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
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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 ...
