Hi,
It looks like the error I was obtaining from mris_preproc looks like it
was due to a failure in stxgrinder-sess that I did not realize had
occurred. I have a feeling that once this problem is resolved mris_preproc
will run correctly, but help here would be much appreciated...The error is
pasted below.
Thanks,
Cameron
[troy:retrievalnewest] (nmr-stable3-env) stxgrinder-sess -sf sessidall -a
retrievalSPMHRF_5cond_40TW -c sh+smvsnh
--------------------------------------------------------------
stxgrinder-sess logfile is
/autofs/space/troy_003/users/retrievalnewest/log/stxgrinder-sess.071026163952.log
--------------------------------------------------------------
Contrast List: sh+smvsnh
MLF is /tmp/stxgrinder-sess-6028.m
-----------------------------------------------------
Warning: Unable to open display iconic, MATLAB is starting without a display.
You will not be able to display graphics on the screen.
Warning:
MATLAB is starting without a display, using internal event queue.
You will not be able to display graphics on the screen.
< M A T L A B >
Copyright 1984-2005 The MathWorks, Inc.
Version 7.1.0.183 (R14) Service Pack 3
August 02, 2005
Warning: Name is nonexistent or not a directory:
/usr/pubsw/common/matlab/7.1/toolbox/matlab/guide.
Warning: Name is nonexistent or not a directory:
/usr/pubsw/common/matlab/7.1/toolbox/matlab/plottools.
Warning: Name is nonexistent or not a directory:
/usr/pubsw/common/matlab/7.1/toolbox/shared/glue.
Warning: Name is nonexistent or not a directory:
/usr/pubsw/common/matlab/7.1/toolbox/simulink/simulink/MPlayIO.
Warning: Name is nonexistent or not a directory:
/usr/pubsw/common/matlab/7.1/toolbox/simulink/dataimportexport.
Warning: Name is nonexistent or not a directory:
/usr/pubsw/common/matlab/7.1/toolbox/shared/hdlshared.
Warning: Name is nonexistent or not a directory:
/usr/pubsw/common/matlab/7.1/toolbox/eml/eml.
Warning: Name is nonexistent or not a directory:
/usr/pubsw/common/matlab/7.1/toolbox/emlcoder/emlcoder.
Warning: Name is nonexistent or not a directory:
/usr/pubsw/common/matlab/7.1/toolbox/emlcoder/emlcodermex.
Warning: Name is nonexistent or not a directory:
/usr/pubsw/common/matlab/7.1/toolbox/fixedpoint/fixedpoint.
Warning: Name is nonexistent or not a directory:
/usr/pubsw/common/matlab/7.1/toolbox/fixedpoint/fidemos.
Warning: Name is nonexistent or not a directory:
/usr/pubsw/common/matlab/7.1/toolbox/slvnv/simcoverage.
Warning: Name is nonexistent or not a directory:
/usr/pubsw/common/matlab/7.1/toolbox/vr/vr.
Warning: Name is nonexistent or not a directory:
/usr/pubsw/common/matlab/7.1/toolbox/vr/vrdemos.
Warning: Name is nonexistent or not a directory:
/usr/pubsw/common/matlab/7.1/toolbox/shared/filterdesignlib.
Warning: Name is nonexistent or not a directory:
/usr/pubsw/common/matlab/7.1/toolbox/dspblks/splibmex.
Warning: Name is nonexistent or not a directory:
/usr/pubsw/common/matlab/7.1/toolbox/shared/sealib.
Warning: Name is nonexistent or not a directory:
/usr/pubsw/common/matlab/7.1/toolbox/wavelet/wmultisig1d.
Warning: Name is nonexistent or not a directory:
/usr/pubsw/common/matlab/7.1/toolbox/shared/spcuilib.
Warning: Name is nonexistent or not a directory:
/usr/pubsw/common/matlab/7.1/toolbox/ident/nlident.
Warning: Name is nonexistent or not a directory:
/usr/pubsw/common/matlab/7.1/toolbox/ident/iddemos/examples.
Warning: Name is nonexistent or not a directory:
/usr/pubsw/common/matlab/7.1/toolbox/shared/slcontrollib.
Warning: Name is nonexistent or not a directory:
/usr/pubsw/common/matlab/7.1/toolbox/optim/optim.
Warning: Name is nonexistent or not a directory:
/usr/pubsw/common/matlab/7.1/toolbox/optim/optimdemos.
