Unfortunately i do not think it works to pass it directly into a
longitudinal run. I tried the following, which exited with errors:
recon-all -long d256a d256_base -FLAIR path/flair.nii.gz -autorecon3
-FLAIRpial
Any suggestions?
Best,
Kasper
2016-05-13 20:01 GMT+02:00 Martin Reuter :
> Hi Kas
Hi Bruce,
Do i just download the following
Development Version
> To install the Development version of FreeSurfer, download the appropriate
> dev build.
on https://surfer.nmr.mgh.harvard.edu/fswiki/Download and install it?
Best,
Kasper
2016-05-10 14:32 GMT+02:00 Bruce Fischl :
> Hi Kasper
>
I would like to know the following:
a) what is the differences between the 3T Atlas (schwartz atlas) and the
standard atlas?
b) what does the 3T-specific NU intensity correction parameters do
differently than the standard?
Best
Kasper
2016-05-10 8:09 GMT+02:00 Kasper Jessen :
> Dear FreeSurfer
Dear FS team,
Thank you for your answers before (email: WmParc). We now realize that we've
formulated our question wrong, since our problem is mainly in creating the
wmparc.a2009s.mgz file. We ran the following command:
mri_aparc2aseg --s --labelwm --hypo-as-wm --rip-unknown --ribbon --o
mri/wm
yes, if you want to try it out. You'll need to replace it with V6 when it
is out
On Tue, 17 May 2016, Kasper Jessen wrote:
Hi Bruce,
Do i just download the following
Development Version
To install the Development version of FreeSurfer, download the
appropriate dev build.
Hi Kasper
what is the error? Can you run it as a separate step at the end (without
the -long flag)?
cheers
Bruce
On Tue, 17 May 2016, Kasper Jessen wrote:
Unfortunately i do not think it works to pass it directly into a
longitudinal run. I tried the following, which exited with errors:
reco
the schwartz atlas is built from 3T data, which has somewhat different
contrast properties due to the field-strength dependence of T1
Hopefully somone else can answer b) as I don't remember.
cheers
Bruce
On Tue, 17 May 2016, Kasper Jessen wrote:
I would like to know the following:
a) what i
Hi Kasper,
> On May 17, 2016, at 10:05 , Kasper Jessen wrote:
>
> I would like to know the following:
>
> a) what is the differences between the 3T Atlas (schwartz atlas) and the
> standard atlas?
> b) what does the 3T-specific NU intensity correction parameters do
> differently than the sta
Hi Kasper,
if I remember correctly, you need to specify it in the cross and the
long runs (see my email below). Also could be you need the dev version,
I have never tested it in 5.3.
Best, Martin
On 05/17/2016 03:54 AM, Kasper Jessen wrote:
Unfortunately i do not think it works to pass it di
Hi Doug,
Yes, you are correct- data I have previously processed without any problems is
no longer being processed.
My version of freesurfer is 5.3.0; I only downloaded it a few weeks ago so I
have not changed my freesurfer version recently.
Thanks!
Joseph Aloi
Graduate Student, MD/PhD Schola
Dear FS team,
I am trying to find the centroid using mri_surfcluster using the following
command but I am getting the same coordinate for all labels. I couldn't
quiet understand what's wrong. Your suggestion would be really appreciated.
NOTE: The coordinates differs for hemisphere.
mri_surfclus
Thanks for the answers :-)
Sebastian: What do you mean with "A somewhat wrong, but intuitive rationale
is with array coils the loops are smaller and hence the coil sensitivity
profiles as well and these modulate the intensity inhomogeneity. But again
that is probably wrong…"
What is it that is pr
Hi Kasper,
> On May 17, 2016, at 17:44 , Kasper Jessen wrote:
>
> Thanks for the answers :-)
>
> Sebastian: What do you mean with "A somewhat wrong, but intuitive rationale
> is with array coils the loops are smaller and hence the coil sensitivity
> profiles as well and these modulate the in
Dear Martin,
Thank you kindly for your prompt response.
I am actually having difficulties with the delineation of White Matter
Hyperintensities at a single time point. I apologize if my question is
redundant and perhaps an answer to it is already mentioned elsewhere.
As it stands, I am finding
Please remember to include previous correspondence otherwise we can't
keep track of the problem!
