Can you send the full terminal output?
On 02/24/2014 09:52 PM, charujing123 wrote:
> Hi doug and others,
> Thanks doug.
> Creating the something.y.ocn.dat,I find it can only creating an
> average thickness for one cluster. When my numbers of clusters in
> *sig.cluster.summary exceeding 1,then it cannot generate the
> something.y.ocn.dat,and error will be exported in the window:memory
> corruption.
> I know how to set the threshold, that is to say p<threshod value. So I
> want to know how to set p>0.1or some other value to get only one
> cluster average thickness.
> Thanks.
> ALL the best.
> Rujing Zha
> 2014-02-25
> ------------------------------------------------------------------------
> charujing123
> ------------------------------------------------------------------------
> *发件人：*Douglas N Greve <greve@nmr.mgh.harvard.edu>
> *发送时间：*2014-02-25 00:28
> *主题：*Re: [Freesurfer] Fw: Re: error in mri_glmfit-sim when using
> --bg and doss
> *收件人：*"freesurfer"<freesurfer@nmr.mgh.harvard.edu>
> *抄送：*
> Try setting the cwpvalthresh to .9 or so. I think this is a numerical
> error that occurs when the cwpthreshold is close to 1
> doug
> On 02/22/2014 04:53 AM, charujing123 wrote:
> > Hi doug and others,
> > I tried to perform it by this command "mri_glmfit-sim --glmdir my_dir
> > --no-sim mc-z.neg.3 --cwpvalthresh 0.999". It worked at first.However
> > it cannot work when I tried it again. It exited error after performing
> > the first contrast. The export message is as below:
> > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
> > Found 4 segmentations
> > Computing statistics for each segmentation
> > 1 1 169 169.000
> > 2 2 135 135.000
> > 3 3 90 90.000
> > Reporting on 3 segmentations
> > Computing spatial average of each frame
> > 0 1 2*** glibc detected *** mri_segstats: malloc(): memory corruption:
> > 0x2e61e810 ***
> > ======= Backtrace: =========
> > /lib/libc.so.6[0x9e11dd]
> > /lib/libc.so.6(__libc_malloc+0x67)[0x9e2d97]
> > /lib/libc.so.6[0x9cf4cf]
> > /lib/libc.so.6(fopen64+0x2c)[0x9d1a7c]
> > mri_segstats[0x80536cd]
> > /lib/libc.so.6(__libc_start_main+0xdc)[0x98ce9c]
> > mri_segstats(__gxx_personality_v0+0x1c9)[0x804f791]
> > ======= Memory map: ========
> > 00958000-00973000 r-xp 00000000 fd:00 60785448 /lib/ld-2.5.so
> > 00973000-00974000 r-xp 0001a000 fd:00 60785448 /lib/ld-2.5.so
> > 00974000-00975000 rwxp 0001b000 fd:00 60785448 /lib/ld-2.5.so
> > 00977000-00acb000 r-xp 00000000 fd:00 60784655 /lib/libc-2.5.so
> > 00acb000-00acc000 ---p 00154000 fd:00 60784655 /lib/libc-2.5.so
> > 00acc000-00ace000 r-xp 00154000 fd:00 60784655 /lib/libc-2.5.so
> > 00ace000-00acf000 rwxp 00156000 fd:00 60784655 /lib/libc-2.5.so
> > 00acf000-00ad2000 rwxp 00acf000 00:00 0
> > 00ad4000-00add000 r-xp 00000000 fd:00 60784725 /lib/libcrypt-2.5.so
> > 00add000-00ade000 r-xp 00008000 fd:00 60784725 /lib/libcrypt-2.5.so
> > 00ade000-00adf000 rwxp 00009000 fd:00 60784725 /lib/libcrypt-2.5.so
> > 00adf000-00b06000 rwxp 00adf000 00:00 0
> > 00b22000-00b2d000 r-xp 00000000 fd:00 60784686
> > /lib/libgcc_s-4.1.2-20080825.so.1
> > 00b2d000-00b2e000 rwxp 0000a000 fd:00 60784686
> > /lib/libgcc_s-4.1.2-20080825.so.1
> > 00c68000-00d48000 r-xp 00000000 fd:00 56176146 /usr/lib/libstdc++.so.6.0.8
>
> > 00d48000-00d4c000 r-xp 000df000 fd:00 56176146 /usr/lib/libstdc++.so.6.0.8
>
