Hi Freesurfer Developers,

I'm trying to map the vertices of entorhinal cortex(EC) in one subject into the space of MNI152 by using mri_label2label.

1) The vertices of EC from subject were extracted using:
mri_annotation2label --subject FreeSurfer --hemi lh  --labelbase FreeSurfer/Vertices/aparc-lh

Those vertices were saved in FreeSurfer/Vertices/aparc-lh-006.label.

2) And I used mri_label2label to map it into the MNI space:
mri_label2label --srclabel /FreeSurfer/Vertices/aparc-lh-006.label --srcsubject FreeSurfer --trglabel /FreeSurfer/Vertices/aparc-lh-006_Reg2MNI.label --trgsubject FreeSurferMNI152 --regmethod surface --hemi lh

So, the mapped vertices were in /FreeSurfer/Vertices/aparc-lh-006_Reg2MNI.label

3) I also extracted the vertices of EC from MNI as a reference:
mri_annotation2label --subject FreeSurferMNI152 --hemi lh  --labelbase FreeSurferMNI152/Vertices/aparc-lh

Vertices of EC from MNI were saved in FreeSurferMNI152/Vertices/aparc-lh-006.label.

To my understanding, the mapped vertices(/FreeSurfer/Vertices/aparc-lh-006_Reg2MNI.label) should cover almost the same surface region as the reference vertices(FreeSurferMNI152/Vertices/aparc-lh-006.label), right? But the reference vertices seem to cover a bigger region, which is shown in the attached picture(Red Points:mapped vertices, Red&Green Points:reference vertices).

We are using freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0, and the computer is CentOS release 6.9.

Thanks!

All the Best,
Hengda

-----------------

Attachment:
1) terminal output from mri_annotation2label --subject FreeSurfer --hemi lh  --labelbase FreeSurfer/Vertices/aparc-lh
subject = FreeSurfer
annotation = aparc
hemi = lh
labelbase = /FreeSurfer/Vertices/aparc-lh
surface   = white

Reading surface
 /FreeSurfer/surf/lh.white
Loading annotations from /FreeSurfer/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
Seg base 1000
max index = 35
...
  6    516 /FreeSurfer/Vertices/aparc-lh-006.label
LabelWrite: saving to /FreeSurfer/Vertices/aparc-lh-006.label
...

2) terminal output from mri_label2label
srclabel = /FreeSurfer/Vertices/aparc-lh-006.label
srcsubject = FreeSurfer
trgsubject = FreeSurferMNI152
trglabel = /FreeSurfer/Vertices/aparc-lh-006_Reg2MNI.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

FREESURFER_HOME /usr/local/freesurfer/5.1
Loading source label.
Found 516 points in source label.
Starting surface-based mapping
Reading source registration
 /FreeSurfer/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
 /FreeSurferMNI152/surf/lh.white
Reading target registration
 /FreeSurferMNI152/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  516 nlabel points
Performing mapping from target back to the source label
Number of reverse mapping hits = 199
Checking for and removing duplicates
Writing label file /FreeSurfer/Vertices/aparc-lh-006_Reg2MNI.label 715
LabelWrite: saving to /FreeSurfer/Vertices/aparc-lh-006_Reg2MNI.label
mri_label2label: Done

3) terminal output from mri_annotation2label --subject FreeSurferMNI152 --hemi lh  --labelbase FreeSurferMNI152/Vertices/aparc-lh
subject = FreeSurferMNI152
annotation = aparc
hemi = lh
labelbase = /FreeSurfer/Vertices/MNI-aparc-lh
surface   = white

Reading surface
 /FreeSurferMNI152/surf/lh.white
Loading annotations from /FreeSurferMNI152/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
Seg base 1000
max index = 35
...
  6    648 /FreeSurfer/Vertices/MNI-aparc-lh-006.label
LabelWrite: saving to /FreeSurfer/Vertices/MNI-aparc-lh-006.label
...