I'm sorry, I don't understand. What resampling fails? How does it fail?
On
Thu, 20 Sep 2007, Jiefeng Jiang wrote:
Hi,
I am using the ?h.sphere.reg files automatically generated by reconall. However, I found
that the area distortion compromise the results of my following resample step. I won
Sorry that I did not make it claer. The resampling did not fail, just the
result was not good.
The resamping process is like this:
I treated reconstructed cortical surfaces as functions defined on a sphere.
Meanwhile, I divided a sphere into 163842 points and 300,000+ triangles by
iterativel
instead of changing the average you can generate a registration with less
distortion by for example invoking mris_register with -dist 1 to increase
the penalty on the metric distortion term
On Thu, 20 Sep 2007, Jiefeng Jiang
wrote:
Sorry that I did not make it claer. The resampling did not fa
Hi,
I asked about this last week, and had a nice discussion with Doug, but
somehow in that we never got the answer to my original question.
When FreeSurfer saves t-values (in F.mgh), what is it actually saving?
The numbers in the file do not have a t-distribution (even when the
source data f
Hi, all:
I am a naive user of fs and fsfast. Now, I am trying to do functional
connectivity analysis with fsfast. But, I actually do not know how to do
correlation analysis with a reference time course (a mean time course from a
specific ROI) in fs and fsfast? Can someone give me some cues on this
Xiangchuan,
I think it would be worth the effort to install ATI's proprietary Linux
x86_64 driver, found by following the links here:
http://ati.amd.com/support/driver.html
It takes a bit of effort (it requires compiling a kernel driver), but I
have done this once on a system (but not FC6) and
Hi Bruce,
Thank you for your suggestions. I just finished the -autorecon1 step with
v4.0.1 for 20 subjects, and checked the talairach registration with
tkregister2. I found that most subjects' talairach volume looked smaller than
the T1 volume. Suppose this is a "not very good" talairach regist
Xaingchuan,
The new v4.0 freesurfer contains an automatic failure detection step to
determine if its talairach alignment is correct. If your -autorecon1
step did not fail, then you can be assured that the alignment is good
enough to complete the rest of the recon-all process. To double-check,
yo
Dear FreeSurfers,
I'm getting odd results from mri_volcluster-the max voxel listed for a given
cluster often does not appear to actually be the max in that cluster. This
most often appears to happen with small clusters and negative significance
values.
Below is an example made with abs thre
Are you sure that it is saving t-values in F.mgh and not F-stats?
From: Glenn Lawyer <[EMAIL PROTECTED]>
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] t-value saved values
Date: Thu, 20 Sep 2007 15:00:44 +0200
Hi,
I asked about this last week, and had a nice discussion with Doug, b
The values in F.mgh are F dist under the null. But you should only have
an F there if it is a multivariate contrast (ie, the contrast matrix has
more than one row).
doug
Don Hagler wrote:
Are you sure that it is saving t-values in F.mgh and not F-stats?
From: Glenn Lawyer <[EMAIL PRO
Hi there,
How can I get a standard deviation map of the thickness measurements ina
subject?
Inês
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what exactly do you mean? Spatial standard deviations? Usually those aren't
terribly interesting, and it's the cross subject ones that are more
useful, but that doesn't sound like what you mean.
Bruce
On Thu, 20 Sep 2007, Inês Souta wrote:
Hi there,
How can I get a standard deviation map o
Well, I'm dealing with a patient with an heterogeneous lesion. Somehow, the
lesion area seems to have misled the algorithm in terms of white and pial
surface definition, leading to an erroneous cortical thickness measure in
that area. What I was interested in analising (if possible) is the
dispersi
if you draw a label outlining the region you can use
mris_anatomical_stats -l to get the thickness standard
deviations I think. Usually they aren't that interesting because the
thickness varies with geometry (e.g. sulci are thinner than gyri).
cheers,
Bruce
On Thu, 20 Sep 2007, Inês Souta w
ok. That's good enough for me by now. Thanks a lot
Inês
2007/9/20, Bruce Fischl <[EMAIL PROTECTED]>:
>
> if you draw a label outlining the region you can use
> mris_anatomical_stats -l to get the thickness standard
> deviations I think. Usually they aren't that interesting because the
> thicknes
Hello,
I was comparing the processing of the "bert" sample data on FreeSurfer
V3.05 with V4.01 and I noticed that the posterior tip of posterior
horns of lateral ventricles both sides were not counted as part of the
lateral ventricles but as cerebral white matter in V4.01. Have I done
something wr
Dear Freesurfer Helpers,
I think 'mri_normalize' might play an important step for the cortical
thickness measurement.
However, I could not find much information regarding 'mri_normalize' except
for a brief description as below:
"mri_normalize converts orig or nu volume from cortical reconstruction
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