External Email - Use Caution Hi Yujing
Thanks for your response, would this only provide the mean cortical thickness though? Is there a way to output cortical thickness values at each vertex in each participant? Im also a bit confused about the segstats call, is this what you are proposing? mri_segstats --i combatlh.thickness.fwhm0.fsaverage.mgh --slabel $SUBJECTS_DIR/fsaverage/label/DLPFC_LH.label --sum lhDLPFClabel.sum Thanks Akansha > On 30 Jun 2023, at 15:16, Huang, Yujing <yhuan...@mgh.harvard.edu> wrote: > > External Email - Use Caution > > Hi Akansha, > > Can you try mri_segstats with option '--slabel subject hemi > full_path_to_label' - > https://secure-web.cisco.com/1_6KUKydZKeVMdsBFIq45SL3FnNI0J0vK1Oc1OGxgUci9ndTV9_ZapgsK_3NzhU8bMJOJY0uIz_LMPNGNff9ofQdi41lbl_z4LOot-PyyIAOkplCuie52WEoC25283K_FLApVE15eUqnyiaVpMRry06hp5_XGPLrNRm50KNv6woZtoPOOJi35Ep6MuRJkBknO4l1bQnjCysJ1851eBgeeHAOcGNtQnlEJSxyMSyXX9hlATC-lcdqDSa3tSwnR3HxF8HRuwC8fhqYKaAFcuhOJ6g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmri_segstats > > Best, > > Yujing > > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Akansha Mahesh Naraindas > Sent: Thursday, June 29, 2023 3:47 PM > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Subject: [Freesurfer] Extracting cortical thickness values for each subject > using labels > > External Email - Use Caution > > Hi > I have made custom labels to use as ROIs, > > I was wondering if there was any way to get thickness values at each vertex > for a participant but just within the areas covered by specific label files, > > So from the lh.thickness.fwhm0.fsaverage.mgh file, would I be able to extract > thickness values from this file, but just within the region covered by > aparc-rh-046.label ? > > Do you know of a way to do this? > > Thanks > Akansha > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1dxT14leTQ7Ksa3Sgg7FIgR2pgu40NDGUaD19UIbwV0y8ZNGQXR9amganjuB0SId6OhqDBw46PFd5Kmdnh5abFjWysy25h5PMuiUsdlGN4-OdtOaTmnQp8KjOQ3KkgnacR8yIuOjlGm_CYBjKu6UjS7tU1lMh9SCP_WHSbWmBeRfMCUF5EhEj5izMkzzylPS06ADMPR4zHJTRT-iU7sNdb9l6WNGj52ISkp6Uxcw9olaXCCVM0oOyNxMjOIhvYmHzRceA9xI42kCUtW3MLFFzfQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1lIcSJz8HcYf7wl6z9BJu2lHEB_fHQYAFk4OjWkh2O38TiGou-3RT8aZjr2O8uw1AzIu3PbnQEkO-yykIkxtTq32auP6LgUWG0k0jKpJ9-QJ8n29q-4915UiiCvX9MDOMYc50y--khBrvTUIIvDUybcNpj1mf_30841Cg-cNrcrZc1DUQNQ9EDUROiD-kzmPQE93cW4IquvQNWZc-f8t4u7oOhzxyvQu3xQdPH_MogCfjgyuQdeg1DbjwYTCrWc0FIiK85qZM9mgtKGEM63lYn2bI20tlSKkm1RFPQQSmtrViIOOl0yz8BlNXiWAxjD8T9-q7HsVUVoUtU6FFoJRisw/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 > https://secure-web.cisco.com/1IiDW8i6LRVYf5Y2vulzMF0f6qdo77QB46Sx6tWGSK6ViogENoKAgUX-AeaQk8dRwOn8s4vap459jaC773FfCLhqi7y38Q23hiG3Uv9dLs3zoK-wstKXi8rSFp_FG430MuoNHnyuKZjjcplA2swHjbTmgnMLuNeezkxf_D3pe4d0qwnn_Ps-YpQnxQkgxbvlxzBgglAejAPpUci2GK0LVuumxt9cXzqx2oLAkqnAcG3wPNc7sGXEw12dIPhVXmP-XZ_yyUvVeklKNrvdj8SdMWSSdkiWjXf8-f0Bir2VY1FA6Hlm6mKQxN9DRi5i7TWe1zD_OnqGX_-KKjis9E6ccLw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > > <https://secure-web.cisco.com/1IiDW8i6LRVYf5Y2vulzMF0f6qdo77QB46Sx6tWGSK6ViogENoKAgUX-AeaQk8dRwOn8s4vap459jaC773FfCLhqi7y38Q23hiG3Uv9dLs3zoK-wstKXi8rSFp_FG430MuoNHnyuKZjjcplA2swHjbTmgnMLuNeezkxf_D3pe4d0qwnn_Ps-YpQnxQkgxbvlxzBgglAejAPpUci2GK0LVuumxt9cXzqx2oLAkqnAcG3wPNc7sGXEw12dIPhVXmP-XZ_yyUvVeklKNrvdj8SdMWSSdkiWjXf8-f0Bir2VY1FA6Hlm6mKQxN9DRi5i7TWe1zD_OnqGX_-KKjis9E6ccLw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . > 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. >
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