Re: [Freesurfer] mris_ca_label: assignment of emty surface to wrong label

2019-03-05 Thread Bruce Fischl 

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/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*
,
/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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Re: [Freesurfer] mris_ca_label: assignment of emty surface to wrong label

2019-03-05 Thread Jörg Stadler 
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/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*
>> ,
>>
>> /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


-- 
Dr. rer. nat. Joerg Stadler
Leibniz Institute for Neurobiology (LIN)
Special Lab Non-Invasive Brain Imaging
Brenneckestr. 6, D - 39118 Magdeburg
Tel.: +49-391-6263-92171 Fax: +49-391-6263-92589
Gnupg-Key:http://keyserver.ubuntu.com search for E-Mail Adress
Key fingerprint:B005 A785 8191 BED1 1B75  9B06 120C F20F 3E08 D20F 


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Re: [Freesurfer] mris_ca_label: assignment of emty surface to wrong label

2019-03-06 Thread Jörg Stadler 
External Email - Use Caution

Got it :)


filling the unassigned vertices with 'unknown' using tksurfer solved my
problem.


cheers,

Joerg


> 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/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*
>>> ,
>>>
>>> /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
>

-- 
Dr. rer. nat. Joerg Stadler
Leibniz Institute for Neurobiology (LIN)
Special Lab Non-Invasive Brain Imaging
Brenneckestr. 6, D - 39118 Magdeburg
Tel.: +49-391-6263-92171 Fax: +49-391-6263-92589
Gnupg-Key:http://keyserver.ubuntu.com search for E-Mail Adress
Key fingerprint:B005 A785 8191 BED1 1B75  9B06 120C F20F 3E08 D20F 


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Re: [Freesurfer] mris_ca_label: assignment of emty surface to wrong label

2019-03-06 Thread Bruce Fischl 

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/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*
,

/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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