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#ViewCSDFi..., 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
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