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
/space/orsay/8/megdev/megsw/mne/matlab/toolbox added to path
/space/orsay/8/megdev/megsw/mne/matlab/examples added to path
ans =
/autofs/space/troy_003/users/retrievalnewest
>> >> >> >> >> >> >> >> >> >> >> >> >> >> >>
nthsess = 1 SM0C1 time=0.009921 --------
/autofs/space/troy_003/users/retrievalnewest/SM0C1
------------------------------------------------------------------------
Segmentation violation detected at Fri Oct 26 16:40:05 2007
------------------------------------------------------------------------
Configuration:
MATLAB Version: 7.1.0.183 (R14) Service Pack 3
MATLAB License: 41630
Operating System: Linux 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:21:39 CDT
2006 i686
Window System: No active display
Current Visual: None
Processor ID: x86 Family 15 Model 2 Stepping 5, GenuineIntel
Virtual Machine: Java is not enabled
Default Charset: UTF-8
Register State:
eax = bfff6ea8 ebx = 417b2d8c
ecx = 6c626174 edx = bfff6ea8
esi = 435dd390 edi = bfff8c40
ebp = bfff76c0 esp = bfff6e80
eip = 00705a39 flg = 00210286
Stack Trace:
[0] libc.so.6:strcat~(0x732f7265, 0x6c626174, 0x622f3465, 0x2f3a6e69) +
9 bytes
Please follow these steps in reporting this problem to The MathWorks so
that we have the best chance of correcting it:
1. Send this crash report to [EMAIL PROTECTED] for automated analysis.
For your convenience, this information has been recorded in:
/homes/13/cameo/matlab_crash_dump.6194
2. Also, if the problem is reproducible, send the crash report to
[EMAIL PROTECTED] along with:
- A specific list of steps that will reproduce the problem
- Any M, MEX, MDL or other files required to reproduce the problem
- Any error messages displayed to the command window
A technical support engineer will contact you with further information.
Thank you for your assistance. Please save your workspace and restart
MATLAB before continuing your work.
------------------------------------------------------------------------
Segmentation violation detected at Fri Oct 26 16:40:05 2007
------------------------------------------------------------------------
Configuration:
MATLAB Version: 7.1.0.183 (R14) Service Pack 3
MATLAB License: 41630
Operating System: Linux 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:21:39 CDT
2006 i686
Window System: No active display
Current Visual: None
Processor ID: x86 Family 15 Model 2 Stepping 5, GenuineIntel
Virtual Machine: Java is not enabled
Default Charset: UTF-8
Register State:
eax = 0000006f ebx = 406a60cc
ecx = 40345c24 edx = e0858bff
esi = 403d3506 edi = bfff8d50
ebp = bfff9c48 esp = bfff9c20
eip = 4041ac9b flg = 00210286
Stack Trace:
[0] libmwm_interpreter.so:(anonymous
namespace)::inPrtlineErrMsg(int)(111, 23, 0x438dd6f0, 0xbfff9c70) + 75
bytes
[1] libmwm_interpreter.so:(anonymous
namespace)::Mfun_call_context::~Mfun_call_context()(0xbfff9cd0, 0,
0x438dd6f0, 1) + 784 bytes
[2] libmwm_interpreter.so:inWordsj(1, 0xbfffa100, 1, 0xbfffa160) + 778
bytes
[3] libmwm_interpreter.so:Mfh_mp::dispatch_file(_mdUnknown_workspace*,
int, mxArray_tag**, int, mxArray_tag**)(0x438dd6f0, 0, 1, 0xbfffa100) +
389 bytes
[4] libmwm_interpreter.so:Mfh_mp::dispatch_file(int, mxArray_tag**, int,
mxArray_tag**)(0x438dd6f0, 1, 0xbfffa100, 1) + 53 bytes
[5] libmwm_dispatcher.so:Mfh_file::dispatch_fh(int, mxArray_tag**, int,
mxArray_tag**)(0x438dd6f0, 1, 0xbfffa100, 1) + 281 bytes
[6] libmwm_interpreter.so:inDispatchFromStack(526, 0x0839fa78
"fast_ldbhdr", 1, 1) + 1422 bytes
[7] libmwm_interpreter.so:.L23(29, 0xffffffd8, 1, 0) + 38 bytes
[8] libmwm_interpreter.so:.L990(1, 0, 57, 0) + 228 bytes
