Paysing Wu
Reply-To: FS Help
Date: Wednesday, August 22, 2018 at 1:56 PM
To: FS Help
Subject: Re: [Freesurfer] mris_smooth error: can't allocate region
External Email - Use Caution
Hi Bruce,
This is the FS version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
I reinstalled the
External Email - Use Caution
Hi Bruce,
This is the FS version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
I reinstalled the MATLAB. Do you think this will result in the issue?
Thanks,
PH
On Wed, Aug 22, 2018 at 4:12 PM Bruce Fischl
wrote:
> what version of FS are you u
what version of FS are you using? I think this is a bug that we had years
ago for only a few weeks. One workaround would be to load each .mgz volume
into matlab and write them back out (which will strip all the tags from
them). I'm not sure why you are having the problem though
Bruce
On Wed,
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Hi Douglas,
Yes, I did try similar way to see if it worked. I deleted the whole folder
and re-ran it. It stoped at the same place. Is there any other suggestion I
could try?
Thanks,
PH
On Wed, Aug 22, 2018 at 1:23 PM Douglas N. Greve
wrote:
> It l
It looks like a corrupted file. Try renaming/deleting lh.orig.nofix,
regenerating it, then seeing if mris_smooth works.
On 08/22/2018 10:44 AM, Paysing Wu wrote:
>
> External Email - Use Caution
>
> Hi FreeSurfer Developers,
>
> I was running recon-all and it stoped at smooth1. The comman
Wow! That was fast.
I am running FreeSurfer 5.3 on top of CentOS6 (64-bit). My hardware is a
PC powered by Intel® Core™ i5 CPU M 520 @ 2.40GHz × 4
Thank you for all help.
Cheers
Marcos.
Em Ter, 2013-10-08 às 09:00 -0400, Bruce Fischl escreveu:
> Hi Marcos
>
> I've fixed this problem, which is a bu
Hi Marcos
I've fixed this problem, which is a bug in one of the open source math
libraries we use. If you email us the details of your hardware/software
environment we'll get you a patch.
cheers
Bruce
On Mon, 7 Oct 2013, Marcos Martins da
Silva wrote:
Hi, Bruce
I proceeded as explained at
ok, I just downloaded it and am trying to replicate your problem now
On Tue,
8 Oct 2013, Marcos Martins da Silva wrote:
Hi, Bruce
Filedrop worked great and fast! Thank you for the tip.
It follows the bath I run for each subject:
mris_smooth -nw -g 5 2 -a 1 -n 1 surfLeftHippo lh.surfHippo
Hi, Bruce
Filedrop worked great and fast! Thank you for the tip.
It follows the bath I run for each subject:
mris_smooth -nw -g 5 2 -a 1 -n 1 surfLeftHippo lh.surfHippo
mris_smooth -nw -g 5 2 -a 1 -n 1 surfLeftHippoHead lh.surfHippoHead
mris_smooth -nw -g 5 2 -a 1 -n 1 surfLeftHippoBody lh
sorry, I don't think it completed as unzip can't find the end of directory
mark in the file. Try our filedrop instead:
https://gate.nmr.mgh.harvard.edu/filedrop2/
cheers
Bruce
On
Mon, 7 Oct 2013, Marcos Martins da
Silva wrote:
Hi, Bruce
I proceeded as explained at
http://surfer.nmr.mgh.h
Hi, Bruce
I proceeded as explained at
http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange .
Using ftp method, it started at good rate but after I transferred about
3/4 of the file the transfer rate decreased to some bytes (not Kbytes)
per second. Tried using curl -T and it seemed to complete a
hmmm, I guess you should upload the subject so that we can track it down
On
Mon, 7 Oct 2013, Marcos Martins da Silva wrote:
Hi, Bruce.
Thank you for your fast answer.
I used a script and It took less than 15 min to process all files from all
subjects, except
the 3 files (surfaces) mris_smooth
Hi, Bruce.
Thank you for your fast answer.
I used a script and It took less than 15 min to process all files from all
subjects, except the 3 files (surfaces) mris_smooth seems to enter a loop.
When I tried to smooth surfLeftHippobody I waited for more than 4 hours.
Comparing to the total time I nee
how long have you waited?
On Fri, 4 Oct 2013, Marcos Martins da Silva wrote:
Hi, Freesurfers
I am getting some interesting hippocampal surfaces with the following steps:
1- recon-all -all -hippo-subfields
2- mri-concat (only CA1, CA23, CA4DG and the tail complement volumes)
3- a custom OCTAVE
Hi Mike,
I don't think there's any randomness in mris_smooth that I can
think
of.
Bruce
On Wed, 12 Dec 2007, Michael Harms wrote:
Hello,
Is the 'NoRandomness' flag (and -seed flag) no longer relevant for
'mris_smooth'?
That is, if I repeat mris_smooth using the same input, I always get th
Hello,
Is the 'NoRandomness' flag (and -seed flag) no longer relevant for
'mris_smooth'?
That is, if I repeat mris_smooth using the same input, I always get the
same output smoothed surface, which was not my expectation. Similarly,
even if I explicitly chose different -seed values, the output is
hmmm, never saw that before. If you can put the data somewhere we can get
to it, we'll take a look.
Bruce
On Wed, 27 Jul 2005, Antao Du wrote:
Hi,
When I run recon-all stage2, I got the following error message but I can't
get the answer from the email list. Can anyone help me what is wrong?
Hi,
When I run recon-all stage2, I got the following error message but I can't
get the answer from the email list. Can anyone help me what is wrong?
thanks,
Antao
- Starting Hemisphere rh
-
Tessellate rh Wed Jul 27 10:23:11 PDT 2005
mri_t
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