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 retrievalS PMHRF_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//space/troy/3/users/retrievalnewest/MC_contrasts/single.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
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 Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 segv@mathworks.com 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 support@mathworks.com 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 Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
That looks like a matlab problem. Maybe something in your startup.m file?
Cameron Ellis wrote:
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, 2005Warning: 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:
Send this crash report to segv@mathworks.com for automated analysis. For your convenience, this information has been recorded in: /homes/13/cameo/matlab_crash_dump.6194
Also, if the problem is reproducible, send the crash report to support@mathworks.com 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 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
There are a couple of problems here. You're specifying sh+smvsnh.mat as the contrast, but it should not have a .mat extension, so it can't find the input. This exposed a bug in mris_preproc, which I have just fixed. Even if you remove the .mat, I think it still fails because there is no contrast volume in the contrast directory (maybe selxavg failed?)
doug
Cameron Ellis wrote:
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 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
freesurfer@nmr.mgh.harvard.edu
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Cameron Ellis -
Doug Greve