Thanks a lot!
Just want to make sure that the “RAS”(FS cords?) and “MNI Talairach” is the
MNI305 coords.
发件人: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] 代表 Douglas Greve
发送时间: 2016年8月30日 21:21
收件人: freesurfer@nmr.mgh.harvard.edu
主题: Re: [Freesurf
Hi Matt
I don't think that counts as a methods paper for the T2-based
deformation. There is no validation or comparison with other methods in
it, and really not enough detail to replicate what we did.
cheers
Bruce
On Tue, 30 Aug
2016, Matt Glasser wrote:
Sure there¹s a publication. See F
Sure there¹s a publication. See Figure 14:
http://www.sciencedirect.com/science/article/pii/S1053811913005053
Peace,
Matt.
On 8/30/16, 10:21 AM, "Bruce Fischl"
wrote:
>Hi Don
>
>the T2 or FLAIR helps us avoid dura. It is still a beta version though as
>we don't have a ton of experience with
Hi,
I am trying to computer the changes of cortical parcellations and fiber
pathways using FreeSurfer v5.3 and Tracula (2014/05/26 update) . I
copied the anatomical and DWI images from the same scan session into
five directories. Run recon-all and trac-all on the 5 same data sets, in
order to
Hi Renata,
In general, mixing’n’matching is not a good idea, since different sequences
bias the volumes in different directions. Now, if the differences in sequences
were independent of whether subjects are patients or controls, it wouldn’t be
*that* bad. But, if patients have different sequence
Hi Mohamad,
For now, our brainstem module separates this structure into midbrain, pons,
medulla and SCP - please see this link:
https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures
If you want to segment more specific nuclei, we don’t have a tool capable of
doing that yet.
Cheers,
/Eu
Hi Iglesias,
Kindly, we would like to know if there are any methods in Freesurfer that can
help to segment that brain stem nucleus. I mean output the nucleus
automatically as a small masks, so these small masks can be used in other
analyses (e.g. fMRI)
I am thinking of creating masks for these
Dear Eugenio,
I have a couple of questions regarding the hippocampus subfields
segmentation on the dev FS 6.0 which I hope you could help me with.
We are comparing the volumes of hippocampal subregions of patients and
controls, and we would like to be as consistent as possible with the input
so t
Greetings,
I want to design a matrix that contains 3 fixed factors. The first is
diagnosis (3 levels), the second is gender (2 levels), and the last is
imaging site (2 levels). However, the thing is that the imaging site factor
only applies to only one level of the diagnosis factor (i.e. patients
Hi Eelco
we've made a bunch of improvements in the T2/FLAIR stream since 5.3 so you
might check them out. Unfortunately I don't think they will be officially
supported in 6.0 as we just don't have the resources to include it in our
unit/system/regression test cycle.
cheers
Bruce
On Tue, 3
Hi Vasudev
probably not. What resolution are they? They are likely to be too low
resolution to be useful and also quite significantly distorted w.r.t. the
T1s. You can try it if you like, but my guess is it will hurt more than it
helps
sorry
Bruce
On Tue, 30 Aug 2016, Dev vasu wrote:
Dea
Hi Don
the T2 or FLAIR helps us avoid dura. It is still a beta version though as
we don't have a ton of experience with it, and no, there is no reference
for it yet (or maybe ever) :)
Bruce
On Tue, 30 Aug 2016, Krieger, Donald N. wrote:
Dear list:
What are the advantages of including
Dear sir,
I was checking for your reply about my question in Freesurfer Forum but
unfortunately i could not your answer although ":Freesurfer Digest, Vol
150, Issue 43 " Today's topics section indicates that you have replied to
my question.
Following is my question :
In order to run my structur
FWIW, we’ve had good success with including the T2w scan as part of the FS 5.3-HCP release.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University S
Sure, any simulation can’t be exhaustive, but my understanding, chatting
with Anderson, is that their 2014 paper simulated a quite large space of
designs and Freedman-Lane is appropriate for the vast majority of the GLMs
that we would encounter in neuroimaging.
Also, again per Anderson, I believe
Hi all,
In the presence of nuisance (orthogonal or not) the permutation test is
only approximate, whatever is the method used. Regressing out the nuisance
introduces dependencies between the residuals that render them strictly not
exchangeable. However, in practice this is not an issue, and the FL
What is paraview? I would contact the developers.
On 8/30/16 10:24 AM, Islem Rekik wrote:
Hi all,
I have a similar problem using Paraview:
When I visualize the surface lh.pial and the anatomical image
brainmask.mgz using FreeView they nicely overlap; however, after I
convert lh.pial to lh.pi
Thank you - very helpful.
Best - Don
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
Sent: Tuesday, August 30, 2016 10:23 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] inclusion of both T1 and T2 in a recon
Hi all,
I have a similar problem using Paraview:
When I visualize the surface lh.pial and the anatomical image brainmask.mgz
using FreeView they nicely overlap; however, after I convert lh.pial to
lh.pial.vtk and brainmask*.mgz* to brainmask*.mha* and visualize them using
Paraview, they are in dif
ps. The 5.3 version is pretty buggy, so I'd wait until 6.0 to test it out
On 8/30/16 10:12 AM, Krieger, Donald N. wrote:
Dear list:
What are the advantages of including a T2 scan when running recon-all
–all ?
Which results can it effect and to what extent?
And how sensitive is freesurfer
Hi Don,
the T2 stream is a work-in-progress, so we don't have a lot of these
answers. In theory, a T2 will allow better placement of the pial surface
allowing it to better exclude dura. No publication on this yet.
doug
On 8/30/16 10:12 AM, Krieger, Donald N. wrote:
Dear list:
What are t
Dear list:
What are the advantages of including a T2 scan when running recon-all -all ?
Which results can it effect and to what extent?
And how sensitive is freesurfer to artifacts in the T2 scan?
Is there a good reference for this/
Thanks and best - Don
You don't need T2w to run FreeSurfer/recon-all. There is an option to
add a T2, but it is not necessary. In any event, you will not be able to
use an fMRI scan for this purpose.
On 8/30/16 7:50 AM, Dev vasu wrote:
Dear Sir,
In order to run my structural analysis pipeline , i require T2w
im
By "wrong" I meant that permutation no longer gives exact p-values in
expectation with non-orthogonal designs. There is no theory to
characterize the accuracy of Freeman-Lane of the other methods. In this
sense, they are not approximations but ad hoc methods that people hope
do a better job t
Hi Woo-Suk
Just adding to Bruce's reply: area isn't a "technically more noisy and
usually thus less sensitive" as the reviewer suggests. Area isn't noisier
on its own right, and it's measured from the very same surfaces from which
thickness is measured. However, there is a much larger variability
tksurfer always uses the ?h.orig coordinates. Also keep in mind that the
vertex index is 0-based whereas matlab is 1-based. When you click on a
point, you should see something like the following print out
selected vertex 123491 out of 163842
current -39.11 15.65 11.26
orig -55.67 -10.37
Dear Sir,
In order to run my structural analysis pipeline , i require T2w images,
but unfortunately we have not performed T2w scans , my colleague suggests
we can use rfMRI instead T2w images Could you please let me know if i can
use rfMRI image instead of T2w image?.
Thanks
Vasudev
___
Dear Experts,
I tried to extract vertex coordinates information from
'fsaverage/surf/lh.pial' file using matlab function 'read_surf', but I found
that the coordinates returned by the function are different from what I saw
in tksurfer, here are the screenshots:
The vertex index starts from 0 in
28 matches
Mail list logo
