|
Size: 1287
Comment:
|
Size: 2137
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 3: | Line 3: |
| {{attachment:flatpconl2inflated2014.jpg}} | |
| Line 4: | Line 5: |
| 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). See Augustinack JC et al, Neuroimage 2013 Jan 1;64:32-42. |
''Author: Jean Augustinack'' |
| Line 7: | Line 7: |
| == Where to find the perirhinal (cytoarchitectural-defined) labels == | 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). |
| Line 10: | Line 9: |
| labels in freesurfer surface space are in subjects dir subj/label/?h.perirhinal.label | Reference for Perirhinal cortex, Cytoarchitecturally-defined labels: |
| Line 12: | Line 11: |
| instructions on how to view in freeview where to get stats on this label (../stats/$hemi.BA.stats) already in freesurfer 5.3 |
Augustinack JC et al, Predicting the location of human perirhinal cortex, Brodmann's area 35, from MRI, Neuroimage 2013 Jan 1;64:32-42. |
| Line 19: | Line 14: |
| == 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+. |
|
| Line 20: | Line 17: |
| The labels are in freesurfer surface space and located in subjects dir: {{{ subj/label/?h.perirhinal_exvivo.label }}} |
|
| Line 21: | Line 22: |
| Alternatively, label in volume space | They are generated by default by: {{{ recon-all -all }}} but can be regenerated with: {{{ recon-all -ba-labels }}} |
| Line 23: | Line 31: |
| -mapping surface label to subjects volume space | 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. |
| Line 25: | Line 45: |
| will be available in v6 | Stats on this label are found in: {{{ subj/stats/?h.BA_exvivo.stats }}} See also: * [[BrodmannAreaMaps]] * [[Entorhinal]] * [[ExVivoEcPcLabelsFsaverage]] |
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: