No, it does not. With version 5 I went to a simple AR1 model instead.
doug
On 11/26/12 10:34 PM, Caspar M. Schwiedrzik wrote:
> Hi Doug,
> thanks for the input. What I meant is that in version 5.1,
> mkanalysis-sess does not seem to recognize the -taumax flag to set the
> maximum delay for the a
Hi Doug,
thanks for the input. What I meant is that in version 5.1,
mkanalysis-sess does not seem to recognize the -taumax flag to set the
maximum delay for the autocorrelation function.
Caspar
2012/11/26 Douglas N Greve :
>
>
> On 11/26/2012 02:12 PM, Caspar M. Schwiedrzik wrote:
>>
>> Hi Doug,
Hi Susan, ok, I see what you are doing now. Let's do it this way:
1. First transfer your label to the volume:
mri_label2vol --temp example_func.nii --reg anat2exf.register.dat
--proj 0 1 .1 --hemi lh --label lh.your.label --o yourlabel.func.nii
2. Then run segstats:
mri_segstats --i cope2.nii
Hi Susan, you can't use func2roi-sess. You'll have to put together some
commands, but it should not be too hard, something like
mri_segstats --i lh.cope2.nii --slabel subjectname lh your.label --mask
lh.zstat1.nii --maskthresh 2 --masksign abs --o sum.dat
where zstat1 is your all/nothing contra
Hi,
I am hoping do a surface-based functional ROI analysis on subject-specific ROIs
that are both defined structurally and are masked by an all/nothing functional
contrast. func2roi-sess seems perfect for this except that my data are not in
an FS-FAST data/analysis structure, but are instead pr
But all four runs into a single bold folder, then try running
selxavg3-sess with the -run-wise option. This will create separate run
analysis in the output directory. I have not tried it with retinotopy
before, so get back to me if it fails.
doug
On 11/26/2012 05:53 PM, Zhou, Wei wrote:
> Hi Do
Michael,
I'm also not aware of any program that will automatically demean by
group when you request an interaction or when you add a covariate.
I still think its important to stress that if you demean the entire
group, you are looking at the "covariate-adjusted group means" rather
than the actual
Hi Doug,
I think I didnt explain clearly last time.
Here's the thing:
I have four runs: 2 eccen and 2 polars. I followed the process
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis and
I hope to view the result of an individual session, e.g. one polar, which could
Just wanted to mention that, to my knowledge no commercial stat package
will mean center by group (Donald's case (C)) if you request an
interaction model. Mean centering by group is a very unusual operation.
cheers,
-MH
--
Michael Harms, Ph.D.
-
Hi Gabriel, how did you create your average subject? with
make_average_subject? If so, try
mri_vol2vol --mov subject/mri/aseg.mgz \
--targ $FREESURFER_HOME/average/mni305.cor.mgz \
--xfm subject/mri/transforms/talairach.xfm --o
subject.aseg.mgz --interp nearest
doug
O
You should have all of your run folders under bold. It looks like you
have only 001 under bold.
doug
On 11/24/2012 12:07 PM, Zhou, Wei wrote:
> Hi Doug,
>
> Thank you for reply.
> As in rtopy.par the stimtype is either polar or eccen, I get separate
> f.nii files for eccen and polar and do one
On 11/26/2012 02:12 PM, Caspar M. Schwiedrzik wrote:
> Hi Doug,
> I'll do that.
> Two quick follow-up questions regarding 5.1:
> - it seems that I cannot specify taumax anymore in mkanalysis-sess. Is
> there another argument that would allow me to set the autocorrelation?
What do you mean by "set
I assume that your 12 columns are: your 6 groups followed by 6 columns
representing your covariate.
You must first test that the slopes are not different with an F-test:
0 0 0 0 0 0 1 -1 0 0 0 0
0 0 0 0 0 0 0 1 -1 0 0 0
0 0 0 0 0 0 0 0 1 -1 0 0
0 0 0 0 0 0 0 0 0 1 -1 0
If you don't find any diffe
Dear FreesSurfers,
**I've checked similar posts on the email-list and still could not find an
answer to my question. I'd really appreciate your attention and feedback:
recon-all -autorecon1 crashes for me in one of the steps before skull
stripping with an error like this:
Done spline_smooth: pos
Hi Caspar, I think I fixed this in later versions. If you upgrade, you
can run the stats from 5.1 with recons from 4.5 (just don't mix recons
from different versions).
doug
On 11/26/2012 01:15 PM, Caspar M. Schwiedrzik wrote:
> Hi!
