Hi freesurfer experts:
1\ when I finished the first step of recon-all(-autorecon1), check
with tkregister2, do i need to check each slice or I just need to check few key
anatomicals (Anterior / posterior commissures, the temporal lobes in the
coronal plane, and the midline cut)? I
Hi,
I'm trying to go over a long list of talairach coordinates and to find their
vertex indices.
I did a bit of research and saw a previous question on the same topic:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12550.html
So I went on to write a tcl script in order to write
Dear all
I am a young researcher just starting on fMRI/ freesurfer analysis in
Cape Town. I got a good start after a Course the MGH guys gave us a
few months back. Ran 53 subjects, T1 MPRAGE 3T Allegra Siemens on our
local cluster (8 core nehalem X 300) (www.chpc.ac.za) : at one subject
per node,
1. You don't need to check each slice - just a few landmarks and overall
alignment.
2. You can go on to the next step, but in general if you rerun we will
retain your edits.
cheers
Bruce
On Thu, 22 Apr 2010, liyari5018 wrote:
Hi freesurfer experts:
1\ when I finished the first
Hello,
While doing a autorecon-all, I experienced an error during the template
deformation step.
writing output transformation to transforms/talairach_with_skull.lta...
registration took 187 minutes and 39 seconds.
mri_watershed -T1 -brain_atlas
Hi Stefan,
that sounds pretty reasonable. Pallidum is hard. We do have some newer
tools that do better on the pallidum, but they are not ready for
distribution yet. If you upload one dataset where the pallidum segmentation
is significantly off, we'll take a look.
And thanks for the positive
Hi Jooman,
sorry, we don't have any of those labels from our collaborators in
Germany yet.
cheers,
Bruce
On Wed, 21 Apr 2010, Jooman Han wrote:
Hi all,
I want to make labels for Brodmann area 9, 24 and 46.
I was wondering if there are corresponding labels in the labels
generated by
is there space left on your disk? Can you see if the file
aseg.auto_noCCseg.label_intensities.txt exists? Do you have permission to
write it?
On Thu, 22 Apr 2010, Guang Zeng
wrote:
Hello, Nick,
Thanks a lot for your help. I downloaded the new version for the website,
and reran the
what is the output of
mri_ca_label --all-info
On Thu, 2010-04-22 at 09:29 -0500, Guang Zeng wrote:
Hello, Nick,
Thanks a lot for your help. I downloaded the new version for the
website, and reran the subject again.
It failed at the same place, it looks like the new version does not
Freesurfers,
I have looked at this subject and original data looks good with no motion.
The betting also looks good on the brainmask.mgz loaded into tkmedit. Any
suggestions on what might be happening? I have attached the relevant log
files, except recon-all.log because I thought it might
i dont think the newer mri_ca_label was installed properly. it should
have the following -all-info output:
ProgramName: mri_ca_label ProgramArguments: --all-info ProgramVersion:
$Name: stable4 $ TimeStamp: 2010/04/22-19:08:18-GMT BuildTimeStamp:
Nov 24 2009 04:00:54 CVS: $Id:
Hey Mailing List,
I'm getting the following error in the smooth2 stage of reconstruction:
#
#...@# Smooth2 lh Wed Apr 21 17:22:08 EDT 2010
mris_smooth -n 3 -nw ../surf/lh.white ../surf/lh.smoothwm
Hi Doug and other Freesurfers,
We are trying to balance the power of different event-related fMRI runs
(each consisting of a different experimental condition with different
interstimulus intervals) using the optseq2 definition for efficiency. Our
outcome metric is the BOLD % signal change
First of all, the number of stimuli should not influence the estimate of
the % change, only its variance (ie, it won't bias you to find a change
that is not there). Having said that, you can get some non-linearities
if stimuli are too close to each other, so you'll want to make sure to
check
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