[9] libmwm_interpreter.so:inInterPcodeSJ(inDebugCheck, int, int,
opcodes, inPcodeNest_tag*, int*)(1, 0, 22, 0) + 474 bytes
[10] libmwm_interpreter.so:inExecuteMFunctionOrScript(Mfh_mp*,
bool)(0x430c42b0, 1, 0xbfffab50, 0) + 537 bytes
[11] libmwm_interpreter.so:inExecCompScript(0, 0xbfffab50, 0x430c42b0,
0x004a7a53) + 296 bytes
[12] libmwm_interpreter.so:Mfh_mp::dispatch_file(_mdUnknown_workspace*,
int, mxArray_tag**, int, mxArray_tag**)(0x430c42b0, 0, 0, 0xbfffab50) +
182 bytes
[13] libmwm_interpreter.so:Mfh_mp::dispatch_file(int, mxArray_tag**,
int, mxArray_tag**)(0x430c42b0, 0, 0xbfffab50, 0) + 53 bytes
[14] libmwm_dispatcher.so:Mfh_file::dispatch_fh(int, mxArray_tag**, int,
mxArray_tag**)(0x430c42b0, 0, 0xbfffab50, 0) + 281 bytes
[15] libmwm_interpreter.so:inDispatchFromStack(523, 0x42c25b84
"fast_stxgrinder2_sess", 0, 0) + 1422 bytes
[16] libmwm_interpreter.so:inDispatchCall(char const*, int, int, int,
int*, int*)(0x42c25b84 "fast_stxgrinder2_sess", 523, 0, 0) + 139 bytes
[17] libmwm_interpreter.so:.L802(2, 0, 0, 0) + 174 bytes
[18] libmwm_interpreter.so:inInterPcodeSJ(inDebugCheck, int, int,
opcodes, inPcodeNest_tag*, int*)(2, 0, 0, 0) + 474 bytes
[19] libmwm_interpreter.so:inInterPcode(2, 0, 0xbfffb1b8 ", 0x40045307)
+ 137 bytes
[20] libmwm_interpreter.so:in_local_call_eval_function(int*,
_pcodeheader*, int*, mxArray_tag**, inDebugCheck)(0, 0xbfffbbb0,
0xbfffbc3c, 0xbfffbc68) + 153 bytes
[21] libmwm_interpreter.so:inEvalStringWithIsVarFcn(_memory_context*,
char const*, EvalType, int, mxArray_tag**, inDebugCheck, _pcodeheader*,
int*, bool (*)(void*, char const*), void*)(0x400b6128, 0x081ac740
"fast_stxgrinder2_sess;\n", 0, 0) + 2416 bytes
[22] libmwm_interpreter.so:inEvalCmdNoEnd(0x081ac740
"fast_stxgrinder2_sess;\n", 1, 2835432, 0) + 135 bytes
[23] libmwbridge.so:ThrowSignal(char const*)(0x081ac740
"fast_stxgrinder2_sess;\n", 0, 0x0804c418 ", 0x41bc7908) + 162 bytes
[24] libmwbridge.so:mnParser(0x402ab0d2 "@@@", 0x402ab3d6 "mnParser", 1,
454334) + 397 bytes
[25] libmwmcr.so:mcrInstance::mnParser()(0x08094f70, 0xbfffc170,
0x08094f98, 0) + 115 bytes
Segmentation violation occurred within signal handler.
Unable to complete stack trace (stack was probably corrupted)
Segmentation fault
Started at Fri Oct 26 16:39:59 EDT 2007
Ended at Fri Oct 26 16:40:05 EDT 2007
stxgrinder-sess completed
> oops. I pasted the original error message incorrectly. below is the error
> with the corrected path.
>
>> Hi,
>> In anattempt to prepare to run a monte carlo cluster threshold
>> simulation
>> with a group of subjects in stable3, I run into the following error
>> using
>> mris_preproc:
>>
>> [troy:retrievalnewest] (nmr-stable3-env) mris_preproc --fsgd
>> SM2_glm_MC_controls.fsgd --target allsubavg --hemi lh --sf
>> sessidallsh+smvsnh --a retrievalSPMHRF_5cond_40TW --c sh+smvsnh.mat
>> --out
>> SM2_glm_MC_controls_sh+smvsnh.mgh
>>
>> ERROR: cannot find
>> /autofs/space/troy_003/users/retrievalnewest/SM0C1/bold/retrievalSPMHRF_5cond_40TW/sh+smvsnh.mat/ces.bhdr
>>
>> I do not know why fsfast is looking for this file here or how to
>> indicate
>> where it is. Am I running in the wrong env? When I try dev I get this
>> error:
>>
>> [troy:retrievalnewest] (nmr-std-env) mris_preproc --fsgd
>> SM2_glm_MC_controls.fsgd --target allsubavg --hemi lh --sf
>> sessidcontrolssh+smvsnh --a retrievalSPMHRF_5cond_40TW --c sh+smvsnh.mat
>> --out SM2_glm_MC_controls_sh+smvsnh.mgh
>> if: Expression Syntax.
>>
>> Any suggestions?
>> Cameron
>>
>> _______________________________________________
>> Freesurfer mailing list
>> [email protected]
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>
>
>
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