External Email - Use Caution Hi,
I'm working with infant (0-30 month) MR data, and iBEAT ( https://secure-web.cisco.com/1T2WKIelhUu8n_wuNR_5gb37RydVg1xrWEVvlUOdcz2UFWoSKKUO8S38cKClNmhjA13keedLju0Te5qHI70cMu686M8Nz33LUMDSdSc5UQuK9Vnl0b2bAEYY3X2pBwXbzaEnuzeLsX13HY7M0H8yFuJubt2wgqrSefkFgQ-XpZoEYeznT5PRAbS3RHGC8kb90A3ZS7a47Zkqz0eN6_e9ebZcBdzOsLlJYdHJwvolLCKV6tVC7wAXDgXrrODdQ0njXnHygdM9DOoJI9dttTpF1R-vsrPxiFk_XgPafiu9Hwi4KZHgiPrc6A_O77CgY-ZWPbJQ3x70CJAnfzYZH0pVTIg/https%3A%2F%2Fwww.nature.com%2Farticles%2Fs41596-023-00806-x) is currently doing a better job than Infant FreeSurfer ( https://secure-web.cisco.com/1M3VIitCZu3azJ0yMsnC2UvSxSyhcRAkbfTg_v1IUkOJObAa_9G8w89RsGzk4Xf4BqDqrThHe1m2ImfRWqSWSe4wlOc42k4ums78aO1mPCguwvDX3eo1ThINBtkLveTLfasbBXqMxqrNUHA3TRlxkBjgCG5QzeEm7x4lvFWhohrGB58jYWKeL3Hz7nABbqZe8ScicauUZNyGrLAEyNnuBsbcf70LrV4-qfWZ5YqKzqzUHzNE405Uh9rPMnIXfxNbNjc0Ybx41EhAM_VRu82VibTKLb1lMTckg3EU5UqhgXtYnTTiplYcAnHlQ1oqG0qxd_viSreko60OHp4aeerH74A/https%3A%2F%2Fwww.sciencedirect.com%2Fscience%2Farticle%2Fpii%2FS1053811920304328) at cortical surface recon in this age range. However, I have custom surface ROI atlases on the fsaverage template and would very much like to leverage FreeSurfer's stats tools to map iBEAT subject surfaces to the template and extract stats from my custom ROIs. To do so, I need to - Bring my iBEAT VTK surfaces (~47K vertices per hemisphere) into FreeSurfer (mris_convert?) - Resample the meshes to FS surface resolution (~12.5K vertices per hemi) - Compute curvature stats on the iBEAT surfaces - Use mris_surf2surf (or equivalent) to map the resampled iBEAT surface to the fsaverage template using curvature - Compute/extract anatomical stats from the regions equivalent to the ROIs in my template space atlas. All of the above are presenting challenges. So far, I tried using mris_convert to bring the VTK into FS format, but when I tried using mris_anatomical_stats, I get errors. Note that I also ran InfantFS on the data, and that I copied the converted (but not downsampled) VTK pial surface from iBEAT to $SUBJECTS_DIR/$subjid/surf/lh.ibeat.pial > mris_anatomical_stats -log test.ibeat.log sub-0001 lh ibeat.pial outputting results to test.ibeat.log... reading volume /scratch/t/tpaus/jhengeni/iBEAT/surface_remapping/sub-0001/sub-0001/mri/wm.mgz... reading input surface /scratch/t/tpaus/jhengeni/iBEAT/surface_remapping/sub-0001/sub-0001/surf/lh.ibeat.pial... Using TH3 vertex volume calc Total face volume 58098.7 Total vertex volume 57390.1 (mask=0) reading input pial surface /scratch/t/tpaus/jhengeni/iBEAT/surface_remapping/sub-0001/sub-0001/surf/lh.pial... error: mrisReadTriangleFile opened /scratch/t/tpaus/jhengeni/iBEAT/surface_remapping/sub-0001/sub-0001/surf/lh.pial okay but surface doesn't match /scratch/t/tpaus/jhengeni/iBEAT/surface_remapping/sub-0001/sub-0001/surf/lh.ibeat.pial. nvertices:46854 != mris->nvertices:12240 || nfaces:93704 != mris->nfaces:24476 error: mrisReadTriangleFile failed. error: mris_anatomical_stats: could not read surface file /scratch/t/tpaus/jhengeni/iBEAT/surface_remapping/sub-0001/sub-0001/surf/lh.pial It appears this approach is failing due to a difference in meshes (the iBEAT mesh is at a different resolution, with more elements, than the lh.pial from InfantFS). Any tips for this and the other steps would be a big help! Thanks, Jim H. -- Jim Hengenius Research Associate Paus Research Group CHU Sainte-Justine Research Centre My Google Calendar <http://secure-web.cisco.com/1NyYdK1uBklqcDSsFMhBiedpJnPC-H6m83iYBtfLt-c-oKzBTwSVYkZEtHRJm20jit2kvoHh5jt8-_bpLVWG7tgMxbJ4Su8MGpCufWWEWDvHAcX9dhQFLeDfjGz9D7RqngZSEUkDY2_NJH_IRlQUylA-G1YdI1digS1CPmzl-aHQ6SiJqQJvSSdOCipdYr7g2ij2udg6xI_MLsXGPrJWj7HwQ_HUf0eVaAwHijfxy4oFp4s-6RbZ7r71HBbYQ4lJie5bkP-ZTBgBcbYgEvyAIAMOMIuJtr8nlS5kmo1o7-nwLg0ejnUKHsJ53Z_7FfyNC1OqSyUEoqzBUIUoZwgeCVg/http%3A%2F%2Fwww.google.com%2Fcalendar%2Fembed%3Fsrc%3Djames.hengenius%40gmail.com>
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