External Email - Use Caution Hi Lilla,
No worries - any help would be appreciated! We're collecting low-field (64mT) infant volumes and also processing some NIHPD2 (1.5T) infant volumes. We've found that iBEAT currently works a bit better than Infant Freesurfer at the younger ages (<6 mo), at least for extracting the pial surface. From another project, we have .annot files specifying our custom atlas parcellation in fsaverage space, and our end goal is the extraction of pial surface area values from atlas ROIs. To get there from iBEAT pial output (one .vtk triangular mesh per hemisphere), I think I will need to - register the iBEAT pial surfaces to fsaverage (possibly minimizing curvature difference as in mris_register) - resample to fsaverage resolution(?) - use the annot files to identify vertices corresponding to our .annot ROIs in the iBEAT surfaces - extract surface area from the ROIs in native space I'm currently working on some of this using the PyVista library in Python, but I'm better with R than Python and would love to avoid reinventing the wheel if you know ways to streamline this process within Freesurfer's tools. Thanks! Jim H. On Wed, Apr 2, 2025 at 3:55 PM Zollei, Lilla,Ph.D. <lzol...@mgh.harvard.edu> wrote: > Hi Jim, > I am sorry I missed your message. Are your questions still relevant? > Apologies, Lilla > ------------------------------ > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of James Hengenius < > james.hengen...@gmail.com> > *Sent:* Friday, December 13, 2024 2:49 PM > *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Subject:* [Freesurfer] Importing surface meshes from 3rd party cortical > surface reconstruction tools for analysis in fsaverage template space > > > External Email - Use Caution > > Hi, > > I'm working with infant (0-30 month) MR data, and iBEAT (*MailScanner has > detected a possible fraud attempt from "secure-web.cisco.com" claiming to > be* > https://secure-web.cisco.com/1wgrR6avzhrKloKIk-lK7SYUO89Nk1mZvx65aN_i4tucrr3ozcqPV2lpqx0RMrrvVLewONwH1Ub4ZNaCSPAfdOZS_EbZphRrMmGyT360MBthjZ_x68P-QlQNZ_vSBeFDOswJ9X1oxnr8tqkPbKhWG-ymp2stCJ4RkMLi3AgiQpdWy_RXy_q4W-2Ce4IMjaM1DFiSEaPqfg4aJF_vFoxLISP33EYPqFCCrX62iMTPmHQzNgDIctnG1osifmDJ9GpjMoO26OLESEl7vVMuwzXQ_jNCnKAOBwEhKUgyu8M7vWjkajC1AliPzhGgdVIrLXc5FUIAyuwCpMk0qtUCTmpHEig/https%3A%2F%2Fwww.nature.com%2Farticles%2Fs41596-023-00806-x > <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 (*MailScanner has > detected a possible fraud attempt from "secure-web.cisco.com" claiming to > be* > https://secure-web.cisco.com/1HPPrCL1b3QKCLpwo16YY3JNX4_vaaGT3zbdy9V_gqn0jnJnQ2Iuz8tMhzRjb-OZpCYqa0HkFWnLi3Mm9KBpOJfV9HXA0fPheWIofIQ7YHZjURR-IGUWqerf2cwNkeunRYhigIZVideDrJmmwRqeq_LYvok5jDf77DzZXW_r-q0_vSLjm4bSnII3GxoCAE1yiJMbERYjIQbVMH4NpZDC_Pw5TDXfVvfR5H9Mufsq6zxKx2uipQMto4yyG5vyVFn9DyVlmgiBAfkyzGvTiypYpsPi1NQwtow7WHcHbm7vnOoyQ6wBDBoS-Zyd7TSBtuskF3LZDMT8YcbR5UL1jmV2etA/https%3A%2F%2Fwww.sciencedirect.com%2Fscience%2Farticle%2Fpii%2FS1053811920304328 > <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> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1wISCCgFsU7PzYbi6Cr7A5XjAj107lDep952lc-Cj9C0lCWzfeFepaNW1wt_Omx4XjGHIDBpteEXekvmMYk4a7bH4-Qmj3P5Bm7y2wbXruiPnkiz1y0fSD90Cc1AtRD4VOw1eo6EDMEHYARZmXYnqlVpy_dp0-Drn6w2sWKeTQGKrfLL4iWN0ujWDtaYNJFDklhjstNhtR6a85OL4WNkJWGN6G9Crkz4xlqW-xT0H1fwFNnSNBolodpXPbftlKn83cliW2EkOV7cpqFmSQ8hjw1J6p9t50hqJaYqX4cWHsDjPUFOGq2sezIRMDOOjjqzwiLmYBX9BJ8xr70uIP7V9gg/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/1wcJY3sP01uyyfd3Us2oMk9lItq4WIJ5a-x7jh-EUG15zxyfksLnYO3vv24CCmasX-w_jyCiekj7CSItHfQCTvG0LxXwICPerAjgnzrolON3B5qYp1uVWmvCIAXysgMkZ4vjRqDmJAHtN12q3oiZmj2Db3ezAzDa2MT7_f8UKi-x4Mm1zfhe8DT8BDdQ54Nv0G64TuNS-lGwv5DYSTU_jvzvdwJlYhSZxdEzJp0p84d-vzSO6JWIMFtNsp7ag1fnB-NKXPo1VFRDSD8WDDOvIM_k0VAJ5EldVXg1mlJig8ljx7xhXmL2kZ-6YdmUunS1gzmOeTNSy8mD7iTtjmpue5A/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/1wcJY3sP01uyyfd3Us2oMk9lItq4WIJ5a-x7jh-EUG15zxyfksLnYO3vv24CCmasX-w_jyCiekj7CSItHfQCTvG0LxXwICPerAjgnzrolON3B5qYp1uVWmvCIAXysgMkZ4vjRqDmJAHtN12q3oiZmj2Db3ezAzDa2MT7_f8UKi-x4Mm1zfhe8DT8BDdQ54Nv0G64TuNS-lGwv5DYSTU_jvzvdwJlYhSZxdEzJp0p84d-vzSO6JWIMFtNsp7ag1fnB-NKXPo1VFRDSD8WDDOvIM_k0VAJ5EldVXg1mlJig8ljx7xhXmL2kZ-6YdmUunS1gzmOeTNSy8mD7iTtjmpue5A/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . > -- Jim Hengenius Research Associate Paus Research Group CHU Sainte-Justine Research Centre My Google Calendar <http://secure-web.cisco.com/17NlTZvemZhoiUNDZxRb-sfRuh_CMF78ghWQ7Cq5D_b7ZdzW0yKM56Kt4MO0g3uqjlfdwo9AN-Dh7ts-6I_zk5BSQsUq1YA_Y8qfeCRTRg6ozeatWm-Zu4izpxfig2J22K9kE_7chFmbB90-YfzvT35t4nLe8y2seGc5IVAyKufTnfNY2NpXU29sI_VMW3pgC2aFFsLI50DFFWQ-6L8KLcnOFCUvGb9MbUBIuiLKCOm31tWnQSKV-h8mO6wEnEu3TQksPTRr5Mxwa6DnUbec6wFw6Rjv3RvjZ0eU_N1CjYO_ewi_aja_x0Q3YbMkFnHJTPfJkJv1R3ACBfLfaADSWcw/http%3A%2F%2Fwww.google.com%2Fcalendar%2Fembed%3Fsrc%3Djames.hengenius%40gmail.com>
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