External Email - Use Caution Thanks for sharing, Mark. One little comment: when you resample the posteriors (which are soft segmentations), why not using linear interpolation? By doing so, you ensure that the sum of the posteriors at a given voxel is still 1 (as it should). Cheers, /Eugenio
-- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Mark Wagshul <mark.wags...@einstein.yu.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Monday, 7 May 2018 at 22:58 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Extracting DTI/NODDI data from hippocampal subfields External Email - Use Caution Eugenio, Not sure if there is any interest in this, but here is our code for converting the data into T1 NIFTI space. Thanks for the help, Mark ____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wags...@einstein.yu.edu<mailto:mark.wags...@einstein.yu.edu> [instein-logo-rgb] This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately. From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Iglesias Gonzalez, Eugenio Sent: Friday, May 4, 2018 2:44 AM To: Freesurfer support list; Freesurfer support list Subject: Re: [Freesurfer] Extracting DTI/NODDI data from hippocampal subfields External Email - Use Caution Hi again, You pick the most probable label at each voxel. In a binary segmentation problem, that amounts to thresholding at 50%. By with more labels, it does not, eg if p(a)=p.4, p(b)=0.3 and p(c)=0.3, you pick a even though p(a)<0.5. Cheers E Sent from my phone, please excuse brevity and typos ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Mark Wagshul <mark.wags...@einstein.yu.edu> Sent: Friday, May 4, 2018 12:24:36 AM To: Freesurfer support list Subject: Re: [Freesurfer] Extracting DTI/NODDI data from hippocampal subfields External Email - Use Caution Eugenio, Yes, we are on the same page, thank you so much for the advice. One followup question - is the threshold on the binary masks 50%? Mark _______________________ Mark Wagshul, PhD Albert Einstein College of Medicine Bronx, NY Sent from my iPhone > On May 3, 2018, at 3:47 AM, Iglesias Gonzalez, Eugenio <e.igles...@ucl.ac.uk> > wrote: > > Eugenio _______________________________________________ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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