Re: [Freesurfer] mri_glmfit-sim with conjunction maps but without pre-cached data

Hi Doug, the script I am running just calls mri_mcsim like this: ~/bin/mri_mcsim \ --surface avg_monkey rh \ --fwhm-max 10 \ --o csd \ --base mcz \ --nreps 10000 \ --no-label \

When I call this from the script or from the command line, I get a segmentation fault. The last line in the terminal reads: 1152 99.89 0 Segmentation fault This seems to be happening after 1152 iterations, which leaves me puzzled. Caspar

2013/11/5 Douglas N Greve greve@nmr.mgh.harvard.edu

I can't tell what is going on in the script. Run mri_segstats from the cmd line and send the terminal output. doug

On 11/05/2013 10:38 AM, Caspar M. Schwiedrzik wrote:

...

Hi Doug, this is not working for me yet. I am using freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0-full, which contains v1.17 of mri_mcsim. I tried the two centos4 versions of mri_mcsim v1.24 that Zeke provided. For the 64bit version, I get the following error: ./cache_csd_surface.script: line 10: 17763 Segmentation fault

For the 32bit version, I get ERROR: ld.so: object '/space/opt/libGL.so.1' from LD_PRELOAD cannot be preloaded: ignored. and then after 1153 iterations, I get 78.91 0 ./cache_csd_surface.script: line 10: 18061 Segmentation fault.

Not sure why this is happening. Thanks, Caspar

2013/11/4 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto: 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>
    <mailto: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>
        <mailto: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>
            <mailto: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
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                    <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>
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                                 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
    <mailto:greve@nmr.mgh.harvard.edu>
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                                         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
                            <greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>
                    <mailto:greve@nmr.mgh.harvard.edu
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                                                 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
    <mailto:greve@nmr.mgh.harvard.edu>
                    <mailto:greve@nmr.mgh.harvard.edu
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                       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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                     >
    https://mail.nmr.mgh.harvard.__edu/mailman/listinfo/__freesurfer


                                                  <

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%3E

                     --
                     Douglas N. Greve, Ph.D.
                     MGH-NMR Center
    greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
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