Re: [Freesurfer] Error: cannot open libXss.so.1?
I had this same problem running on a cluster, if you can get your
sysadmin to install:
libXScrnSaver
It should fix it.
Good luck,
-Sam
On 13/12/2009 2:32 PM, Nick Schmansky wrote:
i'm guessing from the 'compute-0-1.local' bit of your output that this
was run on cluster, which probably doesnt have the X-libs installed
(clusters generally dont include the graphics libs). unfortunately, our
mris_volmask is built against a VTK lib which relies upon linking
against these (even though it doesnt use them: VTK is primarily a
visualization lib, but has some very useful volume/surface routines as
well). the only short-term solution for you is to use
mris_volmask_novtk, which is an alternate binary that doesnt use vtk,
but doesnt produce nearly the quality cortical ribbon that VTK does.
but it will have to do (and is irrelevant if you need only the cortical
and subcortical data: the volmask is used only the create the aparc
+aseg.mgz and wmparc.mgz files).
for the long-term, we are working on a replacement to mris_volmask that
doesnt use the VTK lib, but produces identical (or nearly so) results.
this wont appear for a couple more months though.
n.
On Sun, 2009-12-13 at 10:57 +0900, SG KIM wrote:
Dear Freesurfer,
I ran recon-all with -all flag,
and I've got an error message as below:
mris_volmask.bin: error while loading shared libraries: libXss.so.1:
cannot open shared object file: No such file or directory
Linux compute-0-1.local 2.6.18-92.1.13.el5PAE #1 SMP Wed Sep 24
20:07:49 EDT 2008 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Tue Dec 8 07:43:35 KST 2009
I ran it on {Intel(R) Xeon(R) CPU E5345 @ 2.33GHz (4096 KB cache)}
with {Linux compute-0-1.local 2.6.18-92.1.13.el5PAE #1 SMP Wed Sep 24
20:07:49 EDT 2008 i686 i686 i386 GNU/Linux}
I've googled it, only one case was posted via this mailing list.
Yes, I want to know why this error occur but also how to fix it.
Please help me out here! 'A`
Mr. SG KIM.
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[Freesurfer] T1 and T2 in one recon-all
Hi Freesurfers, Looking through the mail archives it seems T1 and T2 runs for a single subject should not be combined when doing recon-all. Is this still the case? Thank you for your time, Cheers, -Sam ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] T1 and T2 in one recon-all
Thank you for the quick reply Bruce. I'm new to freesurfer, do you know if there is any benefit to including T2 in the process workflow somewhere? Cheers, -Sam On 30/11/2009 11:35 PM, Bruce Fischl wrote: yes, just the T1. cheers, Bruce On Mon, 30 Nov 2009, Samuel Inverso wrote: Hi Freesurfers, Looking through the mail archives it seems T1 and T2 runs for a single subject should not be combined when doing recon-all. Is this still the case? Thank you for your time, Cheers, -Sam ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] T1 and T2 in one recon-all
Ok, I would be interested in your damaged white mater tools when it's released (or even if its in a generally usable form now) as I'm working with a large data set of multiple sclerosis subjects. Cheers, -Sam On 30/11/2009 11:54 PM, Bruce Fischl wrote: not for the default workflow, no. There are other things we are working on such as damaged white matter estimation that would benefit, but nothing released. cheers Bruce On Mon, 30 Nov 2009, Samuel Inverso wrote: Thank you for the quick reply Bruce. I'm new to freesurfer, do you know if there is any benefit to including T2 in the process workflow somewhere? Cheers, -Sam On 30/11/2009 11:35 PM, Bruce Fischl wrote: yes, just the T1. cheers, Bruce On Mon, 30 Nov 2009, Samuel Inverso wrote: Hi Freesurfers, Looking through the mail archives it seems T1 and T2 runs for a single subject should not be combined when doing recon-all. Is this still the case? Thank you for your time, Cheers, -Sam ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
