Hi Aaron
that is for longitudinal analysis. We have been trying to document this
kind of thing, but there are still gaps
cheers
Bruce
On Fri, 27 Apr 2018, Aaron Tanenbaum
wrote:
External Email - Use Caution
Hello FreeSurfers,
I am trying to find what the -l flag does for
External Email - Use Caution
Hello FreeSurfers,
I am trying to find what the -l flag does for the program mri_ca_register
program. Does not seem to be documented anywhere but i could be mistaken.
Aaron Tanenbaum
___
Freesurfer mailing lis
Any help and direction you can provide with this error would be appreciated.
The full log is attached.
I was running with -openmp 5 on a machine with 6 cores and 8 Mbytes of RAM.
0033: dt=73.984000, rms=0.641 (0.133%), neg=0, invalid=96777
0034: dt=73.984000, rms=0.640 (0.104%), neg=0, invalid=967
HI Liesel
is it possible you are running out of RAM? Or disk space?
cheers
Bruce
On Tue, 24 Jun
2014, Liesel-Ann Meusel wrote:
Hi,
I am running recon-all and I am getting the following error during the
mri_ca_register step (full log
file is attached). Please let me know what I need to do t
Hi Matt
you can't skip the careg step if you want an automated recon. It's not
optional. Sorry.
Bruce
On Wed, 24 Oct 2012, Matt Leonard wrote:
Hello,
I'm trying to run a simple recon on a single T1 dataset, and am not interested
in any quantitative measures (this is just for
data presentat
Hello,
I'm trying to run a simple recon on a single T1 dataset, and am not
interested in any quantitative measures (this is just for data presentation
and eventual MRI/CT co-registration). To save time, I tried to skip the CA
registration step, but got the following error:
#---
Ops.. I'm sorry..
the selecting bar of our virtual box changes from green to red at 5.4 GB
(not 4 GB.. i was wrong!)
but if i allocate more than 3.5 GB it does not start!
Thanks!
L. Busti
2011/12/12 Lorenzo Busti
> *No.. it doesn't work. The RAM is not enough.
>
> We abandoned that machine..
*No.. it doesn't work. The RAM is not enough.
We abandoned that machine..
Now we are working with a 64 Bit Computer Dual-core CPU @ 2.10 GHz with 8
GB of RAM.
And.. IT WORKS!
We completed the autorecon1, autorecon2 and autorecon3 stages with succes!!
We use a virtual box under Windows 7 ba
I'm going to check with more ram dedicated.
Many Thanks
Lorenzo Busti
2011/12/5 Nick Schmansky
> 1.5GB is probably not enough. typically we recommend that recon-all
> have at least 3GB available to it, which can be very hard to do on a
> virtual machine (since windows takes 1GB, the vm linux
1.5GB is probably not enough. typically we recommend that recon-all
have at least 3GB available to it, which can be very hard to do on a
virtual machine (since windows takes 1GB, the vm linux takes another
1GB, which leaves 2GB for processes). i would setup your vm to use the
maximum memory allow
*Hi everyone *
*I got this error while running one of my subjects*
*
*
mri_ca_register: GCAMwrite(transforms/talairach.m3z) failed
ERROR: mri_ca_register with non-zero status 252
but continuing despite the error
#--
#@# CA Reg Inv Thu Nov 24 05:15:42 EST 201
can you check to make sure that the partition is not full? If you have
space, upload the dataset and we'll take a look
cheers
Bruce
On Tue, 18 Oct 2011, Oya,
Hiroyuki (UI Health Care) wrote:
Hello ,
I am running recon-all with ?cm switch and getting following error. Is there
any worka
Hello ,
I am running recon-all with -cm switch and getting following error. Is there
any workaround?
Without -cm switch , recon-all completes all the processing just fine.
Thank you.
Hiroyuki
mri_ca_register -invert-and-save transforms/talairach.m3z
mri passed volume size is different fro
al Message-
> From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
> Sent: Thursday, 2 June 2011 10:31 a.m.
> To: Vanessa Lim
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_ca_register error
>
> how much RAM do you have on your machine? For some re
nessa Lim
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_ca_register error
how much RAM do you have on your machine? For some reason gzip needs tons
of it
On Wed, 1 Jun 2011, Vanessa Lim wrote:
> Hi,
>
> I got freesurfer to run with this command:
>
> mri_ca_r
how much RAM do you have on your machine? For some reason gzip needs tons
of it
On Wed, 1 Jun 2011, Vanessa Lim wrote:
> Hi,
>
> I got freesurfer to run with this command:
>
> mri_ca_register -align-after -nobigventricles -mask brainmask.mgz -T
> ~/Desktop/freeSurfer/CG/mri/transforms/talairach.
Hi,
I got freesurfer to run with this command:
mri_ca_register -align-after -nobigventricles -mask brainmask.mgz -T
~/Desktop/freeSurfer/CG/mri/transforms/talairach.lta
~/Desktop/freeSurfer/CG/mri/norm.mgz
$FREESURFER_HOME/average/RB_all_2008-03-26.gca
~/Desktop/freeSurfer/CG/mri/transforms/t
Hi,
I am getting the same error. I did set the environment to an external drive
with LOTS of space. When I run it though I did notice it repeats the subject
path which is the external drive but then says actual path
~/apps/freesurfer/subjects - this doesn't have much space cause it's a
vir
Hi Thomas,
usually that means the partition you are trying to write to is full,
cheers
Bruce
On
Mon, 4 Apr 2011, T. Hagen wrote:
Hello all,
I got this error message while running one of my subjects (freesurfer
version 5.0.0):
gcamFindOptimalTimeStep: Complete in 23335.062 ms
0388: dt=0.000
Hello all,
I got this error message while running one of my subjects (freesurfer
version 5.0.0):
gcamFindOptimalTimeStep: Complete in 23335.062 ms
0388: dt=0.00, rms=0.657 (0.000%), neg=0, invalid=766
GCAMwrite(transforms/talairach.m3z): gzip encountered error.
writing output transformation
Damian,
Yes, it would be worth the effort to try v4.0.3 to see if the problem is
corrected. While the problem with mri_ca_register seemed to manifest
itself only on Darwin, the source of that bug was not Darwin specific,
so in theory it could appear on Linux (but we had never actually
encountered
In addition to this we have several datasets here that have a couple of
subjects failing with:
Killed
ERROR: mri_ca_register with non-zero status
Linux jalapeno14 2.6.20-1.2320.fc5 #1 SMP Tue Jun 12 18:50:49 EDT 2007 x86_64
x86_64 x86_64 GNU/Linux
I see from the new 4.0.3 release notes that the
Hi Alan,
if you can ftp one of the subjects to us I'll take a look.
Bruce
On Sat, 16 Feb 2008, Alan Anticevic wrote:
Hi,
I was hoping someone can help me with this issue.
We are running the recon-all command on a bunch of subjects and most of them
(16/21) process just fine (no errors and
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