Eg, I don't have the previous email to see what the error was. Is it
possible that the disk filled up?
On 05/17/2016 09:49 AM, Aloi, Joseph wrote:
> Hi Doug,
>
> Yes, you are correct- data I have pre
Add --a2009s to your command line. Note that the colors will not differ
between the ctx and wm labels.
On 05/17/2016 07:28 AM, Caroline Beelen wrote:
>
> Dear FS team,
>
> Thank you for your answers before (email: WmParc). We now realize that
> we’ve formulated our question wrong, since our pro
Set the threshold to be something non-zero (eg, ---thmin .0001)
On 05/17/2016 10:47 AM, Nabin Koirala wrote:
> Dear FS team,
>
> I am trying to find the centroid using mri_surfcluster using the
> following command but I am getting the same coordinate for all labels.
> I couldn't quiet unders
Hi Vincent,
I tried it on my machine and it works. No segfault and the registration
looks good. Is your dev version older? I don't specifically remember
fixing anything recently, but it may be best to download a more recent
robust_register binary? It could also be that something else is
incom
Hi Navena,
I am the wrong person to answer questions about the WM lesion stream. I
think the one that is available in FreeSurfer is only based on T1
images, but a prototype of a better stream exists, that can incorporate
different modalities.
Best, Martin
P.S. Changed the subject, to reflec
Hello all,
We are analyzing data from our collaborators and are running into some
difficulties with the accuracy of the pial and wm boundaries. The wm.mgz
appears to follow the actual WM, independent of the wm surface boundary.
Attached is an example showing two types of problems.
1. the WM surface
Hi Corinna
it's hard to tell what's going on from a single slice. If you upload the
subject and tell us the specific coordinates that you see problems in we
will take a look
cheers
Bruce
On Tue, 17 May 2016, Corinna Bauer wrote:
Hello all,We are analyzing data from our collaborators and are
Hello,
I am interested in applying the Yeo 2015 cognitive atlas to structural
data. Basically, I want to quantify networks C1-12 in my structural data by
exporting the voxel size of each network for each subject into an text file
(so I would have left and right hemisphere voxel totals for networks
Postdoctoral research associate positions are available in the Department
of Radiology and Biomedical Research Imaging Center (BRIC) at the
University of North Carolina at Chapel Hill (UNC-Chapel Hill). Our current
focuses are to better understand the dynamic and critical early brain
development in
Hi Gaurang
what volume are you editing? You should be editing the wm.mgz.
cheers
Bruce
On Tue, 17
May 2016, Limachia, Gaurang (NIH/NINDS) [F] wrote:
This is how the white matter changes look like after making corrections and
running recon all.
From: "Limachia , Gaurang (NIH/NINDS) [F]"
I edited the white matter, and then ran recon-all command. The image I
included shows that the white matter changes, but the contour lines have
not changed. Subsequently, how do I change the contour lines to reflect
the changes I made to the white matter. Additionally, is changing the
control point
Hi Gaurang
it looks like you edited the white matter, but not in the wm.mgz, which
is what we require. What volume (i.e. what was the name of the file you
loaded) did you edit?
cheers
Bruce
On Tue, 17 May 2016, Limachia, Gaurang (NIH/NINDS) [F]
wrote:
I edited the white matter, and then r
Dr. Fischl,
I loaded the t1 file from our patient dataset freesurfer>t1>mri>wm.mgz.
When I was editing the white matter, I had the wm highlighted, and not
brainmask under the volumes.
Best,
Gaurang
On 5/17/16, 5:56 PM, "Bruce Fischl" wrote:
>Hi Gaurang
>
>it looks like you edited the white mat
Hi Josh,
Thanks for your interest. The networks are in MNI152 space. My
understanding is that you want to map the networks onto the structural
T1 data of your subjects. Here's my suggestion on how to do it:
1) Assuming you are quite happy with the freesurfer recon-all of your
individual subjects,
Hi Doug,
Sorry- I've added entire correspondence onto the end of this e-mail. I don't
think the disk filled up as I am on a 3 TB hard drive and I still have ~2 TB of
free space on my disk. Anything else you think it could be?
Thanks!
Joseph Aloi
Please remember to include previous c
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