External Email - Use Caution 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 >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://secure-web.cisco.com/1H0IKdQpT4zPZkmsDE3dEGynFAqJ8gZgI246QYuKuK97UhcDquJXljQPDYuZm1nsEd_TfqRUWyTJzsLvzK-zsS02IcjaG6T1sc7ZtOOoYw28b-SrbS5ROL8YyokLKHYMhZ3pobWIa4-nyDFy9mhjeUL74LNbw9KKRBf31fiMplXV1I5uhqhlfnDF7422q8hEgoZdLHeqIAY9vvm9-3pq42cqekDvbMZmZCNtDpEKqEkB3SRscF0mmGcV7VvUdjSM1-S30JEo0h2FLL3IUPMY89w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1H0IKdQpT4zPZkmsDE3dEGynFAqJ8gZgI246QYuKuK97UhcDquJXljQPDYuZm1nsEd_TfqRUWyTJzsLvzK-zsS02IcjaG6T1sc7ZtOOoYw28b-SrbS5ROL8YyokLKHYMhZ3pobWIa4-nyDFy9mhjeUL74LNbw9KKRBf31fiMplXV1I5uhqhlfnDF7422q8hEgoZdLHeqIAY9vvm9-3pq42cqekDvbMZmZCNtDpEKqEkB3SRscF0mmGcV7VvUdjSM1-S30JEo0h2FLL3IUPMY89w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > 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 Mass > General Brigham Compliance HelpLine at > http://secure-web.cisco.com/12A9Z86cVvIfejvHmhAmkm_jsUjdevBGws-rp-pt7Q-bo06wpk1KlUNhCQtEranmsD4u0mO-8lFvORRCRhHKhbV8WTxcy7nzvs5oRq6kSPzP8Ywn1YGXqlTSS0RbU7vQDlRzMLpJHyjDs9bjtcKIKIPtFNMggN4elDqk7_9hESJPhEk8qb68NJp1_e9EuqA_2WOPj6mAoAtBN7i-nj2WpTSLVhUYtLn8_CCiA7qld1WfqVH1Y8-NwdaSqB85LH80S7X4hkOTtkDZun3bOJ-lqBQ/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > . 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. > Please note that this e-mail is not secure (encrypted). If you do not > wish to continue communication over unencrypted e-mail, please notify > the sender of this message immediately. Continuing to send or respond > to e-mail after receiving this message means you understand and accept > this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
