what server? On 02/27/2014 02:14 AM, charujing123 wrote:
Hi doug, As file drop fail to me, so I try use ftp. And it work. I sent these 2 files in the server. Thanks doug.Looking forward your help. ALL the best. Rujing Zha 2014-02-27
charujing123
*发件人：*Douglas N Greve greve@nmr.mgh.harvard.edu *发送时间：*2014-02-27 01:54 *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：* Can you send me rh.38sb_score.dods.glmdir/38sb_score-dods/mc-z.neg.3.sig.ocn.mgh and /mnt/sdb1/psylab16/BACKUP/freesurfer/freesurfer/subjects/glm/rh.38sb_score.10.mgh
through our file drop https://gate.nmr.mgh.harvard.edu/filedrop2 On 02/26/2014 01:16 AM, charujing123 wrote:
Hi doug, OK. Terminal output of "mri_glmfit-sim --glmdir ../ --no-sim mc-z.neg.3 --cwpvalthresh */0.5/*" is included in */file1/*, which cannot create something.y.ocn.dat as its several clusters. Terminal output of "mri_glmfit-sim --glmdir ../ --no-sim mc-z.neg.3 --cwpvalthresh */0.1/*" is included in */file2/*, which can create something.y.ocn.dat as it has only one cluster. Thanks. All the best. Rujing Zha 2014-02-26
charujing123
*发件 人：*Douglas N Greve greve@nmr.mgh.harvard.edu *发送时间：*2014-02-26 00:29 *主题：*Re: [Freesurfer] Fw: Re: error in mri_glmfit- sim when using --bg and doss *收件人：*"charujing123"charujing123@163.com *抄 送：*"freesurfer@nmr.mgh.harvard.edu"
freesurfer@nmr.mgh.harvard.edu
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#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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-- 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 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing:
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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 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing:
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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 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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