It is hard to tell what is happening in that image, but it looks like the overlap is pretty close? One does not expect the overlap to be perfect, esp since the MNI152 is not a real subject. It would be easier to judge if you rendered the labels on the surface.
On 05/31/2017 02:55 PM, Hengda He wrote:
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.
- 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.
- 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
- 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:
- 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 ...
- 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
- 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 ...
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