Hi folks!
I just like to send some information regarding "awk" problems under MacOs
which occurs at least on "German" systems. I am not quite sure if FS uses
awk at any point - but it might help when processing FS results:
With the Region Setting "Germany" in the general settings of MacOs (
sys
I've gotten as far as running the mris_make_surfaces on the RMS, but after
running for a bit it stopped with this error
mghRead (file/path/s_MEMPRAGE/mri/0010.mgz -1): coult not open file
mris_make_surfaces: could not read 0th echo for dura localization from
file/path/s_MEMPRAGE/mri/0010.mgz
fo
can you send details about the steps you carried out including full
command lines?
On Fri, 10 May 2013, Jonathan Holt wrote:
> I've gotten as far as running the mris_make_surfaces on the RMS, but after
> running for a bit it stopped with this error
>
> mghRead (file/path/s_MEMPRAGE/mri/0010.mgz
$ export SUBJECTS_DIR=/net/data4/ALSSCI/FreeSurfer201211/FreeSurfer
$ mris_make_surfaces -dura 001%d.mgz 4 s_MEMPRAGE lh
it's entirely possible I'm specifying the wrong mgz? After running
recon-all on the RMS the usual directories were created, etc... including
001.mgz which is in s_MEMPRAGE/mri/o
did you run recon-all -all all the way through? you should name your echoes
something different like echo1.mgz, echo2.mgz... then specify -dura
echo%d.mgz 4
cheers
Bruce
On Fri, 10 May 2013, Jonathan Holt wrote:
$ export SUBJECTS_DIR=/net/data4/ALSSCI/FreeSurfer201211/FreeSurfer $
mris_make
I ran mri_convert on the RMS'd nifti, then recon-all on that. I don't
understand how I can go from 1 RMS'd mgz back to 4 separate echos?
jon
On May 10, 2013, at 12:41 PM, Bruce Fischl wrote:
> did you run recon-all -all all the way through? you should name your echoes
> something different lik
how are the echoes stored now? If they are in separate series just convert
the individually. If in a single multi-frame file, use
foreach echo (0 1 2 3)
mri_convert -nth $echo echo${echo}.mgz
end
cheers
Bruce
On Fri, 10 May 2013, Jonathan Holt wrote:
> I ran mri_convert on the RMS'
will convert individually, should they eventually be stored in the same
directory as the RMS'd mgz, with the same file name + invidivual numbers?
after which I'd proceed with mris_make_surfaces?
jon
On May 10, 2013, at 12:48 PM, Jonathan Holt wrote:
> I ran mri_convert on the RMS'd nifti, the
it doesn't matter what you name them as long as you tell
mris_make_surfaces. Store them in the subject's mri dir
On Fri, 10 May 2013,
Jonathan Holt wrote:
> will convert individually, should they eventually be stored in the same
> directory as the RMS'd mgz, with the same file name + invidivual
Thanks very much for your response, Bruce. We already collect T2 in our
scanner -- not sure about FLAIR. Is there a way for them to work
analogously with the mri_make_surfaces command (as outlined here)?:
FreeSurfer command to correct dura:
mris_make_surfaces–dura filename_%d.mgz
Dear all,
I know you run Centos at the Martinos center. Are there any known issues
or concerns that differentiate between running Freesurfer on Centos or
Ubuntu? Reasons to prefer one or the other?
Thanks for your help,
Katie Surrence
--
Research Coordinator
Social Cognition Laboratory
New Yo
Hi,
Has anybody got problems using FS with NFS v4?
We cannot write subjects if the SUBJECTS_DIR is in a NFS v4 system.
Many thanks,
Gari
-- Forwarded message --
From: Garikoitz Lerma-Usabiaga
Date: Tue, May 7, 2013 at 5:25 PM
Subject: NFS v4 on CentOS 5.4 or Red Hat 6.2
To: Frees
How have you configured NFS? e.g. a simple check is to type
# system-config-nfs
Then choose the filesystem and click "Properties". Make sure the bullet
point labeled "Read/write" is chosen.
On 05/10/2013 01:45 PM, Garikoitz Lerma-Usabiaga wrote:
Hi,
Has anybody got problems using FS with NFS
Hi Katie,
yes, give mris_make_surfaces the -T2dura after recon-all has completed.
cheers
Bruce
On Fri, 10 May 2013, Katie Surrence wrote:
Thanks very much for your response, Bruce. We already collect T2 in our
scanner -- not sure about FLAIR. Is there a way for them to work
analogously wit
Gari,
At the NMR Center we use NFS v4 without problems with freesurfer. Is the
SUBJECTS_DIR writable? Note that in the default freesurfer distribution,
the freesurfer/subjects directory is not writable (contains sample and
template subjects).
Nick
> Hi,
> Has anybody got problems using FS wit
Katie,
The next release, v5.3 (hopefully next week), will fix a problem with
running on Ubuntu 13, but freesurfer works on Ubuntu 12 as well (with one
modification described on our download page).
So there are no reasons not to pick Ubuntu other than who will maintain
it. If its just one machine
Thanks for the answers.
I am not the sys admin, but I think I can answer both questions:
> I assume the system is in read-write mode since the rest of the programs
(i.e. Matlab) are working.
> The SUBJECT_DIR is in each personal space, I mean:
--- FS is installed in a Linux CentOS 5 machine, I have
Gari,
Hi, your situation seems odd. Freesurfer does not require anything
special in terms of a file system, or modify system settings of any sort,
so I'm not sure what is happening in your situation. The recon-all script
does set 'umask 002', which clears the write-bit for 'other' users.
Perhap
Thanks Nick!
I'll pass your answer to the sysadmin, let's see how it goes :)
On Sat, May 11, 2013 at 12:08 AM, Nick Schmansky
wrote:
> Gari,
>
> Hi, your situation seems odd. Freesurfer does not require anything
> special in terms of a file system, or modify system settings of any sort,
> so I'
Can you check that the UID and GID both match on the client and server
sides? Is it the same user that is able to use other programs, yet
unable to write via Freesurfer? Is your user an NIS account?
Can you output
# ls -l $SUBJECTS_DIR
I assume that since you say other programs can write to th
Thanks Chris,
> ls -l $SUBJECTS_DIR: it works
> This is the output of the command (I cannot make sense out of it):
[glerma@cajal ~]$ cat /etc/fstab
/dev/VolGroup00/LogVol00 / ext3defaults1 1
LABEL=/boot /boot ext3defaults
Can you paste the output of "ls -l $SUBJECTS_DIR", so we can see what
the permissions are? You may also want to paste the output of the parent
directory as well.
On 05/10/2013 06:18 PM, Garikoitz Lerma-Usabiaga wrote:
Thanks Chris,
> ls -l $SUBJECTS_DIR: it works
> This is the output of the co
Yes,
first two lines for example in SUBJECTS_DIR (I had to change SUBJECTS_DIR
since now I have it in the app server, as said before):
drwxr-xr-x 77 glerma domain users 4096 Dec 20 17:25 BERTSO
drwxr-xr-x 10 glerma domain users 2048 Feb 14 16:27 BERTSO_MRI
and for the parent directory:
drwxr-x
For a workstation machine I prefer Ubuntu rather than Centos. There are
available drivers for graphic cards in Ubuntu that make the experience with
graphic tools (eg. tksurfer) much better than it is with Centos. In addition,
by default every developer tool (eg. the GNU compilers, debugger and
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