Try sending me another file (even junk.mgh). Until I get a valid file, I cannot do much doug
On 03/01/2014 02:14 AM, charujing123 wrote:
Hi doug, Thanks very much doug for your help all the time. I try mri_convert rh.38sb_score.10.mgh junk.mgh,and it display this: ===================================================== mri_convert rh.38sb_score.10.mgh junk.mgh mri_convert rh.38sb_score.10.mgh junk.mgh $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from rh.38sb_score.10.mgh... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to junk.mgh... ====================================================== I found junk.mgh after this done. So it worked. And I have many files like rh.38sb_score.10.mgh(i.e. rh.allsb_score.10.mgh, rh.36sb_score.10.mgh), all of these files have the same question. Doug, I donot know why.As it creates *.y.ocn.dat for only one cluster, may I try this: 1,generate a mask which only has one cluster from ocn.mgh:mri_binarize --i ocn.mgh --match 2 --o cluster2.mgh
2,The run mri_glmfit with --mask cluster2.mgh
3,Then run mri_glmfit-sim with simulation 4,So there is only one cluster in the *.cluster.summary, so it can create a *.y.ocn.dat. 5,So I can use this *.y.ocn.dat file to get the time course of specific cluster. Doug, is that appropriate, or is there any method to deal with my question? Thanks. All the best. Rujing Zha 2014-03-01
charujing123
*发件人：*Douglas N Greve greve@nmr.mgh.harvard.edu *发送时间：*2014-03-01 00:20 *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：* There appears to be something wrong with rh.38sb_score.10.mgh. Try running this mri_convert rh.38sb_score.10.mgh junk.mgh If that fails, then regenerate rh.38sb_score.10.mgh On 02/27/2014 08:12 PM, charujing123 wrote:
Hi doug, Thanks doug. I try to ftp by this manu,so I think server is "surfer.nmr.mgh.harvard.edu": $ ftp surfer.nmr.mgh.harvard.edu Connected to surfer.nmr.mgh.harvard.edu (132.183.202.158). 220 surfer.nmr.mgh.harvard.edu FTP server (Version
wu-2.6.2-15.7x.legacy) ready.
Name (surfer.nmr.mgh.harvard.edu:fsurfer): anonymous 331 Guest login ok, send your complete e-mail address as password. Password: 230 Guest login ok, access restrictions apply. Remote system type is UNIX. Using binary mode to transfer files. ftp> this information is available on the website:http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange All the best. Rujing Zha 2014-02-28
charujing123
*发件 人：*Douglas N Greve greve@nmr.mgh.harvard.edu *发送时间：*2014-02-28 01:01 *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：* 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 > > > _______________________________________________ > 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 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 The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error
and
the e-mail
contains patient information, please contact the Partners
Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was
sent to
you in error
but does not contain patient information, please contact the
sender
and properly
dispose of the e-mail.
-- 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
-- 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
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 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
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 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer