2013/11/4 Douglas N Greve <greve@nmr.mgh.harvard.edu>

Caspar, is this resolved yet? What version of FS is your base installation and for what platform?
doug

On 11/01/2013 01:29 PM, Caspar M. Schwiedrzik wrote:

Hi again,
I keep getting segmentation fault errors (this time with the centOS4 version).
After 1153 iterations, I get 78.91 0 ./cache_csd_surface.script: line 10: 18061 Segmentation fault ~/bin/mri_mcsim --surface avg_monkey rh --fwhm-max 10 --o csd --base mcz --nreps 10000 --no-label
This version also signaled "ERROR: ld.so: object '/space/opt/libGL.so.1' from LD_PRELOAD cannot be preloaded: ignored" when it started.
With the centOS4 64bit version, I got a segmentation fault error with the first iteration, or even before.
Caspar

2013/11/1 Caspar M. Schwiedrzik <cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>

just a quick update. I just saw that the centOS4 version threw the
following error message:
ERROR: ld.so: object '/space/opt/libGL.so.1' from LD_PRELOAD
cannot be preloaded: ignored.
Do I need to worry about this?
Thanks, Caspar

2013/11/1 Caspar M. Schwiedrzik <cschwiedrz@rockefeller.edu
<mailto:cschwiedrz@rockefeller.edu>>

Hi Zeke,
thanks for making these available. The centOS4 version seems
to work so far, for the
centOS4_x86_64 version I got the following error message:
./cache_csd_surface.script: line 10: 17763 Segmentation fault
Caspar

2013/11/1 Z K <zkaufman@nmr.mgh.harvard.edu
<mailto:zkaufman@nmr.mgh.harvard.edu>>

Casper,

This email thread is kinda long and Im not able to clearly
decipher what has been tried and what hasn't, so Im
sending you a link to all 3 dev versions of mri_mcsim that
we build.

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/casper/

This includes the following:

-centOS4
-centOS4_x86_64
-centOS6_x86_64

Unfortunately we do not have a centOS5 build of that binary.

-Zeke

On 11/01/2013 08:09 AM, Caspar M. Schwiedrzik wrote:

Hi Doug, Nick, and Zeke,
just following up: Is there a version of mri_mcsim
>1.17 that is
compatible with centos5?

Thanks!
Caspar

2013/10/30 Douglas N Greve <greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>

Nick/Zeke, do we have anything that will run under
CentoOS5?

On 10/30/2013 12:00 PM, Caspar M. Schwiedrzik wrote:

Hi Doug,
with the new version, I am now getting the
following error
(excerpt):
after it dispalys the average vertex area,
*** glibc detected *** .../bin/mri_mcsim:
malloc(): smallbin
double linked list corrupted:
0x00000000281efc40 ***
followed by a backtrace and a memory map.
This did not happen when I ran it with
--checkopts.
Caspar

2013/10/30 Douglas N Greve
<greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
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<mailto:greve@nmr.mgh.harvard.>__edu

<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>>

OK, I put a centos4 build there, that
should work

On 10/30/2013 11:05 AM, Caspar M.
Schwiedrzik wrote:

Hi Doug,

that would be Red Hat Enterprise
Linux Server release 5.9
(Tikanga)
Caspar

2013/10/30 Douglas N Greve
<greve@nmr.mgh.harvard.edu
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<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>>>

what OS platform are you using?

On 10/30/2013 11:00 AM, Caspar M.
Schwiedrzik wrote:

Hi Doug,

thanks for the advice.
When I try to use the new
mri_mcscim, I get the
following
error messages:
/usr/lib64/libstdc++.so.6: version
`GLIBCXX_3.4.11'
not found
/usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9'
not found
/lib64/libc.so.6: version `GLIBC_2.7' not found
Caspar

2013/10/30 Douglas N Greve
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<mailto:greve@nmr.mgh.harvard.edu>>>>>>

On 10/30/2013 08:51 AM,
Caspar M.
Schwiedrzik wrote:

Hi Doug,
thank you very much!
I have two follow-up
questions for your two
suggestions:
1) If I want to use mri_glmfit-sim but my
conjunctions
are not
from contrasts that are all from the
same GLM,
I guess
I can
still do what you suggested but I will
have to
come up
with a
fwhm.dat for the conjunction, correct?
Is there a way to compute this from the
conjunction
sig map,
or should I use the average or the max
or the
min of the
contrasts that go into the conjunction?
This
is for
functional
data.

If they are not from the
same GLM, then I would
use the
larger of
the two FWHMs.

