Hi Amy,
what version are you running? This looks really strange. Maybe a huge
topological defect that was corrected improperly?
Bruce
On Thu, 6 Dec 2007, Amy
DeLuca wrote:
Hi All,
I am having difficulties with a subject and would like advice on anything
else I can try. I've attached a j
Can you send a pic?
Ryan Muetzel wrote:
Hello,
We are running Freesurfer version 4.0.1 and seem to be having problems
with the white matter/gray matter parcellation borders. When viewing
the pial and the main white surfaces in tkmedit, everything looks good
against the t1 brain. However, wh
FDR assumes that the collection of values has both positives and
negatives. It assumes that the pvalues of the negatives are uniformly
distributed between 0 and 1, and this model is used to estimate the
total number of positives (both true and false). When you cluster, you
are setting all voxel
Hi All,
I'm interested in the relationship between estimated total intracranial
volume (eTIV), and the volume measures generated in aseg.stats and
lh/rh.aparc.stats. I have used freesurfer v3.0.3 for this data set.
Here I am using the output of aseg.stats for all volumes except the
cerebral
Hello All,
I wanted to convert the brainmask volume to analyze format. I'm not very
familiar with the analyze format and had two questions.
1) The wiki mentions that converting to SPM-Analyze format could involve
converting to multiple or single frames. What exactly are multiple or single
frames?
Paul,
The eTIV calc in freesurfer is an estimate of the total intracranial
volume based on a scaling factor determined by the alignment with an
atlas. The technique is described in the paper referenced here:
http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV
To my knowledge, its relationship to the
Anil Roy wrote:
Hello All,
I wanted to convert the brainmask volume to analyze format. I'm not
very familiar with the analyze format and had two questions.
1) The wiki mentions that converting to SPM-Analyze format could
involve converting to multiple or single frames. What exactly are
m
the total will be brain plus ventricles. eTIV also includes sulcal csf,
so it won't be the same
On Thu, 6 Dec 2007, Nick Schmansky wrote:
Paul,
The eTIV calc in freesurfer is an estimate of the total intracranial
volume based on a scaling factor determined by the alignment with an
atlas. The
Dear FreeSurfers,
I'm having some trouble with my brain masks. Below I have inserted a
subject's T1.mgz and brain.nii overlay (made with preproc-sess). As you can
see, the mask goes well beyond the boundaries of the brain. Any ideas what
could cause this-perhaps noisy functional scans? The majo
I would not worry about it. It is just used to help exclude voxels for
whitening.
Dan Dillon wrote:
Dear FreeSurfers,
I’m having some trouble
with my brain masks. Below I
have inserted a subject’s T1.mgz and brain.nii overlay (made with
preproc-sess).
As you can see, the m
Hello,
I am having trouble with one subject during the recon-all process. It has
failed twice at CA Reg:
status file for recon-all
Thu Nov 8 15:11:20 EST 2007
[EMAIL PROTECTED] MotionCor Thu Nov 8 15:11:20 EST 2007
[EMAIL PROTECTED] Nu Intensity Correction Thu Nov 8 15:18:50 EST 2007
[EMAIL
Hi Caroline,
can you send us the end of the recon-all.log when it fails?
Bruce
On Thu, 6 Dec
2007, Caroline Chapman wrote:
Hello,
I am having trouble with one subject during the recon-all process. It has
failed twice at CA Reg:
status file for recon-all
Thu Nov 8 15:11:20 EST 2007
[EMAI
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