yes, give mris_inflate the -w n flag, and the surface will be written
out every n iterations. This is pretty useful, as some of the intermediate
surfaces can be very nice for visualization as they still have the major
folds, but you can see into all of them.
Bruce
On Fri, 19 Dec 2003,
Dear all:
I use
freesurfer to process a brain data and I met a problem.
Inrunning "Process volume" . Itcan't
finish and the message pop up said:
_
|Alert|
Images(brain)
/tmp/lab/exp/subject/bee04/mri/brain/cor-001...
not found .. stripskull first.
but in the process display, it
yes, the white matter intensity is around 110 in /mri/T1 directory.
I put the zipped file of bee04 directory in the following address.
www.ee.cuhk.edu.hk/~zjzhang/bee04.zip
Would you please view this data?
regards,
zhang zhijun
- Original Message -
From: Bruce Fischl [EMAIL
Hello all,
I have a few questions regarding the feature, mris_anatomical_stats. My
first is really just to clarify the output of the command
mris_anatomical_stats using the label (-l) feature. Please correct me if I
have this wrong
total white matter volume -- of the hemisphere?
total
On Thu, 18 Dec 2003, Bob Thoma wrote:
Hello all,
I have a few questions regarding the feature, mris_anatomical_stats. My
first is really just to clarify the output of the command
mris_anatomical_stats using the label (-l) feature. Please correct me if I
have this wrong
total white
hi Rob,
try making a label on the surface, which it sounds like you have done for
the average brain you mapped your sigt's to.
you can map this label to other subjects using mri_label2label.
(in this example, i made the label on subject 017 and called it
lh.temp.label, then mapped it to
Hi all, we'd like to average some MPRAGE's in
preparation to use FreeSurfer. In a
piloting study we acquired a pair of MPRAGE's on a verywell-behaved
subject on one day, and then another pair of MPRAGE's on another day.
Although motion artifact is small within day, it is large across day
FSL has some code for this, but the problem is really an MR one. If the
subject placement in the scanner is substantially different then the
gradient nonlinearities will cause the volumes to be warped differently.
In addition, different shim settings will cause different B0 distortions,
which
Thanks for the tips, Bruce. I'll try FSL, although I suspect that you're
right, this is more of an MR problem. I *did* have a suspicion that there
was some geometric distortion between the scans acquired on different days,
just from visual inspection.
Joe
- Original Message -
From:
Joe:
There are various reasons why 3dvolreg may not do the job. In addition to
what Bruce mentioned (basically geometric incompatibility), 3dvolreg can
fail due to the MRIs starting off too far out of alignment, or very
different intensity values, or even things like you've got the right-left
Hi, All:
After the topology correction, we are supposed to get a triangle mesh which
has the same topology as a sphere, right? but I didn't. The Euler
characteristic of the mesh is not 2. Can any one tell me why?
Sincerely,
Shijie
after the spherical registration, run the script:
parcellate_subject $subject
this will take about 10 minutes and generate two files in the subject's
label directory named lh.aparc.annot and rh.aparc.annot. In tksurfer you
can visualize them with file-import annotation, and
Then the labelling is a by product of the spherical registration?
If I have the sulci labeling obtained by using other method, such as using
the Brainvisa software,
can these labelling be used into the spherical registration to reduce the
matching ambiguity?
regards,
zhang zhijun
- Original
Hi, Professor Fischl, Thank you for your reply,
there are 114090 vertex and 228348 triangles, so EC=-84
- Original Message -
From: Bruce Fischl [EMAIL PROTECTED]
Date: Thursday, December 18, 2003 9:16 pm
Subject: Re: about the toplogy
what is the euler number?
On Thu, 18 Dec
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