> > 00d4c000-00d4d000 rwxp 000e3000 fd:00 56176146 /usr/lib/libstdc++.so.6.0.8
>
> > 00d4d000-00d53000 rwxp 00d4d000 00:00 0
> > 00d72000-00d84000 r-xp 00000000 fd:00 60784662 /lib/libz.so.1.2.3
> > 00d84000-00d85000 rwxp 00011000 fd:00 60784662 /lib/libz.so.1.2.3
> > 08048000-08817000 r-xp 08048000 00:00 0
> > 08817000-2e63b000 rwxp 08817000 00:00 0 [heap]
> > f6300000-f6321000 rwxp f6300000 00:00 0
> > f6321000-f6400000 ---p f6321000 00:00 0
> > f6498000-f7e61000 rwxp f6498000 00:00 0
> > f7f02000-f7f04000 rwxp f7f02000 00:00 0
> > f7f04000-f7f2b000 r-xp 00000000 fd:00 60784705 /lib/libm-2.5.so
> > f7f2b000-f7f2c000 r-xp 00026000 fd:00 60784705 /lib/libm-2.5.so
> > f7f2c000-f7f2d000 rwxp 00027000 fd:00 60784705 /lib/libm-2.5.so
> > f7f2d000-f7f42000 r-xp 00000000 fd:00 60784716 /lib/libpthread-2.5.so
> > f7f42000-f7f43000 ---p 00015000 fd:00 60784716 /lib/libpthread-2.5.so
> > f7f43000-f7f44000 r-xp 00015000 fd:00 60784716 /lib/libpthread-2.5.so
> > f7f44000-f7f45000 rwxp 00016000 fd:00 60784716 /lib/libpthread-2.5.so
> > f7f45000-f7f47000 rwxp f7f45000 00:00 0
> > f7f47000-f7f4a000 r-xp 00000000 fd:00 60784670 /lib/libdl-2.5.so
> > f7f4a000-f7f4b000 r-xp 00002000 fd:00 60784670 /lib/libdl-2.5.so
> > f7f4b000-f7f4c000 rwxp 00003000 fd:00 60784670 /lib/libdl-2.5.so
> > f7f4c000-f7f4d000 rwxp f7f4c000 00:00 0
> > f7f6f000-f7f79000 r-xp 00000000 fd:00 60784678 /lib/libnss_files-2.5.so
> > f7f79000-f7f7a000 r-xp 00009000 fd:00 60784678 /lib/libnss_files-2.5.so
> > f7f7a000-f7f7b000 rwxp 0000a000 fd:00 60784678 /lib/libnss_files-2.5.so
> > f7f7b000-f7f7c000 rwxp f7f7b000 00:00 0
> > ff8e2000-ff8f7000 rwxp 7ffffffe9000 00:00 0 [stack]
> > ffffe000-fffff000 r-xp ffffe000 00:00 0
> > Writing to ../rh.demo.glmdir/demo-doss-CON2IA/mc-z.neg.3.y.ocn.dat
> > Abort
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
> > Thanks.
> > All the best.
> > Rujing Zha
> > 2014-02-22
> > ------------------------------------------------------------------------
>
> > charujing123
> > ------------------------------------------------------------------------
>
> > *发件人：*"charujing123"<charujing123@163.com>
> > *发送时间：*2014-02-22 10:22
> > *主题：*[Freesurfer] Fw: Re: error in mri_glmfit- sim when using --bg
> > and doss
> > *收件 人：*"freesurfer@nmr.mgh.harvard.edu"
> <freesurfer@nmr.mgh.harvard.edu>
> > *抄送：*
> > Hi doug and others,
> > I am sorry for pasting files in my first contrast directory, if it can
> > help me desolve the question:
> > cache.th23.abs.pdf.dat mc-z.abs.2.sig.cluster.summary
> > mc-z.neg.3.sig.cluster.summary mc-z.pos.3.sig.cluster.summary
> > cache.th23.abs.sig.cluster.mgh mc-z.abs.2.sig.masked.mgh
> > mc-z.neg.3.sig.masked.mgh mc-z.pos.3.sig.masked.mgh
> > cache.th23.abs.sig.cluster.summary mc-z.abs.2.sig.ocn.annot
> > mc-z.neg.3.sig.ocn.annot mc-z.pos.3.sig.ocn.annot
> > cache.th23.abs.sig.masked.mgh mc-z.abs.2.sig.ocn.mgh
> > mc-z.neg.3.sig.ocn.mgh mc-z.pos.3.sig.ocn.mgh
> > cache.th23.abs.sig.ocn.annot mc-z.abs.2.sig.voxel.mgh
> > mc-z.neg.3.sig.voxel.mgh mc-z.pos.3.sig.voxel.mgh
> > cache.th23.abs.sig.ocn.mgh mc-z.abs.3.pdf.dat mc-z.neg.3.y.ocn.dat
> > mc-z.pos.3.y.ocn.dat
> > cache.th23.abs.sig.voxel.mgh mc-z.abs.3.sig.cluster.mgh
> > mc-z.neg.pdf.dat mc-z.pos.pdf.dat
> > C.dat mc-z.abs.3.sig.cluster.summary mc-z.neg.sig.cluster.mgh
> > mc-z.pos.sig.cluster.mgh
