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. LZOLLEI@mgh.harvard.edu wrote:

Hi Jim, I am sorry I missed your message. Are your questions still relevant? Apologies, Lilla

---

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of James Hengenius < james.hengenius@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_i4tucrr3... 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_gqn0jnJ... 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-Cj9C0lCW... 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-EUG15zxy... < https://secure-web.cisco.com/1wcJY3sP01uyyfd3Us2oMk9lItq4WIJ5a-x7jh-EUG15zxy... .