> I ran into a funny problem when calculating contrasts in Frees
Hi!
I ran into a funny problem when calculating contrasts in Freesurfer 4.5.0.
Namely, the center of my cluster of significant voxels has a p-value
of -0.0, resulting in a funny whole where you would otherwise expect
to find the most significant voxel(s).
It seems that the p-value is too small. Is
Dear all,
I have difficulty sorting out the problem with some tracts in several
subjects, tracts are incomplete or missing. As it has come up quite a few
times on the list, for this sort of problem I have first set "reinit=1" and
then increased control points to 7, and re-ran trac-all with "-prior
Mahinda,
As I understand it, you have 3 groups (Controls, P1, and P4) in your
analysis and have done three contrasts:
(1) P1vP4 --> no differences
(2) P1vControls --> no differences
(3) P4vControls --> significant differences
Your first question about the difference in the analysis --> three
cont
Hi Doug and Donald,
Again many thanks for the advice. With regard to the analysis described
previously - I have n=21 in my control group while P1=4 patients, P2=7
patients, P3=3 patients and P4=5 patients. Given that i have small numbers I
elected to compare only 2 patient groups (p1 and p4) r
hmmm, I guess the only thing you can really do is edit the
brain.finalsurfs.mgz and replace the hyperintense voxels with lower
intensities (around 50 or so I would think). We don't usually see
hyperintensitities in GM in T1-weighted images unless they are
MR-distortions caused by low bandwidth
Hi Marie,
I don't think so, since your volume does have a small but real rotation
away from coronal. Any idea why that is? I guess we could avoid
resampling if the direction cosines are close enough to what we want.
Bruce
On
Fri, 16 Nov 2012, Marie Schaer wrote:
>
> Hi everyone,
>
> I have a
1. Use:
recon-all -i MRI-image.nii -s test_subject -all
this will produce an aseg.mgz that is our segmentation. You can extract the
left (17) and right (53) hippocampi using mri_extract_label. Soemthing
like:
mri_extract_label aseg.mgz 17 53 hippocampi.mgz
note that we also generate hippoc
yes, that would retain edits
cheers
Bruce
On Mon, 26 Nov 2012, Catherine Bois wrote:
> Ps. To make it clearer; would this command recon-all -autorecon1 -autorecon2
> -autorecon3, incorporate all the edits amde, or would it merely overwrite
> them and just regenerate the brain surface from scratch
Hi Cathy
you will waste a lot of processor time this way, but all edits should be
retained no matter how early you start in the process.
cheers
Bruce
On Mon, 26 Nov 2012,
Catherine Bois wrote:
> Hi,
>
> I am currently in the process of reconstructing my brains after performing
> edits. I am s
Ps. To make it clearer; would this command recon-all -autorecon1
-autorecon2 -autorecon3, incorporate all the edits amde, or would it merely
overwrite them and just regenerate the brain surface from scratch?
Thanks
On 26 November 2012 13:13, Catherine Bois wrote:
> Hi,
>
> I am currently in the
Hi,
I am currently in the process of reconstructing my brains after performing
edits. I am submitting them to a system named condor, which allows them to
be processed in parallel, reducing time. However, I am unsure of how to
best use the script that takes into account all the changes made. Is it
17 is the intensity value for left hippocamus, and 53 for the right hippocamus.
Then you can view with tkmedit ( to view aseg.mgz) for more clearance. Then
use matlab to extract this label base on the intensities value.
Azeez Adebimpe
Date: Mon, 26 Nov 2012 13:48:09 +0100
From: andrea.ta.
Hello,
I am working on segmentation of the hippocampus and I need a comparing method.
I am approaching for the first time to FreeSurfer method.
I would like your courteous help.
I have three questions for you:
1 - I have input a MRI-image.nii showing all head. As output I would like a
b
28 matches
Mail list logo
