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. > > 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 > ... > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
