Hi, I've just started using the newest freesurfer v 5.3 and I've noticed in the labels folder that every .label has a thresh.label. When overlaying the two, they can be quite different (for example MT.label is much larger than MT.thresh.label) or quite similar (V1.label is just a tiny bit larger than V1.thresh.label). What is the difference between the two and which is best to use?
Thanks! Krista
Hi Krista
the unthresholded labels give every point that has a non-zero probability of being in the label, no matter how unlikely. The .thresh ones are thresholded to pick the most likely vertices that give a label that is the right surface area.
cheers Bruce On Sun, 17 Nov 2013, krista kelly wrote:
Hi, I've just started using the newest freesurfer v 5.3 and I've noticed in the labels folder that every .label has a thresh.label. When overlaying the two, they can be quite different (for example MT.label is much larger than MT.thresh.label) or quite similar (V1.label is just a tiny bit larger than V1.thresh.label). What is the difference between the two and which is best to use? Thanks! Krista
Great thanks Bruce! I'm assuming then that using the thresh.label is the best choice.
On Sun, Nov 17, 2013 at 12:50 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Krista
the unthresholded labels give every point that has a non-zero probability of being in the label, no matter how unlikely. The .thresh ones are thresholded to pick the most likely vertices that give a label that is the right surface area.
cheers Bruce
On Sun, 17 Nov 2013, krista kelly wrote:
Hi, I've just started using the newest freesurfer v 5.3 and I've noticed
in the labels folder that every .label has a thresh.label. When overlaying the two, they can be quite different (for example MT.label is much larger than MT.thresh.label) or quite similar (V1.label is just a tiny bit larger than V1.thresh.label). What is the difference between the two and which is best to use? Thanks! Krista
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.
for most purposes, yes Bruce On Sun, 17 Nov 2013, krista kelly wrote:
Great thanks Bruce! I'm assuming then that using the thresh.label is the best choice.
On Sun, Nov 17, 2013 at 12:50 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Krista
the unthresholded labels give every point that has a non-zero probability of being in the label, no matter how unlikely. The .thresh ones are thresholded to pick the most likely vertices that give a label that is the right surface area. cheers Bruce On Sun, 17 Nov 2013, krista kelly wrote: Hi, I've just started using the newest freesurfer v 5.3 and I've noticed in the labels folder that every .label has a thresh.label. When overlaying the two, they can be quite different (for example MT.label is much larger than MT.thresh.label) or quite similar (V1.label is just a tiny bit larger than V1.thresh.label). What is the difference between the two and which is best to use? Thanks! KristaThe 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.
Ok perfect. Just one last question, how would I use the thresholded option for the annotations (i.e. aparc.DKTatlas40.annot, aparc2009s.annot) when doing whole brain analyses?
Thanks!
On Sun, Nov 17, 2013 at 1:20 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
for most purposes, yes
Bruce On Sun, 17 Nov 2013, krista kelly wrote:
Great thanks Bruce! I'm assuming then that using the thresh.label is the
best choice.
On Sun, Nov 17, 2013 at 12:50 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: Hi Krista
the unthresholded labels give every point that has a non-zero probability of being in the label, no matter how unlikely. The .thresh ones are thresholded to pick the most likely vertices that give a label that is the right surface area. cheers Bruce On Sun, 17 Nov 2013, krista kelly wrote: Hi, I've just started using the newest freesurfer v 5.3 and I've noticed in the labels folder that every .label has a thresh.label. When overlaying the two, they can be quite different (for example MT.label is much larger than MT.thresh.label) or quite similar (V1.label is just a tiny bit larger than V1.thresh.label). What is the difference between the two and which is best to use? Thanks! KristaThe 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.
no, those are whole-brain parcellations so ever vertex is already assigned the most likely label for it
cheers Bruce On Sun, 17 Nov 2013, krista kelly wrote:
Ok perfect. Just one last question, how would I use the thresholded option for the annotations (i.e. aparc.DKTatlas40.annot, aparc2009s.annot) when doing whole brain analyses? Thanks!
On Sun, Nov 17, 2013 at 1:20 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: for most purposes, yes Bruce On Sun, 17 Nov 2013, krista kelly wrote:
Great thanks Bruce! I'm assuming then that using the thresh.label is the best choice. On Sun, Nov 17, 2013 at 12:50 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Krista the unthresholded labels give every point that has a non-zero probability of being in the label, no matter how unlikely. The .thresh ones are thresholded to pick the most likely vertices that give a label that is the right surface area. cheers Bruce On Sun, 17 Nov 2013, krista kelly wrote: Hi, I've just started using the newest freesurfer v 5.3 and I've noticed in the labels folder that every .label has a thresh.label. When overlaying the two, they can be quite different (for example MT.label is much larger than MT.thresh.label) or quite similar (V1.label is just a tiny bit larger than V1.thresh.label). What is the difference between the two and which is best to use? Thanks! Krista 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.
Ok great! Thanks for the quick responses, and for your help.
Best, Krista
On Sun, Nov 17, 2013 at 1:26 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
no, those are whole-brain parcellations so ever vertex is already assigned the most likely label for it
cheers Bruce On Sun, 17 Nov 2013, krista kelly wrote:
Ok perfect. Just one last question, how would I use the thresholded option
for the annotations (i.e. aparc.DKTatlas40.annot, aparc2009s.annot) when doing whole brain analyses? Thanks!
On Sun, Nov 17, 2013 at 1:20 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote: for most purposes, yes Bruce On Sun, 17 Nov 2013, krista kelly wrote:
Great thanks Bruce! I'm assuming then that using the thresh.label is the best choice. On Sun, Nov 17, 2013 at 12:50 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Krista the unthresholded labels give every point that has a non-zero probability of being in the label, no matter how unlikely. The .thresh ones are thresholded to pick the most likely vertices that give a label that is the right surface area. cheers Bruce On Sun, 17 Nov 2013, krista kelly wrote: Hi, I've just started using the newest freesurfer v 5.3 and I've noticed in the labels folder that every .label has a thresh.label. When overlaying the two, they can be quite different (for example MT.label is much larger than MT.thresh.label) or quite similar (V1.label is just a tiny bit larger than V1.thresh.label). What is the difference between the two and which is best to use? Thanks! Krista 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.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
krista kelly