oh, yes, I think that is probably your problem. The left/right topology
fixing alone took more than 10 hours I think, so probably you got to 24
and they killed it. If they gave you 48 or even 30 it might have finished
On
Thu, 1 Jun 2017, Jasmin Alves wrote:
Hi Bruce,
I waited 24 hours, and th
Hi Bruce,
I waited 24 hours, and then the job, at that point it was killed by the
computing center I use. They have a max analysis time of 24 hours. Perhaps
the last steps are not being reached due to the large topological defects,
however I never encountered this problem before with FS5.3, what d
Hi Jasmin
how long did you wait? Is the process still running? The last step in the
log is not a very long one. Maybe someone/something killed your job
prematurely? I see no reason in the log that it wouldn't have finished
Bruce
On Thu, 1 Jun 2017, Jasmin Alves wrote:
Hi Bruce,
So it does
Hi Bruce,
So it does not matter that the recon-all.done script never appeared in the
script folder? Or that the isrunning.lh+rh script is still in the folder?
I plan to run the hippocampal subfield analysis on these folders, so I am
wondering if the subfield analysis can still function without t
Hi Jasmin
actually things look pretty reasonble given the degree of motion
corruption. Is it still running? I would expect it to finish ok. I doubt
you can get realiable thickness estimates off this kind of data, but you
should be able to do e.g. fMRI analysis.
There were a bunch of big defe
Hi Bruce,
I uploaded two subjects directories to the FTP site.
Thanks,
Jasmin
On Wed, May 31, 2017 at 3:24 PM, Bruce Fischl
wrote:
> you can put it on our ftp site:
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.
> nmr.mgh.harvard.edu_fswiki_FtpFileExchange&d=DwIDaQ&c=clK7kQ
>
you can put it on our ftp site:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
but at that point you might as well tar and gzip the entire subject dir
and upload it
On Wed, 31 May
2017, Jasmin Alves wrote:
Hi Bruce,
Thanks for the reply, below is a couple of sentences from the re
Hi Jasmin
typically that means there is a big topological defect, which definitely
can be caused by motion. What is the last couple of lines of the
recon-all.log file of one of the subjects? Can you upload an image we can
look at?
cheers
Bruce
On Wed, 31 May 2017,
Jasmin Alves wrote:
H
You probably have cerebellum or some extra cerebral structure attached
to the brain. Check the wm.mgz
On 05/31/2017 02:15 PM, Jasmin Alves wrote:
> Hello,
>
> I have used FS6.0 to do recon-all on about 57 brains, but for some
> reason, recon-all is not working on some brains, recon-all is not
Hi Cheng
why can't you visualize them? You should be able to load them on the
command line in freeview via:
freeview -f surf/lh.orig surf/lh.orig.nofix
or from the GUI.
cheers
Bruce
On Tue, 17 Jun 2014, Cheng Peng
wrote:
Hi!
I am a relative beginner with freesurfer and was going through
This is the output of env | grep MNI:
MNI_PERL5LIB=/usr/local/imsw/freesurfer/mni/lib/perl5/5.8.5
MNI_DIR=/usr/local/imsw/freesurfer/mni
MNI_DATAPATH=/usr/local/imsw/freesurfer/mni/data
I am using Red Hat Enterprise Linux 5
Dev
On Fri, Dec 5, 2008 at 1:57 PM, Nick Schmansky <[EMAIL PROTECTED]>w
what OS are you using? what version of perl does it have? what is the
output of:
env | grep MNI
On Fri, 2008-12-05 at 13:51 -0600, Devdutta W wrote:
> Nick,
> When I type nu_estimate_np_and_em, I did indeed see the message you
> mentioned. I also checked and found perl at /usr/bin/.
> I didn'
Nick,
When I type nu_estimate_np_and_em, I did indeed see the message you
mentioned. I also checked and found perl at /usr/bin/.
I didn't find any other installations of the mni tools in my path.
Are these the only things that usually cause recon-all to fail like this?
Any other ideas why it is fa
Dev,
What happens when you type:
nu_estimate_np_and_em
you should see:
nu_estimate_np_and_em, version 1.10
Usage: nu_estimate_np_and_em [-help] [options] input_volume.mnc
nu_field.imp
Incorrect number of arguments
do you have perl installed at /usr/bin/perl ?
do you have another installati
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