Hi all,
I am trying to examine the interaction of 2 factors (2 x 4 groups) and have
difficulties to find the right contrast matrix for mri_glmfit.
We have patients and controls at four different aquisition sites and want to
know if the changes (i.e. thickness) between patients and controls are equ
I wonder how log does it ususally take to complete cluster-wise correction for
multiple comparisons using mri_glm-sim. I have a group analysis of 19
subjects with 1 continuous and 1 discrete factor (two levels) and the
mri_glm-sim is running now for about 4 days. Is there any way to track the
p
Hi:
The command:
recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas -s
only runs the skullstrip procedure ?...
Which is the "clone" tool ?...
Sincerely,
--
Gonzalo Rojas Costa
Department of Radiology
Las Condes Clinic
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Te
Hi all,
I am working with QDEC and I would like to know if it is possible to do
subcortical structures (e.g. hippocampus, amygdala, putamen) analyses in qdec??
I only have cortical structures mapped in my analyses.
Thanks for the help,
Miguel.
I am planning an analysis using freesurfer to compare 2 groups. The SPGRs
that will be used vary in regard to slice thickness (from 0.86 to 1.5 in
each axis), number of slices acquired (100-256), and orientation (axial;
coronal) due to the fact that these were collected over a number of years on
t
Miguel,
No, not yet. Sorry.
You can use the command-line tool mri_glmfit to do the analysis though.
Also, its pretty easy to export a table of the data and use a plain
stats tools. See:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI
Nick
On Tue, 2009-10-06 at 08:45 -0700,
the clone tool is useful for copying parts of the unstripped volume back
into the stripped one if parts of the brain are incorrectly removed (it's
part of tkmedit)
Bruce
On Tue, 6 Oct 2009, Gonzalo Rojas wrote:
> Hi:
>
> The command:
> recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgc
Hi Aize,
what is your definition of hippocampus? Does it coincide with our's? Is
fimbria included? Alveus?
Bruce
On Tue, 6 Oct 2009, caoaize wrote:
Hello Bruce,
We did manual and freesurfer auto segmentation on hippocampus for 39 subjects.
I attached the comparison plot here. As seen in
Hi James,
it certainly can. If one group had all one scan type and another all a
different one then you wouldn't be able to tell if the effects you find are
due to the group membership or the scan differences.
cheers,
Bruce
On Tue, 6 Oct 2009, James Root wrote:
> I am planning an analysis usi
I don't know what "two samples" refers to.
doug
Asaf Kaftory wrote:
> Hey Doug - first of all, thanks for the reply. second -
>
> 1. I'm afraid i didn't get the explanation. what is the FIR, and what
> does it mean "two samples in the FIR" ?
>
> 2. ok, thanks. isn't it strange though? how do res
It would be the same as your 2nd matrix with the right four columns negated.
doug
Stefan Brauns wrote:
> Hi all,
>
> I am trying to examine the interaction of 2 factors (2 x 4 groups)
> and have difficulties to find the right contrast matrix for mri_glmfit.
>
> We have patients and controls at f
It means that you don't have permission to write into that directory.
The images look a little off. What kind of scanner are you using?
doug
Weisinger, Brian (NIH/OD) [E] wrote:
> When I try to use tkregister2 I get this message, how do I go about changing
> not being able to save the changes I
Hi, all,
I am new to FreeSurfer world. I am trying to do the surface-based
registration using FreeSurfer. I found a tool called mris_register,
which is defined as a command registering a surface to an average
surface template(or another single-subject's surface). But I don't
understand how to use
Does each group have a mix of parameters or does each group have its own
set of parameters. If the latter, then it is a real problem.
doug
Bruce Fischl wrote:
> Hi James,
>
> it certainly can. If one group had all one scan type and another all a
> different one then you wouldn't be able to tell
The surface-based registration is usually done as part of recon-all
(which runs mris_register with all the appropriate arguments). You
trying to do something different?
doug
Xiaojing Long wrote:
> Hi, all,
>
> I am new to FreeSurfer world. I am trying to do the surface-based
> registration us
Hi Xiaojing,
the inputs are an individual subject sphere created with mris_sphere, and
statistics in an atlas coordinate system, usually stored in a tif file that
we supply.
cheers,
Bruce
On Tue, 6 Oct 2009, Xiaojing Long wrote:
> Hi, all,
>
> I am new to FreeSurfer world. I am trying to do
Hi, Bruce,
Thank you so much for your help.
Now my understanding on 'mris_register' is that：
1. I need to construct the 'xx.sphere' for all my inputs;
2. For the 'source.sphere', I also need to provide 'source.curv'
and 'source.sulc'.
