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.
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/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
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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
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