what version are you using? what is your command line? Can you send the
full terminal output?
doug
Lena Palaniyappan wrote:
>
>
>
> On 26/12/2010 12:08, "Lena Palaniyappan"
> wrote:
>
> For some of my data, label2label (one of the PALS labels from
> fsaverage being mapped on to a subje
The only two things that should be different are the number of
iterations and the amount of smoothing. The cached simulations used 10k
iterations (you have 5k). When you use the cached, it uses the FWHM
that is closest to and higher than whatever is in your data. But this
should make it more c
Dear Freesurfer users,
I am using mri_glmfit-sim to do clusterwise correction for multiple
comparisons. I ran the Z Monte Carlo simulation for 5000 iterations for my 43
subjects (vertex wise threshold of 2.0 or p < 0.01), but I received different
results than when I ran the correction using the
Hello,
I'm trying to make a surface for a monkey volume that is 256 by 296 by 256
voxels in size. I know that if I use recon-all -autorecon, I can add the
-cw256 flag to deal with that FOV of 296. But with a monkey volume, my
understanding is that I can't use recon-all. Instead, I need to us
On 26/12/2010 12:08, "Lena Palaniyappan"
wrote:
For some of my data, label2label (one of the PALS labels from fsaverage being
mapped on to a subject) gives this message
Performing mapping from target back to the source label
ERROR: srcvtxno = -1 < 0
trgvtxno = 140122, dmin = 1000
trgregxyz
You can't analyze 3 levels in QDEC, you'll have to create an FSGD file
and use mri_glmfit. See
https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
doug
Lena Palaniyappan wrote:
> I have a single factor with three levels (diagnosis) and trying to
> setup qdec, but I get the following message
Try using mris_preproc with "--meas curv". Create a list of your
subjects in a text file which you then pass with the --f flag. The
output will be all the curvs from your subjects stacked together. You
can then use mri_concat with the --mean option to get the mean, or the
--std to get the stand
It might be that the sequence was not so good. You might try setting the
prestim to 0 (to match your optseq cmd line).
doug
Yuko Yotsumoto wrote:
> Hi all,
>
> ( freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0 )
>
> I created sequences for event-related design, using optseq2.
>
Hi Thomas,
you can specify -s to generate means and variances, but I'm
pretty sure Doug has something more up-to-date to do this.
cheers
Bruce
On Thu, 6 Jan
2011, Thesen, Thomas wrote:
> Hi,
>
> I am using mris_average_curvature to create an average thickness map across
> subjects (registere
Hi Liesbeth
if it's the eTIV you are looking at, that is computed from the determinant
of the Talairach transform and is independent of the skull stripping.
cheers
Bruce
On Fri, 7 Jan 2011 l.hoeks...@psy.umcn.nl wrote:
> Dear Freesurfer users,
>
> We were suprised to find out in two cases tha
Dear Freesurfer users,
We were suprised to find out in two cases that after adjusting watershed
(because of skull that was left) and autorecon2 and autorecon3, the ICV was
exactly the same as the ICV measured by pipeline--> autorecon-all. If we didn't
adjust watershed in one case the skull was
Hi all,
( freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0 )
I created sequences for event-related design, using optseq2.
optseq2 --ntp 150 --tr 2 --psdwin 0 20 1 --ev TG1 2 22 --ev IG1 2 22 --ev CNT 2
22 --ev TGIG 2 22 --ev TGCN 2 22 --nsearch 2000 --focb nCB10pt --nkeep 15 --o
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