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Hi FreeSurfer experts,
I have recently been wondering about the correct unit for curvature and local
gyrification index.
For curvature I find inconsistent information like:
mm^-2 (https://onlinelibrary.wiley.com/doi/epdf/10.1002/ima.20138, page 47),
It has not changed (and is no longer supported)
On 11/19/19 6:48 AM, Steve Petersen wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer experts,
>
> What freesurfer version do you recommend to perform the local
> gyrification index, version 6 or 6 development version?
>
>
> Thanks
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Dear Freesurfer experts,
What freesurfer version do you recommend to perform the local gyrification
index, version 6 or 6 development version?
Thanks in advance.
Best regards,
___
Freesurfer mailing list
F
Sorry, the person who used to support the gyrification software has left.
You're kind of on your own unfortunately.
On 10/11/2019 6:04 AM, LOSKE, PHILIPP (PGR) wrote:
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Hello FreeSurfer Team,
I am trying to compute the local Gyrification index on my subjects
External Email - Use Caution
Hello FreeSurfer Team,
I am trying to compute the local Gyrification index on my subjects with
recon-all -s -localGI. Running this under FS 6.0 runs without errors,
with FS 5.3. I get:
mesh_outer =
struct with fields:
vertices: [68598x
On 02/21/2018 11:47 AM, C.P.E. Rollins wrote:
> Dear Freesurfer Developers,
>
> I'm following the very well-documented steps proposed by Marie Schaer
> for measuring local gyrification index in the paper "How to Measure
> Cortical Folding from MR Images: a Step-by-Step Tutorial to Compute
> Local
Dear Freesurfer Developers,
I'm following the very well-documented steps proposed by Marie Schaer
for measuring local gyrification index in the paper "How to Measure
Cortical Folding from MR Images: a Step-by-Step Tutorial to Compute
Local Gyrification Index"
(https://www.ncbi.nlm.nih.gov/pmc/
Hi:
To compute local Gyrification Index is necessary Matlab... Complete
installation or only runtime?
Sincerely,
Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of Radiology
Clínica las Condes
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
C
Don't know what you mean by "extract lGI values from surface data" if
not using mri_segstats as we've discussed. I think you can do the
comparison you want in the GLM using a "two group" analysis where one
group only has one subject.
On 11/09/2017 01:46 AM, Buse Merve Ürgen wrote:
> Thank you
Thank you so much! Can I also learn whether running vertex-wise analysis
without GLM analysis in Qdec is possible or not? As I said, I will compare a
single patient with a group of healthy controls, so GLM would not work. What
would you suggest for this? Is it possible to extract lGI values from
Intensity Mean will be the mean value of the input (lGI) averaged over
the ROI.
STD, Max, Min, and Range are the intensity stddev maximimum mininum
andrange=max-min over the ROI
On 11/07/2017 12:57 PM, Buse Merve Ürgen wrote:
> Dear Freesurfers,
>
> I have two questions:
>
> 1) In the last sta
Dear Freesurfers,
I have two questions:
1) In the last stage of the recon-all -s -localGI analysis, local
gyrification index values are calculated at each pial vertices. Is there
any way (command?) to extract *vertex-wise local gyrification index values*
(of individual subjects) *before running
Dear Freesurfer developers,
I would like to run Local Gyrification Index analysis for a group of
healthy controls and a single patient. After running recon-all -s
-localGI command, we get lh.pial_lgi and rh.pial_lgi surf files. In the
last stage of this analysis, local gyrification index values
The problem is that your variable is always0 for the HC group. This
creates a regressors of all 0s when using DODS. One way around this is
to use DOSS (--fsgd your.fsgd doss) and change the contrast matrix. This
may not be the model you want (it will assume that the change due to
Antipsychotic
Hello FreeSurfer Group
I would like to make a two group comparison controlling for both gender and
medication status. The only way that I have sorted out doing this is to
make eight groups (ClinicalGroup x Sex x Meds) but I get an error that my
design is poorly scaled:
--
Hello,
I am trying to obtain estimates for the local gyrification index (LGI) using
Freesurfer. I have tried to compute LGI via two different commands...
"mris_compute_lgi --i lh.pial" and " recon-all -lgi -s subjectName." Both of
these return the same error after running for a while...
..
Hi
I would like to analyse local gyrification data for a number of brains in
Matlab. I have ran the command
mris_compute_lgi -i lh.pial
which results in a file called lh.pial_lgi. However, I was expecting an output
of the form lh.pial_lgi.mat which could be immediately read into Matlab. Do you
Dear Nathan,
There are usually 2 workarounds with this error: the first option is
simply to try to rerun the lgi for this surface, you may have a little
chance that it works fine until the end, which will solve your
problem. If not, the second option is to recreate the problematic
surface
Hi All,
I'm running the lGI script on my subjects, and recently received this error:
... remeasuring lGI value for vertex iV = 64101. It may take a few minutes.
WARNING -- Problem for vertex iV = 64101, lGI value is aberrantly high
(lGI=59.4571)...
...lGI computation will be stopped. This may be
Hi Holly,
Can you please try to launch it on the fsaverage subject that you have
downloaded with the distribution? Just to see if you get the same
error, because I don't seem to get an error neither with fsaverage nor
with the average subject I just created.
Marie
On 20 août 09, at 15:
We are trying to compute a pial_lgi surface for an average brain.
When we run mris_compute_lgi, we get this error at the mris_fill
stage:
conforming output volume
setting resolution for intermediate calculations to 1.
reading surface from lh.pial...
reading group avg surface area 1015
Dear Freesurfer's users,
Just a small e-mail to announce the availability of a new feature for
quantifying cortical morphology in the latest Freesurfer release. It
is called local Gyrification Index (lGI) and is derived from the
surface-based Gyrification Index which was traditionally meas
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