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#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

> > >

> > > _______________________________________________

> > > Freesurfer mailing list

> > > Freesurfer@nmr.mgh.harvard.edu

> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

> > --

> > 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

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> > _______________________________________________

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> > The information in this e-mail is intended only for the person to

> whom it is

> >

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> >

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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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> _______________________________________________

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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

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