3. For the 'target.sphere', I need to have a statistical f
yes, that is correct. All that info is generated as a matter of course
during recon-all.
Bruce
On Tue, 6 Oct 2009, Xiaojing Long wrote:
Hi, Bruce,
Thank you so much for your help.
Now my understanding on 'mris_register' is that£º
1. I need to construct the 'xx.sphere' for all my inputs;
2. F
Hi, Douglas,
Thank you so much for your help.
I once ran the recon-all for my subjects and I got the 'xx.sphere.reg's.
Are these results the warped sphere surfaces to the atlas?
I am trying to register the wm surface of subject1 to surface of subject2,
so I am seeking for help to use 'mris_regis
there is -1 switch you can give mris_register to directly register one
surface to another, but in our experience using the atlas statistics and
the measures of cross-subject variability stabilizes the whole procedure
On Tue, 6 Oct 2009, Xiaojing Long wrote:
> Hi, Douglas,
>
> Thank you so much
Thank you all so much.
I will first try to figure out how 'mris_register' works for
registering a subject to the atlas. Then think about
my problem.
Best,
Xiaojing
2009/10/6 Bruce Fischl
> there is -1 switch you can give mris_register to directly register one
> surface to another, but in ou
Hi:
I do all the steps of the "Manual Editing" process that appears in
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix, but
the "save main volume as.." option appears in gray (off)... Why ?... I
thought it might be a access permission related issue, but it was not...
Si
Would it be a problem to skip this step by using the -notal-check or would
that mess the results up too much?
On 10/6/09 2:03 PM, "Douglas N Greve" wrote:
That might be a problem as (I think) our target is made from 3T data,
and the contrast might be different. Pratap, is your anatomical data
Depends on what you want to do with it. It probably won't affect the
surface/subcortical analysis. But if you try to report tal coordinates
for this subject or try to make an average subject using this subject
(and/or other subjects that have a bad tal), then the coordinates will
be off.
doug
So if I wanted to do the longitudinal stream it would be important to fix these
then. Is it possible to do this longitudinal stream if the scanner was a 1.5t
and therefore the talairach will be off since the target was 3t and the
contrast may be off?
On 10/6/09 2:23 PM, "Douglas N Greve" wrot
I don't think it will affect the longitudinal stream, but Martin would
know more.
Weisinger, Brian (NIH/OD) [E] wrote:
> So if I wanted to do the longitudinal stream it would be important to fix
> these then. Is it possible to do this longitudinal stream if the scanner was
> a 1.5t and therefor
Hello list,
attached is my first post plus my new questions underneath every paragraph.
thanks.
> >
> > I'm new to optseq, and would like your help with the following issues:
> > 1. What exactly does DPSD mean? and why does the TR has to be an
> integer of it?
>
> Doug: Delta Post-Stimulus Dela
FIR stands for "Finite Impulse Response". You define a time window that
brackets your stimulus response then compute the average response at
each time point inside the window. Eg, the window might start at
stimulus onset (psd=0) and be sampled at each TR (eg, 2 sec) until the
end of the window
Hi Brian,
yes it looks like this is slightly too small. A little stretching does
not hurt. The talairach transform from the base is used for all the
longitudinal runs, so if it is wrong, this will have an influence. In
your case, however, I think it might not be a big problem (as the
difference is
Bruce recently wrote that you could run mris_expand like this:
mris_expand -t lh.white 0.5 lh.graymid
I found that didn't work, but this did:
mris_expand -thickness lh.white 0.5 lh.graymid
I am using version 4.4.
By the way, is there a way to increase the resolution of the surfaces before
cre
oops, you're right. -t does something else that is irrelevant. There is
code around for supersampling the surface, but it's not integrated into
anything yet. I assume you have the source so you should be able to try it
out if you want.
cheers,
Bruce
On Tue, 6 Oct 2009, Don Hagler wrote:
>
>
Hello,
I want to do a quality check of the cortex for 140 subjects, as far as
making sure it is segmented correctly. What files are the best ones to load
up to check this in fs 3? If I load the aseg.mgz file up in tkmedit and
look at the cortical regions, there are some regions where there is no
Hi Jeff,
just for the cortex I would run:
tkmedit $subject norm.mgz lh.white -aux-surface rh.white -aux wm.mgz
and check to see if the gray/white and pial surfaces are accurate. Don't
worry about the cortex labels in the aseg - it's not what we use
cheers
Bruce
On Tue,
6 Oct 2009, Jeff Sadino
Dear all,
I am a PH. D. student at KAIST in KOREA.
I am researching cortical surface analysis.
So I'd like to anaylize the source code, and it seems that the source code is
open.
However, I couldn't find any link or cvs ID in the freesurfer wiki.
Please let me know whether the code is really open
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