> > cnr.mgh mc-z.abs.3.sig.masked.mgh mc-z.neg.sig.cluster.summary
> > mc-z.pos.sig.cluster.summary
> > F.mgh mc-z.abs.3.sig.ocn.annot mc-z.neg.sig.masked.mgh
> > mc-z.pos.sig.masked.mgh
> > gamma.mgh mc-z.abs.3.sig.ocn.mgh mc-z.neg.sig.ocn.annot
> > mc-z.pos.sig.ocn.annot
> > gammavar.mgh mc-z.abs.3.sig.voxel.mgh mc-z.neg.sig.ocn.mgh
> > mc-z.pos.sig.ocn.mgh
> > maxvox.dat mc-z.abs.3.y.ocn.dat mc-z.neg.sig.voxel.mgh
> > mc-z.pos.sig.voxel.mgh
> > mc-z.abs.2.pdf.dat mc-z.neg.3.pdf.dat mc-z.pos.3.pdf.dat
> > mc-z.pos.y.ocn.dat
> > mc-z.abs.2.sig.cluster.mgh mc-z.neg.3.sig.cluster.mgh
> > mc-z.pos.3.sig.cluster.mgh sig.mgh
> > Thanks.
> > All the best.
> > Rujing Zha
> > 2014-02-22
> > ------------------------------------------------------------------------
>
> > charujing123
> > ------------------------------------------------------------------------
>
> > *发件人：*"charujing123"<charujing123@163.com>
> > *发送时间：*2014-02-22 10:18
> > *主题：*Re: [Freesurfer] error in mri_glmfit-
> sim when using --bg and doss
> > *收件 人：*"freesurfer@nmr.mgh.harvard.edu"
> <freesurfer@nmr.mgh.harvard.edu>
> > *抄送：*
> > Hi doug and others,
> > Thanks doug.
> > According this information
> > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#ViewCSDFile,
>
> > I try to find the csd files in the csd folder(I am not sure this is
> > what you just told me). But there are the csd files as I run
> > simulation with --bg option.
> > Also I try to find the csd files in the first contrast directory, but
> > I think, maybe I am wrong, none of these is csd files that you suggest.
> > Doug, would you please describe it more detailly, as I am a new user
> > for FS?
> > Thanks doug and others.
> > All the best.
> > Rujing Zha
> > 2014-02-22
> > ------------------------------------------------------------------------
>
> > charujing123
> > ------------------------------------------------------------------------
>
> > *发件 人：*Douglas Greve <greve@nmr.mgh.harvard.edu>
> > *发送时间：*2014-02-21 23:49
> > *主题：*Re: [Freesurfer] error in mri_glmfit-
> sim when using --bg and doss
> > *收件 人：*"freesurfer"<freesurfer@nmr.mgh.harvard.edu>
> > *抄送：*
> >
> > When you actually run the simulation, it only runs it for the first
> > contrast. The simulation is the same for all contrasts, so you can
> > just copy the csd files from the first contrast to the others, then
> > run mri_glmfit-sim with the --no-sim option
> > doug
> >
> >
> >
> > On 2/21/14 5:47 AM, charujing123 wrote:
> >> Hi FS experts,
> >> I ran the mri_glmfit with DOSS, followed by the
> >> mri_glmfit-sim(running with --bg option). I have 4 contrasts, but
> >> only the first one has some files of corrected results(i.e.
> >> mc-z.neg.3.sig.cluster.summary). I donot know why. So I upload the
> >> log file in the attachment. However, previously I ran mri_glmfit by
> >> DODS, and mri_glmfit-sim with --bg option.All the contrasts have
> >> corrected results.
> >> Thanks.
> >> All the best.
> >> Rujing Zha
> >> 2014-02-21
> >> ------------------------------------------------------------------------
>
> >> charujing123
> >>
> >>
> >> _______________________________________________
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
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> >
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu
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