.
‘recon-all’ steps are described in this wiki page
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Quah, Bryan
Sent: Thursday, February 27, 2025 1:06 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Unknown error
check the talairach.xfm transform and see if it is accurate.
cheers
Bruce
On Tue, 12 Jan
2010, Xiantong Zhen wrote:
Hi experts,
I run freesurfer to compute the thickness, but I find some subjects failed with
error.
Would you please tell me how to handle this error. Thank you very much!
And
Hi experts,
I run freesurfer to compute the thickness, but I find some subjects failed with
error.
Would you please tell me how to handle this error. Thank you very much!
And the error is as follow:
talairach_af
Thanks again!
I'm working on some other analyses right now, but I will report back once i
get a chance to run this again...!
- Jerry
On Tue, Apr 29, 2008 at 11:52 AM, Bruce Fischl <[EMAIL PROTECTED]>
wrote:
> 1. It should be very sensitive to this - just make sure the white matter
> is at least 1
1. It should be very sensitive to this - just make sure the white
matter is at least 100 or so in the image (it can be more).
2. You shouldn't need to erase anything - just rerun recon-all
cheers,
Bruce
On Tue, 29
Apr
2008, Jerry Yeou-Wei Chen wrote:
Okay, thanks! I'll give that a shot...
Okay, thanks! I'll give that a shot... but I have a couple of questions
beforehand:
1) How would you recommend that I decide what scale factor to use? Trial and
error to get a peak of ~116?
2) Should I run cp and mri_convert, then erase all other existing files and
folders, and rerun recon-all from
Hi Jerry,
I think you can do something like:
cp 001.mgz 001_orig.mgz
mri_convert --scale 3 001_orig.mgz 001.mgz
then the same for the other runs and see how that works in recon-all.
Usually we detect and account for this, but I guess something is failing in
your case.
cheers,
Bruce
On
Mo
Hi Bruce,
Looking at one of the successfully processed subjects in tkmedit, I would
guesstimate the range in the brain to be ~20-65. The corresponding 001.mgz
is equally dark.
Regarding the scale option, would I run that initially ( with --scale ), and then run autorecon as normal?
Do I find the
p.s. are the 001.mgz and 002.mgz dark? The orig.mgz? Sometimes nu_correct
can create very dark images, and there are some switches you can loo
through to correct them. Alternatively if it is the 001.mgz, mri_convert
has a scale option you can use.
cheers,
Bruce
On Fri, 25 Apr 2008, Jerry Yeo
it can be trouble if they are that low, as you lose dynamic range in the
8-bit representation. What are the ranges in orig.mgz?
On Tue, 22 Apr 2008,
Nick Schmansky wrote:
Jerry,
At this point, I think Bruce will need to jump-in to answer (he is out-
of-town today). I think he will ask about
Okay, thanks for your help again Nick!
Regarding the scan data: I am actually working with data collected by a
previous member of our lab, and there were indeed some problems... (related
to the SCIC algorithm on our GE scanner). So, our technician created a
program to "uncorrect" the intensity scal
Jerry,
At this point, I think Bruce will need to jump-in to answer (he is out-
of-town today). I think he will ask about your scan parameters, ie, how
is your scanner setup? It sounds as if something is not quite right in
the data coming-off the scanner.
Nick
On Tue, 2008-04-22 at 14:26 -0400
Thanks for the reply, Nick. I think you correctly identified the problem.
nu.mgz is oriented correctly, but looks very dark... However, it looks
decent if I adjust the brightness/contrast
I have other scans that were processed without error, and the orig.mgz, and
nu.mgz also appear quite dark (
Jerry,
I'm not sure why it exited without giving a better message, but this is
a clue why it exited:
before smoothing, mri peak at 0
after smoothing, mri peak at 0, scaling input intensities by inf
the mri peak is at zero, which is wrong (it should be around 116/117 or
so).
if you view nu.m
Hello,
I am having trouble deciphering why I got the error attached below. Any
suggestions would be greatly appreciated!
Thanks,
- Jerry
Tue Apr 22 10:15:22 EDT 2008
talairach_avi done
cp transforms/talairach.auto.xfm transforms/talairach.xfm
#
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