label/?h.perirhinal_exvivo.thresh.label }}} which is a thresholded version, more suitable as an ROI. |
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| where to get stats on this label (../stats/$hemi.BA.stats) | Stats on this label are found in: {{{ subj/stats/?h.BA_exvivo.stats }}} |
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| already in freesurfer 5.3 label in volume space mapping surface label to subjects volume space will be available in v6 or if you have freesurfer, run this to map from surface space to volume space and then this is how you view it. label in fsaverage volume space [[attachment:perirhinal_fsaverage.nii]] label in mni152 volume space [[attachment:perirhinal_mni152.nii]] |
See also [[BrodmannAreaMaps]] and [[Entorhinal]]. |
Perirhinal Cortex
Author: Jean Augustinack
Perirhinal cortex (area 35) is located in the parahippocampal gyrus. Perirhinal area 35 usually sits on the medial bank of the collateral sulcus but also on the lateral bank of the rhinal sulcus anteriorly, if the rhinal sulcus is present. Using high-resolution ex vivo imaging, we mapped perirhinal cortex (area 35) onto a surface template. Two different resolutions were collected 1) a "standard" 1 mm isotropic scan and 2) a high resolution 100 um isotropic scan. The high resolution scan showed architectural features (lamina and boundaries) while the standard 1mm scan provided the surface template that works with FreeSurfer. This perirhinal label was validated with histological staining and thus cytoarchitecturally-defined for perirhinal cortex (Brodmann's area 35).
Reference for Perirhinal cortex, Cytoarchitecturally-defined labels:
Augustinack JC et al, Predicting the location of human perirhinal cortex, Brodmann's area 35, from MRI, Neuroimage 2013 Jan 1;64:32-42.
Where to find the perirhinal (cytoarchitectural-defined) labels in FreeSurfer
Right and left labels for perirhinal are available in freesurfer 5.3 and 6.0+.
The labels are in freesurfer surface space and located in subjects dir:
subj/label/?h.perirhinal_exvivo.label
They are generated by default by:
recon-all -all
but can be regenerated with:
recon-all -ba-labels
In freeview, after loading a surface, the label can be viewed either by loading the Annotation file:
subj/label/?h.BA_exvivo.annot
or by loading the Label file:
subj/label/?h.perirhinal_exvivo.label
(which allows selection of 'Heat Scale' viewing mode to display the probability mapping), or by loading the Label file:
subj/label/?h.perirhinal_exvivo.thresh.label
which is a thresholded version, more suitable as an ROI.
Stats on this label are found in:
subj/stats/?h.BA_exvivo.stats
See also BrodmannAreaMaps and Entorhinal.