Hi Freesurfer users!
We are performing such analysis on Matlab using cartesian coordinates of
the control points for the study of cortical thickness.
We have some problems to exactly localize control points from matlab
viewing to freview or tkmedit: if the localization in Matlab is fine, in
freevie
Hello everyone,
I've got some problems with qdec. I have .levels with more than 2 factors. For
example a "grpe.levels" with three factors : children (enfant), adults
(adultes) and nothing (rien). But if I want to exclude some subjects like
children qdec doesn't work anymore (attachmen
Hi,
I have some mesh and label files I would like to use with my Freesurfer data
however they are in an alternative format (connectome workbench).
I would like to get the labels into the space of a typical Freesurfer subject
(e.g. fsaverage), followed by pushing the labels to subject native spa
Hi Maryam
I'm looking at it now - it's very noisy and has a huge I/S bias field
(brainstem WM is almost twice as bright as superior WM). Can you send me
the coords of the crossing and also tell me something about the
acquisition (coil, sequence, field-strength)?
cheers
Bruce
On
Tue, 8 Ma
Hi Andrea
our coordinate systems are documented here:
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
the control points are stored in RAS (either "surface ras" or "scanner ras"
depending on the header). By default it is "surface ras" (if not otherwise
specified at the top of the
Hi David
I'm pretty sure that the Wash U HCP group has sorted this out. Have you
asked them?
cheers
Bruce
On Tue, 8 Mar 2016, Slater David wrote:
Hi,
I have some mesh and label files I would like to use with my Freesurfer data
however they are in an alternative format (connectome work
It is the case for qdec that a factor cannot have more than two levels.
You'll have to use the "command line" stream, creating an FSGD file,
running mris_preproc, mri_surf2surf, mri_glmfit, and mri_glmfit-sim. See
the wiki
On 03/08/2016 05:29 AM, Lisa Delalande wrote:
> Hello everyone,
>
> I've
Dear. Freesurfer experts.
Hi.
I'm using freesurfer version 5.3.0.
I tried:
mkanalysis-sess -analysis retino -TR 2 -paradigm para.para -event-related
-funcstem fmc -nconditions 4 -timewindow 34 -inorm -gammafit 2.25 1.25
-polyfit 2 -mcextreg -force -fsd bold_retino -per-run -native -refeventdur
Dear. Experts.
I appreciate your help in advance.
I also tried:
selxavg3-sess -s $SUBJECT -analysis retino -df sessdirfile
Then I
got the error:
-
selxavg3-sess logfile is
/home/jbang/Projects/replay/log/log/selxavg3-sess-bold_retino-
Dear Douglas,
My command lines were, e.g. right thickness and right white surface (using
the same ad_hv.fsgd and group_diff.mtx files in the command lines):
ad_hv.fsgd
GroupDescriptorFile 1
Title AD_HV_GroupAnalysis
Class AD
Class HV
Input AD_003 AD
Input AD_005 AD
...
Input HV_AB HV
Input HV_A
Kaiming, can you include my previous correspondence with your email?
On 03/08/2016 05:48 PM, Kaiming Yin wrote:
> Dear Douglas,
>
> My command lines were, e.g. right thickness and right white surface
> (using the same ad_hv.fsgd and group_diff.mtx files in the command lines):
>
>
> ad_hv.fsgd
>
>
Dear Douglas,
I saw the previous tutorials didn't include this "-th3" flag, is there any
difference between the following two command lines?
mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f
../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c
../label/aparc.annot.ctab subje
Dear Douglas,
Sorry for this, but could I ask how to include the previous correspondence?
I just saw your responses from Freesurfer Digest, Vol 145, Issue 19, and I
don't know how to do that. I use gmail.
Best,
Kaiming
On Tue, Mar 8, 2016 at 10:50 PM, Douglas N Greve
wrote:
> Kaiming, can you
Dear Freesurfer Experts:
I would appreciate your help in clarifying one issue I have
when applying Monte Carlo simulation to control for multiple comparisons.
First, I did the correction via QDEC GUI. In the section of Monte Carlo Null-Z
simulation, I set Threshold: 2.0 (0.01) and Sign: neg. Thi
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