Hi Jim,
I am sorry I missed your message. Are your questions still relevant?
Apologies, Lilla
________________________________
From: [email protected]
<[email protected]> on behalf of James Hengenius
<[email protected]>
Sent: Friday, December 13, 2024 2:49 PM
To: Freesurfer support list <[email protected]>
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://www.nature.com/articles/s41596-023-00806-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://www.sciencedirect.com/science/article/pii/S1053811920304328<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
[email protected]
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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://www.massgeneralbrigham.org/complianceline
<https://www.massgeneralbrigham.org/complianceline> .
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.
