Dear FreeSurfer gurus,
We are trying to conduct a simple group analysis, employing
freesurfer. However, our aim is to use the software only up to the
point where the functional data is projected to a common space, and
from that point on export the data to a text file and conduct the
analysis usin
Dear All,
I tried to extract a surface from a MRI scan (T1, 1.5T) using Freesurfer
3.0.3 on a Linux computer. I just run "recon-all" script for the same scan
6 times (same computer, no human interaction). To my supprise, I got 6
different results ( different #triangles, #vertices). Go back to che
Hi Emily,
don't use .w files as they might generate a different number of data
points. The number of nodes is constant, but the .w file will attempt to
do a "compression" by eliminating nodes that are 0. This, of course,
turns into a bookkeeping mess, which is why I discourage the use of .w
f
Li-Chen,
Some of the utilities make use of random number generation in their
algorithms, specifically: mris_smooth, mris_sphere, mris_topo_fixer and
mris_ca_label. While the number of vertices can change because of this,
the resulting stats (cortical thickness) should not differ by more than
0.5%
Hi Li-Chen,
there is some intentional randomness in the algorithms. Try overlaying the
surfaces and you'll see that they are visually identical I would think.
Nick: is there a switch to recon-all to specify what the seed should be for
the random # generators?
thanks,
Bruce
On Tue, 5 Dec 20
On Tue, 2006-12-05 at 13:31 -0500, Bruce Fischl wrote:
> Hi Li-Chen,
>
> there is some intentional randomness in the algorithms. Try overlaying the
> surfaces and you'll see that they are visually identical I would think.
> Nick: is there a switch to recon-all to specify what the seed should be
Hi Doug,
I tried commands like this one initially, originally getting a "Segmentation
fault" error. It was my understanding from the help file that using the -c
flag specified that I want to convert the curv file to .asc. What I would
like to do is convert a functional file to .asc. A command lik
I've rigged the curv format reader to recognize volume files used to
encode surface values, so anything that accepts curv will also accept
mgh. The issue on the number of vertices is whether the rh.white is that
of the target subject used with mri_vol2surf. Are you using fsaverage?
doug
E
hi doug,
the target subject of mri_vol2surf was ico7 when i got the error in
mris_convert. i tried using the command you gave when the target was the
individuals sphere.reg, and got a text file with 5 columns. is the last
column the intensity values? is there a way to use this command on data
map
Hi all,
I used mris_preproc to generate a surface file from 4 feat directories, as
described in the tutorial:
mris_preproc --out lh.cope1.nii.gz --target fsaverage --hemi lh \
--iv fbert1.feat/stats/cope1.nii.gz
fbert1.feat/reg/freesurfer/anat2exf.register.dat
--iv fbert2.feat/stats/cope1.nii.gz
hi emily,
let's back up a minute. Try running mri_vol2surf using fsaverage as
the target (this is basically the same as ico7). Then when running
mris_convert, specify the ?h.white in the fsaverage/surf dir.
doug
On Tue, 5 Dec 2006, Emily Cooper wrote:
hi doug,
the target subject of mri_
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