Dear Freesurfers,
I have come across a problem with viewing the significant clusters on qdec
display tab.
When a particular query is selected after analyzing for a selected design
there are multiple clusters of varying size which appear. This query when
run (corrected) with Monte carlo simulation
Hi all,
I used FDR correction method to correct for multiple comparison after
mri_glmfit. And I have a cluster covering multiple regions. I want to extract
the thickness, surface area, lgi values for local maxima (or, multiple regions
covered by the big significant cluster). I see it is not stra
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Hi - If I would like to try to perform mass-univariate statistics at the vertex
level (thickness, area, vol at each vertex) without using the mri_glmfit, is
this order a sound step (in general) for mapping stats parameter of choice
(p-val or t s or weights for example) to the surface?
1. Use
Hello,
I have created my own subcortical ROI in freesurfer (saved as .label file), and
am trying to generate an intensity stats file for this ROI. Reading the mailing
list, I think that the best way to do this is to:
1) mri_label2vol to convert my ROI to a volume file
2) mri_label_volume to ge
Hi Sabrina
if you have drawn the label in freeview you can use mri_label_vals to
generate a file of the value of each voxel in the label in whatever
volume you specify. You can then do whatever you want with them (e.g. fit
a Gaussian to it, etc...)
Bruce
On Tue, 24 May 2016, Sabrina Yu wrote
Freesurfer Support,
I'd like to create a design matrix for a group analysis outside of the DODS
and DOSS models. I understand that in order to do this the -X flag must be
used. However, I have been unable to find examples of how to do this.
I am hoping to reveal a difference in thickness or gyrif
Dear Han,
if controls have only 1 time point, you cannot compare/analyse any
measurement of change across the groups (such as atrophy rates). You can
only do a cross sectional analysis at baseline.
For patients you could separately look at atrophy rates (if they differ
from zero, which should
Hi Doug, I¹m curious why the newer mris_preproc does not use sphere.reg as
the default srcsurfreg when the target is not fsaverage - see below
Thanks for any info! (not urgent)
On 2016-5-24, 11:30, "Z K" wrote:
>Good question, and I dont know the answer. mris_preproc is Dougs baby so
>I sugges
Hi Yoonho,
the steps look good. Take a look at
https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels
which basically describes exactly these steps for the case of linear
mixed effects models. Note that we have dedicated code for that as part
of FreeSurfer (see also the references e
Dear All,
I want to segment white matter into 131xx and 141xx label series. I used
aparc.a2009s but it just gave me cortex labels (111xx and 121xx). Can anyone
guide me how could I do this?
Regards,
Fari
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That looks fine. If you are going to use the monte carlo sim, then
you'll need an estimate of the FWHM. In mri_glmfit, we get that by
running mris_fwhm on the residuals. So, assuming that your analysis has
residuals, then you should save those out too.
On 05/24/2016 01:55 PM, Chung, Yoonho wrot
You'll need a regressor for each of the 8 classes you describe below.
You can use mri_glmfit to generate this (Xg.dat file)
You'll need two more regressors for age, one for each diagnosis. If a
subject (ie, row) is a control then the two values will be AGE 0. If the
subject of the row is a pati
see
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg47157.html
On 05/24/2016 05:44 PM, Mahmoudi, Fariborz wrote:
>
> Dear All,
>
> I want to segment white matter into 131xx and 141xx label series. I
> used aparc.a2009s but it just gave me cortex labels (111xx and 121xx).
> Can
Dear Douglas N Greve,
Today, I tested the previous group analysis on other computer, and saw the
same error massage.
I attached the tested fsgd and mtx files.
command:
mri_glmfit --y 052416_lh.Pa_Co_G2V2_dods_sm15.mgh --fsgd
052416_PA_CO_G2V2.fsgd dods --glmdir 052416_lh.Pa_Co_G2V2_dods_sm15.glm
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