Thanks Nick and Anil! I tried with the Bert data set in its original
location, and got a different kind of error:
ERROR: talairach_afd::Load_xfm(): could not parse transforms/talairach.xfm
Manual Talairach alignment may be necessary, or
include the -notal-check flag to skip this test,
making sure
Thanks Anil! Tudor, sounds like you should give this a try.
I'm re-posting this to the freesurfer list to archive it.
Nick
>
> Hi
>
> I am having the same problem but I have an idea where it's occurring.
>
> I have Windows XP Virtualbox Ubuntu Install where I have an windows share
> on the Li
Tudor,
In the default installation, there should be 2GB of free space on the
default disk, so somehow it got filled. Try deleting unnecessary stuff
(packages added during an upgrade I think mentioned doing, or subjects in
the freesurfer/subjects dir). Freeing just a few tens of MB should be
enou
Tudor,
Now that there is free space on the virtualbox ubuntu disk, are you able
to complete recon-all's on data that is located on your external disk? I
ask because although i'm not certain, i think nu_correct uses tmp space on
the ubuntu local drive, which if it was full would cause recon failur
Tudor,
I dont have any other suggestions, other than to make sure, as i
mentioned before, then you have free space on the disk that appears
within Xubuntu. That is, from a terminal, when you type:
df -h
you should see that /dev/sda1 has about 2GB of space. the nu_correct
tools will fail if ther
Tudor,
Sorry to hear its not working. There is a plan B: scrap our VirtualBox
instance entirely and instead install FSL's VMWare (from their website).
This has a 64b Centos, so upon successful installation of it, you would
download our 64b centos freesurfer distribution.
Nick
On Wed, 2013-02-0
..I also did the following in the meantime, to make sure that the problem
isn't due to a path error:
- ran nu_estimate_np_and_em and nu_correct: both seem to respond fine, and
they return their version number
- checked env variables $MNI_PERL5LIB and $MNI_DATAPATH: both point into
$FREESURFER_HOME/
Hi NIck,
I too thought disk space might be an issue, however I''ve been running the
recon-all from a mounted partition (shared folder in Virtualbox) that has
plenty of space:
*FreeSurfer:~> df -h
FilesystemSize Used Avail Use% Mounted on
/dev/sda1 11G 9.8G 0 100% /
Tudor,
I'm a bit at a loss as to why it wont work. It appears you have plenty of
available memory. Also, another person on the list confirmed that bert
will run to completion in the fsv5.1 WindowsVM.
I noticed though that it appears you have the buckner tutorial data. I
dont have my virtual mac
Tudor,
the log indicates that you need to run this:
rm /media/Dell/_FS/buckner_data/tutorial_subjs/bert/scripts/IsRunning.lh+rh
to get recon-all to run again.
Nick
> Hi Nick,
>
> Thanks for your reply! I increased the memory available to FS in the
> virtualbox to the maximum allowed value (80
I was able to verify that 'recon-all -s bert -nuintensitycor' works on
the windows virtualbox instance of fs5.1. bert is the sample data that
comes with the distribution, and nuintensitycor is the stage that runs
nu_correct.
I noticed in your recon-all.log file this line:
total
Hi Nick,
Thanks for your help, I'm on Windows XP SP3 & VirtualBox 4.2.4
Tudor
On 28 January 2013 18:30, Nick Schmansky wrote:
> Tudor, Greg, and Petr,
>
> I'm currently attempting to replicate this problem. In the meantime,
> can you tell me which Windows and which VirtualBox version you are
Tudor, Greg, and Petr,
I'm currently attempting to replicate this problem. In the meantime,
can you tell me which Windows and which VirtualBox version you are
running this on? I'm at a loss as to why this build no longer works.
Nick
On Mon, 2013-01-28 at 18:19 +, Tudor Popescu wrote:
> De
Dear Nick,
I was wondering whether you (or indeed anyone else reading this!) know
where the error that I report earlier in this thread might be coming from.
Many thanks in advance!
Tudor
On 20 December 2012 05:27, Douglas Greve wrote:
> Hi Tudor, I don't know how to solve this problem. Maybe
Hi Tudor, I don't know how to solve this problem. Maybe Nick knows.
doug
On 12/19/12 6:59 AM, Tudor Popescu wrote:
Hi Doug, thanks for replying, here is the file attached. In case the
attachment doesn't go through please let me know if I should send it
to a different address.
Tudor
On 18 Dec
Can you send the recon-all.log file (located in the subject/scripts folder).
doug
On 12/18/2012 11:41 AM, Tudor Popescu wrote:
> Hello,
>
> First of all, apologies for asking for help three times today! THings
> will hopefully become clearer once I get used to FS a bit; I really do
> appreciat
Hello,
First of all, apologies for asking for help three times today! THings will
hopefully become clearer once I get used to FS a bit; I really do
appreciate the amazing support provided by the team behind FreeSurfer!
I ran the following command on one of my structurals:
*recon-all -subject M01
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