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"<charujing...@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"<charujing...@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 <gr...@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
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