External Email - Use Caution Uuummm I don’t think this would work, as a lot of our intermediate files (eg norm.mgz) are not comparable to their counterparts in the standard recon-all stream. Sorry!
-- Juan Eugenio Iglesias http://secure-web.cisco.com/1R9UOepVdGkzRhS_JbSZ7bkBYP0OujnEdjEaN6GrFG8xXfSYD4kdXxV5RSS22Efrjae1iNxYRieIPx_TYVzRGrhKR7IazpuzMz4Ym84t7daDKT2lROIZG2Ix9Ai0MCDWZBnw16XZaiV9NWdiAJEcywTAurIVkUFYUAh3Khky2RB1R2o14oO0NzRlpuI44mZpcM2bAbkTFbsInupFmBGqsCS3RpDiM9pgiOl8BTnlZa4P9JEsI7qWo6gmVLlhag_YbwWjigMA54QiSxrmN-r_iDg/http%3A%2F%2Fwww.jeiglesias.com From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgr...@mgh.harvard.edu> Date: Tuesday, June 20, 2023 at 9:32 AM To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>, Iglesias Gonzalez, Eugenio <e.igles...@ucl.ac.uk>, Gopinath, Karthik <kgopin...@mgh.harvard.edu> Subject: Re: [Freesurfer] recon-all-clinical External Email - Use Caution On 5/26/2023 5:39 PM, Andrew Dedinas Geoly wrote: External Email - Use Caution Hello Freesurfer experts! I am conducting a longitudinal GMV and CT analysis of mTBI participants who received an experimental single-dose pharmacological treatment. We collected GE Bravo (0.9mm isotropic) T1w data pre, immediately after (~ 4 days after intervention) and 1-month following the intervention. I have been working with the recon-all longitudinal pipeline stream (7.1.1) but have noticed pretty significant errors in terms of skull stripping and segmentation (participants are veterans with somewhat random lesion / atrophy patterns). I have tested your new recon-all-clinical program (7.4.0) on some of my worst cases and it is performing remarkably well. I am doing some more digging into the various synth segmentation packages available in FS newest versions and was wondering what the best course of action would be for integrating recon-all-clinical or synthseg into a longitudinal workflow. 1.Could I use the recon-all-clinical outputs as the "cross" for later base and long template construction? I don't know. Hopefully Eugenio/Karthik will weigh in 2. SynthSeg and SCLimbic seem to have very good test-retest reliability-- would it be feasible to use the independent segmentation extractions from those and bypass the longitudinal stream entirely (not saying I would want to but I am curious)? sclimbic generates segs that are not in the long stream, so there is no long option. My experience with synthseg is that it is inferior to the long stream on long data Any and all help here would be greatly appreciated, and I thank you very much for your time. Warmest regards, Andrew --- Andrew D. Geoly, MS Research Data Analyst 1 Brain Stimulation Lab Department of Psychiatry and Behavioral Sciences Stanford University School of Medicine _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1XZ5Z95aOXJ85Fce4l7oGja6HZWq5WgzorMDBXS-cV_e_hPkYHzZribEccRf4kFVcvkuE3Yo3aghyKt3TQDhyKbOKLDpnoahNz3xdL2T_6IOwha0EbvfUXPSTsHDc2epWBC7zcjBIrMhMnNMN6ITFozgZsXNrSppIPU0aOALIZpk7whwNzVHzmUd9h5_xNgz2oYiqqB02JFXqMBF51tW9OspSrPppueOoTPTHPiN8QKXSF5QQBL5CpFz5wZlZPaCOgu-o1SvRNPILCbICrzdjfw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/1MtioKA64TCULuiinjIH4QyWe2hiHaKCHzIns0CxttO-bay2yQP1b-yM33qjobcBSCOJbAn6m5bQDnHZM1XpmFJzov32JerbQUAyXpnhaYNQ7tjIf6vpxHF8VhbD1vMBnk53WlXFwCWKkfaKJuBIUzwMhCcJgBmAaFK6hx_i9R8exatmS1KgagAElywIDmtKqFE5HbZPeV_uw8CCtR4LR9qgH5-SzOCIO-uhB9lGjsEu_1bPju38goO_WMIBTYJh9EMQxYr44BcIV7tylTx3Jlw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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.
