Lusineh,
Which version of freesurfer do you have? To find out, type:
cat $FREESURFER_HOME/build-stamp.txt
Per the release notes page (which documents updates), a fix was included
in v3.0.4 (and newer) that addresses a problem where the pial surface
crosses the midline:
http://surfer.nmr.mgh
Hi Jackie,
you need to rename the T1.xfm to be talairach.xfm and put it in the
mri/transforms dir.
When you say "after this step, the orientation of the target volume is
mixed up" do you mean after applying the tal transform? The orientation of
all the .mgz (e.g. orig.mgz, T1.mgz, brain.mgz)
Hi Xin,
I will Doug handle this one. And please email the list in your replies.
Best,
rahul
On Mon, 30 Apr 2007, Wang, Xin wrote:
Many thanks, Rahul. I found readings in /stats/*h.aparc.stats. I am a freesurfer
beginner. I have another question. I want to compare the cortical thickness betw
Hi Jenni,
The orig volume is in the correct orientation when I viewed it with
tikmedit. But after I fixed the Talairach transform by using mri_convert
T1.mgz T1.mnc , mritotal -protocol icbm T1.mnc T1.xfm.,(and I viewed it
in tkregister2, which looks quite fine), then I ran recon-all -subjid
Hi Xin,
Within the *h.aparc.annot files for each subject, there should be
individual label files for *h.precentral.label and *h.postcentral.label.
If you take a look at your *h.aparc.stats, there should be a value for the
thickness and volume. You can, of course, take this *h.aparc.stats file
Hi Xin,
What exactly do SI and MI cortices refer to?
rahul
On Mon, 30 Apr 2007, Wang, Xin wrote:
Hello, group
I need to compare thickness of left v.s. the right SI and MI cortices. I saw
some matlab tools for comparsion of left and right hippocampus in
Lundervold.pdf. I could not find simil
Hello, group
I need to compare thickness of left v.s. the right SI and MI cortices. I saw
some matlab tools for comparsion of left and right hippocampus in
Lundervold.pdf. I could not find similar tools in the matlab folder of
Freesurfer stable release 3.0.5 that I just installed. Could anybody
Hi,
I'm a little confused, so please correct me if I've made the wrong
assumptions. It sounds like your problem is becuase your orig volume is
in the wrong orientation when you view it in tkmedit (ie., the coronal
view in tkmedit does not show a coronal view, but shows the sagital view).
It
Dear list,
After fixing the Talairach transform automatically, (by mri_convert , the final
objective funciton value is fine, ca.0.06)
So I replaced the talairach.xfm with T1.xfm and named it as talairach.xfm, and
it looked pretty fine with tkregister2.
Then I runed recon-all -subjid -autore
Hi all,
I wanted to have whitematter, gray volume and avg.thickness for each
hemisphere. So when I run
mris_anatomical_stats -t thickness
I get the following data:
mris_anatomical_stats -t thickness lh
using thickness file thickness.
total white matter volume = 729800 mm^3
tota
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