2) It seems that there is a version of
mri_mcsim that
allows
one to specify a range of FWHM with the
flag
--fwhm-max;
however, version 1.17 that comes with
the 5.1
and 5.3
releases
does bot have that option. Is the
version of
mri_mcsim
that
understands --fwhm-max available?

Try
ftp://surfer.nmr.mgh.harvard.__edu/transfer/outgoing/flat/__greve/mri_mcsim

<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_mcsim>
doug

Thanks again, Caspar

2013/10/24 Douglas N Greve
<greve@nmr.mgh.harvard.edu
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<mailto:greve@nmr.mgh.harvard.>__edu

<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>>>>>

Hi Caspar, there are a couple of things
you can do:

1. Go into the mri_glmfit folder
used to
create
the input
contrasts to
the conjunction. Create a
subfolder. Save the
conjunction as
sig.mgz and
create a file called "C.dat" (it can be
empty) in
this folder.
Then run
mri_glmfit-sim specifying to do the
simulation
rather than
using
cached
data.

2. Create cached data by running
mri_mcsim. This
may take
longer than
#1, but once you have the cached
data you
do not
need to
run it again,
which could be useful if you are
going to
do more
analyses
with this
template

doug

On 10/23/2013 02:55 PM, Caspar M.
Schwiedrzik wrote:
> Hi,
> I have a question regarding
cluster size
thresholding using
> mri_glmfit-sim. Namely, I have a
sig.nii
conjunction map
that I made
> with mri_concat.
> The analyses that serve as input
to the
conjunction map
are done
on a
> custom surface template.
> If I want to run mri_glmfit-sim, how
would that
work? I
obviously do
> not have precached data.
> Thanks, Caspar
>
>
>
>
>
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--
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<tel:617-726-7422 <tel:617-726-7422>
<tel:617-726-7422 <tel:617-726-7422>>>>
<tel:617-726-7422
<tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>>
<tel:617-726-7422 <tel:617-726-7422>
<tel:617-726-7422 <tel:617-726-7422>>>
<tel:617-726-7422 <tel:617-726-7422>
<tel:617-726-7422 <tel:617-726-7422>>
<tel:617-726-7422 <tel:617-726-7422>
<tel:617-726-7422 <tel:617-726-7422>>>>>
<tel:617-726-7422 <tel:617-726-7422>
<tel:617-726-7422 <tel:617-726-7422>>
<tel:617-726-7422 <tel:617-726-7422>
<tel:617-726-7422 <tel:617-726-7422>>>

<tel:617-726-7422
<tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>>
<tel:617-726-7422 <tel:617-726-7422>
<tel:617-726-7422 <tel:617-726-7422>>>>

<tel:617-726-7422 <tel:617-726-7422>
<tel:617-726-7422 <tel:617-726-7422>>
<tel:617-726-7422 <tel:617-726-7422>
<tel:617-726-7422 <tel:617-726-7422>>>
<tel:617-726-7422 <tel:617-726-7422>
<tel:617-726-7422 <tel:617-726-7422>>
<tel:617-726-7422 <tel:617-726-7422>
<tel:617-726-7422 <tel:617-726-7422>>>>>>

Bugs:
surfer.nmr.mgh.harvard.edu/__fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/__fswiki/BugReporting>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>

<http://surfer.nmr.mgh.__harvard.edu/fswiki/__BugReporting
<http://harvard.edu/fswiki/__BugReporting>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>

<http://surfer.nmr.mgh.__harvard.edu/fswiki/__BugReporting
<http://harvard.edu/fswiki/__BugReporting>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>

<http://surfer.nmr.mgh.__harvard.edu/fswiki/__BugReporting
<http://harvard.edu/fswiki/__BugReporting>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>

<http://surfer.nmr.mgh.__harvard.edu/fswiki/__BugReporting
<http://harvard.edu/fswiki/__BugReporting>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
FileDrop:
https://gate.nmr.mgh.harvard.__edu/filedrop2
<https://gate.nmr.mgh.harvard.edu/filedrop2>
www.nmr.mgh.harvard.edu/__facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/__facility/filedrop/index.html>
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

<http://www.nmr.mgh.harvard.__edu/facility/filedrop/index.__html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>

<http://www.nmr.mgh.harvard.__edu/facility/filedrop/index.__html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>

<http://www.nmr.mgh.harvard.__edu/facility/filedrop/index.__html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>

<http://www.nmr.mgh.harvard.__edu/facility/filedrop/index.__html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>

Outgoing:
ftp://surfer.nmr.mgh.harvard.__edu/transfer/outgoing/flat/__greve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>

_________________________________________________

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