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
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> _______________________________________________
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> Freesurfer@nmr.mgh.harvard.edu
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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