are they currently labeled 0? Where did you get your color LUT from?
On Wed,
6 Mar 2019, Jörg Stadler wrote:
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Hi Bruce,
this did not change anything. But I tried the process of mris_ca_train,
mris_ca_label with lh.oasis.chubs.annot and this worked fine.
A closer look to my source annot file from mris_seg2annot showed that
the label 'unknown' is missing.
How can I add the unknown to all unlabeled vertices?
cheers,
Joerg
Hi Joerg
I'm not positive that I understand, but have you tried giving
mris_ca_label the switch:
mris_ca_label -l $SUBJECTS_DIR/$subject/label/$hemi.cortex.label ...
that should remove non-cortical regions from your output annot
cheers
Bruce
On Tue, 5 Mar 2019, Jörg Stadler wrote:
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Hi,
I transfered the SPM Anatomy Toolbox
(http://www.fz-juelich.de/inm/inm-1/DE/Forschung/_docs/SPMAnatomyToolbox/SPMAnatomyToolbox_node.html)
from Collin space to fsaverage using
Wu J, Ngo GH, Greve DN, Li J, He T, Fischl B, Eickhoff SB, Yeo BTT.
*Accurate nonlinear mapping between MNI volumetric and FreeSurfer
surface coordinate systems*
<http://people.csail.mit.edu/ythomas/publications/2018VolSurfMapping-HBM.pdf>,
/Human Brain Mapping/ 39:3793–3808, 2018.
mris_seg2annot --seg rh_Anatomy_v22c.nii.gz --ctab-auto Anatomy_v22c --s
fsaverage --hemi rh --o rh.anat_v22c
mris_seg2annot --seg lh_Anatomy_v22c.nii.gz --ctab-auto Anatomy_v22c --s
fsaverage --hemi lh --o lh.anat_v22c
This gave me the annot files for fsaverage (annotation.png) and a
template for the color lookup table.
Training of the classifier:
mris_ca_train -t Anatomy_v22c_LUT.txt lh lh.sphere.reg anat_v22c.annot
fsaverage lh.Anatomy_v22c.gcs
mris_ca_train -t Anatomy_v22c_LUT.txt rh rh.sphere.reg anat_v22c.annot
fsaverage rh.Anatomy_v22c.gcs
Transfer to individual subject fsaverage:
mris_ca_label fs_average lh sphere.reg lh.Anatomy_v22c.gcs
Anatomy_v22c.annot
mris_ca_label fs_average rh sphere.reg rh.Anatomy_v22c.gcs
Anatomy_v22c.annot
Now the miracle occurred and the whole surface got labeled.
(mris_ca_label.png)
How can a keep unassigned regions unlabeled?
Joerg
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