I can't see anything wrong either. Does it happen repeatedly? Can you
try running it without the -parallel flag?
On 1/7/2025 1:42 PM, Aaron Tanenbaum wrote:
External Email - Use Caution
You are correct. Attached is the correct one
On Tue, Jan 7, 2025 at 8:08 AM Douglas N. Greve
w
Are you sure this is the right recon-all.log file? At the end it says it
finished without error
On 1/6/2025 4:12 PM, Aaron Tanenbaum wrote:
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Hell All,
I am testing recon-all and found that it returned with an error. I am
not sure where the error is. The r
External Email - Use Caution
Thank you!
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: 23 June 2020 05:09
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] error in "recon-all -all -s su
You have to run through all of recon-all before running the subfields,
so just add -all to the command line
On 6/22/2020 2:06 PM, Shimura, Yuki wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I'm attempting to compute calculate hippocampal volumes, as described
on
hmmm, not sure. Your surface is very big with lots of defects and that is
also a very big defect. Can you bring up the lh.inflated.nofix and see if
anything is dramatically wrong with it (e.g. cerebellum or skull attached).
cheers
Bruce
On Tue, 15 Aug 2017, 王康程 wrote:
Hello FreeSurfer Devel
Thank you, we did that, and it was indeed an issue with the way we ran it.
Diana
> El 9 feb 2017, a las 18:19, Douglas Greve
> escribió:
>
> It says that it was "Killed" which sounds like the job exceeded some resource
> on the supercomputer. You should contact the administrators to see what
It says that it was "Killed" which sounds like the job exceeded some
resource on the supercomputer. You should contact the administrators to
see what the limits are and whether you exceeded them. You can also run
the same subject on a regular computer and see if it dies in the same place.
On
Dear FreeSurfer developers,
I am a new FreeSurfer user and I am trying to run it in a supercomputer
for the first time.
Recon-all finished with errors (see log attached) during skull stripping.
I have searched the archives and only found that it could be a memory
problem, but I am unsure ab
Hi Noam
it looks like the talairach alignment failed. You can usually find answers
on our wiki for what to do in this type of case. For example:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_tktools
cheers
Bruce
On Mon, 9 Feb 2015, Ben Eliezer, Noam wrote:
Hi Freesurfer su
Hi Freesurfer support,
I am receiving an error from recon-all and would be happy to get your opinion.
This dataset, I am processing, is generated by a 3D MPR (Sagittal orientation)
protocol.
It’s only one of many datasets I have and this is the only one giving me
problems…
The run seems to gen
Hi Stefano
do you have the perirhinal labels? If not, I'll attach them. Just copy them
into the fsaverage/label dir and you should be all set.
cheers
Bruce
On Thu, 31 Jul 2014, std...@virgilio.it
wrote:
Hi list,
during recon-all, I have this error in three subjects (some months ago I
an
Use this version
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.linux
doug
On 11/08/2012 10:01 PM, Zheng Hui wrote:
> Hi Doug,
>
> After updating the mri_segstats, all our recon-all encounter errors as
> follow log suggest. Please advice a work around.
>
> Thank you,
>
what version of freesurfer is being run? that error is from an old
version (prior to v4.5 i think). i suggest updating to v5.1.
n.
On Wed, 2011-06-15 at 08:52 +0800, Sophy Zhu wrote:
> Hello, Freesurfers,
>
> When I use *recon-all -all -s ...*
> there exists the error *mris_volmask.bin: error
Hello, Freesurfers,
When I use *recon-all -all -s ...*
there exists the error *mris_volmask.bin: error while loading shared
libraries:
/usr/local/freesurfer//lib/vtk/lib/vtk-5.2/libvtkRendering.so.5.2: cannot
restore segment prot after reloc: Permission denied*
Would you please tell me how to sol
http://www.nmr.mgh.harvard.edu/martinos/itgroup/seychelles.html
describes the cluster use. It will tell you how to check errors (there
are pbsjob files in your folder that contain output and error messages.
Best, Martin
On Thu, 2011-06-02 at 14:54 -0400, Chindhuri Selvadurai wrote:
> I'm not su
I'm not sure how to get that information. It does not give me an error
message in the terminal. Is there a log I could look at? Is there anything
that I need to do prior to the recon-all?
> Hi Chindhuri,
>
> we'll need to know what the error was that resulted in the non-zero exit
> status.
>
> che
Hi Chindhuri,
we'll need to know what the error was that resulted in the non-zero exit
status.
cheers
Bruce
On Thu, 2 Jun 2011, Chindhuri Selvadurai wrote:
> Hello,
>
> I am not able to do a regular recon-all of my data on seychelles-- I am
> doing the same thing I used to do. We have started m
Hello,
I am not able to do a regular recon-all of my data on seychelles-- I am
doing the same thing I used to do. We have started moving our data to a
different location, however, since this is all new data, I don't see how
this could be the problem.
I am using freesurfer 4, so I set this var bef
Dear Paola,
I think the problem might be that your operating system ships
libtiff.so.4 instead of libtiff.so.3 and that is why mris_volmask.bin
cannot find libtiff.so.3.
As far as I know you can just create a symbolic link from libtiff.so.3
to libtiff.so.4. In case your libraries are in /usr
Dear FS list,
I am trying to finish my first analyses with freesurfer; however, I have
some problems when running the last stages of recon-all.
In summary what I did:
1) recon-all -autorecon1 (worked well)
2) some minor brain strip editing
3) recon-all -autorecon2 (worked well)
4) some edi
I am running v4.5.0
On Jul 26, 2010, at 8:49 AM, Bruce Fischl wrote:
> Hi Philip,
>
> what version were you running? I think Martin Reuter fixed this bug.
>
> cheers
> Bruce
>
> On Mon, 26 Jul 2010, York, Philip wrote:
>
>> Dear Freesurfer experts,
>>
>> one of my recent recon-all processes
Hi Philip,
what version were you running? I think Martin Reuter fixed this bug.
cheers
Bruce
On Mon, 26 Jul 2010, York, Philip wrote:
> Dear Freesurfer experts,
>
> one of my recent recon-all processes exited with errors as seen here
>
> mri_ca_label GCA sequential renormalization: label 28 not
Dear Freesurfer experts,
one of my recent recon-all processes exited with errors as seen here
mri_ca_label GCA sequential renormalization: label 28 not consistently computed.
not using caudate to estimate GM means
setting label Right_VentralDC based on Left_VentralDC = 1.15 x + 0
estimating mea
Hi Everyone,
We're having a problem in our preprocessing (see below).
Any ideas what the problem may be?
Many thanks,
Massih
#
#...@# Nu Intensity Correction Thu Nov 19 13:40:47 EST 2009
mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2
/usr/local/
Juergen,
There is a bug in mri_segstats which causes these huge files. You will
also want to get mris_wm_volume. You can get them here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/stable
Nick
On Fri, 2008-09-26 at 08:15 +0200, Juergen Haenggi wrote:
> Dear FS experts
>
>
Jurgen,
I think it comes from the fact that FS could not find some file. I had similar
situation here a while ago, when I had almost full partition with FS data. FS
created about 4GB logfile.
Just a guess, didn't you move the data from your mac to linux to be
re-analyzed or finish the analysis
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