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Dear Freesurfer Community,
I wish to manually reassign/edit cortical parcellation performed by FS.
We use the cortical parcellation done by FS and it has worked very well for most of our subjects. However, we have two subjects where the parcellation has not been done correctly. It seems that the central sulcus has been mis-classified to be one sulcus too far posterior in the brain - this has resulted in incorrect labeling of surrounding gyri. Curiously, it is only one hemisphere for both subjects (rh for one and lh for the other), where the other hemisphere is correctly parcellated.
In our two mis-parcellated subjects, how might we manually reassign or guide FS to correctly classify the central sulcus and thus correctly label the surrounding gyri?
I have attached a picture of an erroneous parcellation. Freesurfer version: freesurfer-linux-centos6_x86_64-dev-20201011-4d2b06a Platform: Ubuntu 16.04
Best, Helena-Céline Stevelt Danish Research Centre for Magnetic Resonance
Can you try an experiment for me? cd $SUBJECTS_DIR/subject/surf cp lh.sphere.reg lh.sphere.reg.auto # make a backup mris_register -norot -rotate 0 0 +15 -curv rh.sphere $FREESURFER_HOME/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif rh.sphere.reg Then run recon-all -s subject -autorecon3 -nosphere -nospherereg And see if that fixes the problem
ps. It looks like you are using a development of FS from Jan 11, 2020. In general, you should only use released versions
On 6/1/2021 5:10 AM, Helena-Céline Stevelt wrote:
External Email - Use Caution Dear Freesurfer Community,
I wish to manually reassign/edit cortical parcellation performed by FS.
We use the cortical parcellation done by FS and it has worked very well for most of our subjects. However, we have two subjects where the parcellation has not been done correctly. It seems that the central sulcus has been mis-classified to be one sulcus too far posterior in the brain - this has resulted in incorrect labeling of surrounding gyri. Curiously, it is only one hemisphere for both subjects (rh for one and lh for the other), where the other hemisphere is correctly parcellated.
In our two mis-parcellated subjects, how might we manually reassign or guide FS to correctly classify the central sulcus and thus correctly label the surrounding gyri?
I have attached a picture of an erroneous parcellation. Freesurfer version: freesurfer-linux-centos6_x86_64-dev-20201011-4d2b06a Platform: Ubuntu 16.04
Best, Helena-Céline Stevelt Danish Research Centre for Magnetic Resonance
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Dear Doug,
With some adjustments from our resident freesurfer expert, that fixed our problem! Thank you so much for your help.
Best, Helena-Céline Stevelt Danish Research Centre for Magnetic Resonance
On 2021-06-03 19:19, Douglas N. Greve wrote:
Can you try an experiment for me? cd $SUBJECTS_DIR/subject/surf cp lh.sphere.reg lh.sphere.reg.auto # make a backup mris_register -norot -rotate 0 0 +15 -curv rh.sphere $FREESURFER_HOME/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif rh.sphere.reg Then run recon-all -s subject -autorecon3 -nosphere -nospherereg And see if that fixes the problem
ps. It looks like you are using a development of FS from Jan 11, 2020. In general, you should only use released versions
On 6/1/2021 5:10 AM, Helena-Céline Stevelt wrote:
External Email - Use Caution Dear Freesurfer Community,
I wish to manually reassign/edit cortical parcellation performed by FS.
We use the cortical parcellation done by FS and it has worked very well for most of our subjects. However, we have two subjects where the parcellation has not been done correctly. It seems that the central sulcus has been mis-classified to be one sulcus too far posterior in the brain - this has resulted in incorrect labeling of surrounding gyri. Curiously, it is only one hemisphere for both subjects (rh for one and lh for the other), where the other hemisphere is correctly parcellated.
In our two mis-parcellated subjects, how might we manually reassign or guide FS to correctly classify the central sulcus and thus correctly label the surrounding gyri?
I have attached a picture of an erroneous parcellation. Freesurfer version: freesurfer-linux-centos6_x86_64-dev-20201011-4d2b06a Platform: Ubuntu 16.04
Best, Helena-Céline Stevelt Danish Research Centre for Magnetic Resonance
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Douglas N. Greve -
Helena-Céline Stevelt