External Email - Use Caution

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:

...

External Email - Use Caution Hi,

I transfered the SPM Anatomy Toolbox (http://www.fz-juelich.de/inm/inm-1/DE/Forschung/_docs/SPMAnatomyToolbox/SPMA...)

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

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

are they currently labeled 0? Where did you get your color LUT from? On Wed, 6 Mar 2019, Jörg Stadler wrote:

   External Email - Use Caution

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:

...

External Email - Use Caution Hi,

I transfered the SPM Anatomy Toolbox (http://www.fz-juelich.de/inm/inm-1/DE/Forschung/_docs/SPMAnatomyToolbox/SPMA...)

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

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer