I've found the article "Within-subject template estimation for unbiased
longitudinal image analysis" by Reuter et al. It only examines a limited
number of structures for the reproducibility of longitudinal Freesurfer.
Are there any other paper that examines the cerebellum as well? Any
suggestion fr
Hello Gabor,
a few quick comments:
i) Although we typically aim for maximizing both, accuracy and
reproducibility are different things. In a longitudinal study you are
often particularly interested in the reproducibility of the findings, in
the sense of their repeatability across different ti
sorry, I don't remember this case. please repost with our previous
correspondence included
On 12/12/16 5:40 PM, Dowling, Kevin Francis wrote:
Hi Doug,
Thank you for your note and my apologies for a delayed response. To
create the sig.mgh file we used a volume specific mri_glmfit analysis,
o
To get the t-score, compute the square root of the F, like
fscalc F.mgh sqrt -o t.mgh
You can then get the clusters with
mri_surfcluster --in t.mgh --thmin t-threshold --sign sign --no-adjust
--sum sumfile --ocn ocn.mgh
ocn (output cluster number) will be a map with the custer number as the
here you go ...
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_apply_reg
On 12/9/16 4:01 PM, Matthew Defenderfer wrote:
Hi All,
I am trying to mirror labels across hemispheres and found various
threads using mris_apply_reg. Unfortunately the version of that
command I have does not rec
Hi Freesurfer experts,
I am new to freesurfer. I installed the last freesurfer version
(freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) and I am trying to compute
the shortest cortical path between two sets of vertices.
1- Using the command mris_pmake updated
If I understand correctly ac
Yes. I immediately tried to enter the command in manually, checked the
paths, and looked at the command manual for any format errors.
[ksd770@katelinux Temple_Tracula]$ xfmrot
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.ecclog
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bve
Ok, if you also send me the first file,
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.ecclog, I'll see if I
can replicate the error.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine Damme
[
On Tue, Dec 13, 2016 at 8:34 AM, Yendiki, Anastasia <
ayend...@mgh.harvard.edu> wrote:
> Ok, if you also send me the first file, /media/Data/Temple/Temple_
> Tracula/31313422_10128/dmri/dwi.ecclog, I'll see if I can replicate the
> error.
>
> --
> *From:* freesurfer-bou
Dear experts
I am trying to compute the local gyrification index but I am not sure how I
have to do the following:
"You will also need $FREESURFER_HOME/matlab in your matlab path set up in your
~/matlab/starup.m script."
Can you please quickly help me what I need to type in the terminal to do
The LGI routines run matlab (even though you never actually run any
matlab commands yourself). But you have to make sure that matlab knows
where the LGI matlab routines are. To do this you must modify your
matlab ~/matlab/startup.m file to add the path to the LGI routines to
your path. To do th
Many thanks for your help. According to your suggestion, I modified the
start.up file in Users/andre/matlab/startup.m (see attached).
However, I got the following error:
Andres-MacBook-Pro:~ andre$ export FREESURFER_HOME=/Applications/freesurfer
Andres-MacBook-Pro:~ andre$ source $FREESURFER_HOM
Dear Freesurfers,
Could anyone tell me what the white.H and white.K measures in Qdec are?
Thank you so much!
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The information in thi
white.H is the mean curvature of the ?h.white surface and white.K is the
Gaussian curvature
cheers
Bruce
On Tue, 13 Dec 2016, tom parker wrote:
> Dear Freesurfers,
>
> Could anyone tell me what the white.H and white.K measures in Qdec are?
>
> Thank you so much!
>
>
__
I believe they are mean and Gaussian curvature respectively.
Cheers,
Kevin Aquino
> On 13 Dec 2016, at 17:23, tom parker wrote:
>
> Dear Freesurfers,
>
> Could anyone tell me what the white.H and white.K measures in Qdec are?
>
> Thank you so much!
> __
Hi Freesurfer's experts
Is there an easy way to create automatically a circular label with a radius
centered on a vertex with predifined RAS/Tailarach coordinates on the fsaverage
surface?
Thanks
Cris
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Freesurfer mailing list
Freesurfer@nmr.mgh.ha
Not that easy. I would do it by selecting a vertex that is close to the
coordinate you want, then
1. Create a surface overlay with all vertices = 0 except your chosen vertex
mri_volsynth --template $FREESURFER_HOME/fsaverage/surf/lh.thickness
--delta vertexno 0 0 0 --o delta.mgh
2. Smooth
Is matlab in your linux path? On my mac, I had to add this path to my
linux path: /Applications/MATLAB_R2011b.app/bin/matlab
On 12/13/16 11:16 AM, André Schmidt wrote:
Many thanks for your help. According to your suggestion, I modified
the start.up file in Users/andre/matlab/startup.m (see at
Does this cover your situation?
https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V
On 12/9/16 9:54 AM, Emmanuel Nwosu wrote:
Hi All
Am not sure if I can do this in mri glmfit
I want to investigate the relationship between cortical thickness and
a continuous variable (A) while accounting fo
You will need a registration between the space where the ROIs are and
the anatomical. We usually do this with bbregister, but you will need to
identify a volume that is in the ROI space that has anatomical contrast
so that the registration can be done (ie, dont use the ROI mask for
registration
1) Don't use DOSS in QDEC as it sometimes generates the wrong results.
2) Yes
On 12/7/16 11:50 PM, Rodrigo Gonzalez Huerta wrote:
Hey Doug,
First, thanks for your previous answer, it helped me to clarify some
issues. Lately, I’ve been doing what you suggested. But something just
caught m
Dear FS Wiki
I run my scan in FS without any problem
example:
#@#%# recon-all-run-time-hours 8.342
recon-all -s 877 finished without error
then I do some edits to the aseg in freeview
edits include: relabelling correctly lateral ventricles voxels mostly in the
posterior horn of the lateral
Hi Katherine - Can you please use the attached version and tell me if it works?
You'll have to copy it into $FREESURFER_HOME/bin, to overwrite the version of
xfmrot that you have now. If it works, we'll include it in the next version.
Thanks!
a.y
From: freesurf
Postdoctoral Scientist - Neurocardiovascular Disease and Depression
*THE POSITION:*
Interested postdoctoral applicants will be joining a dynamic and highly
successful collaborative research program aimed at applying cutting edge
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