Yes, same thing!
On Wed, 27 Jul 2016, Harms, Michael wrote:
Thanks for clarifying. Is the same true for the --pthr option of
dmri_pathstats as well?
i.e., --pthr is specifying the portion of the 99th percentile, not the
strict maximum?
thx,
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO 63110Email: mha...@wustl.edu
On 7/26/16, 11:40 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
ayend...@nmr.mgh.harvard.edu> wrote:
Hi Dillan - Thank you for your support!
Because the maximum value can sometimes be an outlier, we use the values
of the 99th percentile instead. In the absence of an outlier this would be
very close to the maximum.
Best,
a.y
On Tue, 26 Jul 2016, Newbold, Dillan wrote:
Hi everyone,
I’m having a little trouble understanding the exact meaning of the 20%
default threshold used in the freeview -tv option and dmri_pathstats
--pthr. I’ve seen multiple threads where Anastasia said that it is 20% of
the maximum value in the probability distribution—which corresponds to
the maximum number of sample paths intersecting a single voxel—but the
default thresholds I’ve seen set by the -tv option are generally lower
than that. For example, I have one subject in whom the right CST has a
maximum value in its path.pd.nii.gz file of 300. I would expect based on
what I’ve read in the mail archives that the threshold would be set at
60, but when I open the merged file with the -tv option the default
threshold for the right CST is 35.
My current best guess is that the default threshold is set to produce a
volume that has a probability sum equal to 20% of the sum of the
pre-threshold volume. (That is, the sum of intensities of all voxels in
the path.pd.nii.gz file should be 5 times the sum of the voxels above the
default threshold.) Is that accurate?
Thanks for all you’ve done to develop this tool. It’s brilliant and I
want to understand as much of it as I can.
-Dillan
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
________________________________
The materials in this message are private and may contain Protected Healthcare
Information or other information of a sensitive nature. If you are not the
intended recipient, be advised that any unauthorized use, disclosure, copying
or the taking of any action in reliance on the contents of this information is
strictly prohibited. If you have received this email in error, please
immediately notify the sender via telephone or return mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
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.
