Unexpected problem in simulation, output file does not exist

[siatjiasen]

Hi,

I successfully installed Qt5.5 and sequencetree4_master on Ubuntu 14.04 LTS. No compilation error.

Then I run ./st4, then GUI was displayed. I started compiling SPGR.sts squence. I got the following output:
simulating...
Duration=0 seconds; 0 blocks; Rel.SAR=0
Simulation finished...
Unexpected problem in simulation, output file does not exist.

In the terminal running ./st4, I got:

Running: "/home/jiasen/sequencetree4/bin/simulator_executable2.exe" ("stat", "/home/jiasen/sequencetree4/bin/../tmp/sequence_parameters_in.txt", "/home/jiasen/sequencetree4/bin/../tmp/sequence_parameters_out.txt", "/home/jiasen/sequencetree4/bin/../tmp/simulation_output.dat", "/home/jiasen/sequencetree4/bin/../tmp/results_output_stat.txt", "-1", "-1")

There is simulator_executable2.exe, but no /tmp folder contains the txt files and dat file.

Is this error induced by my wrong installation of sequencetree4 and Qt4 , or the sequence parameters were not set correctly, or something else?

Thank you for help.
Best wishes,
Jia Sen

[magland]

Does the tmp folder exist? If not, try creating it manually. Otherwise I can try to reproduce on my ubuntu

[siatjiasen]

Thank you very much for help.
The tmp folder didn't exist.
I created it manually, then compile SPGR.sts sequence, still:
Simulation finished...Unexpected problem in simulation, output file does not exist.
I attached the full log file recording the output of building and running ./st4.
Thank you again.Best wishes,Jia Sen

Date: Wed, 21 Oct 2015 05:54:39 -0700
From: [email protected]
To: [email protected]
CC: [email protected]
Subject: Re: [sequencetree4] Unexpected problem in simulation, output file does not exist (#3)

Does the tmp folder exist? If not, try creating it manually. Otherwise I can try to reproduce on my ubuntu

―
Reply to this email directly or view it on GitHub.

[siatjiasen]

Thank you very much for help.

The tmp folder didn't exist.

I created it manually, then compile SPGR.sts sequence, still:

Simulation finished...
Unexpected problem in simulation, output file does not exist.

I attached the full log file recording the output of building and running ./st4.

Thank you again.
Best wishes,
Jia Sen

[licheng2002]

Did you attach the log file? Try to take a look at the simulator folder,
and delete the temporary object file, i.e. the file with extension ".o".
Then compile the sequence again.

On Wed, Oct 21, 2015 at 10:41 AM, siatjiasen [email protected]
wrote:

Thank you very much for help.

The tmp folder didn't exist.

I created it manually, then compile SPGR.sts sequence, still:

Simulation finished...
Unexpected problem in simulation, output file does not exist.

I attached the full log file recording the output of building and running
./st4.

Thank you again.
Best wishes,
Jia Sen

—
Reply to this email directly or view it on GitHub
#3 (comment)
.

Regards!

Cheng Li
Email: [email protected]

[siatjiasen]

Thank you for help.

I did as you said. But I still got: Unexpected problem in simulation,
output files does not exist.

[licheng2002]

Hi,
I just tried a fresh compilation, it seems working fine on my PC,
Ubuntu 14.04, qmake v3.0 using Qt v5.2.1

Following the steps:

1. git clone https://github.com/magland/sequencetree4.git

2. cd sequence4/src

3. qmake

4. make

5. cd ../

6. mkdir tmp

7. cd bin

8. ./st4

   Could you please try again from a fresh download? Thanks!
   Cheng

On Thu, Oct 22, 2015 at 8:03 PM, siatjiasen [email protected]
wrote:

Thank you for help.

I did as you said. But I still got: Unexpected problem in simulation,
output files does not exist.

The log file was:

jiasen@jiasen:$ cd sequencetree4/
jiasen@jiasen:/sequencetree4$ cd simulator/
jiasen@jiasen:/sequencetree4/simulator$ cd build
jiasen@jiasen:/sequencetree4/simulator/build$ ls
createsequence.o foundationclasses.o main.o stsimscannerblocklist.o
customclasses.o loadparametersfile.o st4.o stsimscanner.o
jiasen@jiasen:/sequencetree4/simulator/build$ sudo rm *.o
[sudo] password for jiasen:
jiasen@jiasen:/sequencetree4/simulator/build$ ls
jiasen@jiasen:/sequencetree4/simulator/build$ cd ..
jiasen@jiasen:/sequencetree4/simulator$ cd ..
jiasen@jiasen:/sequencetree4$ ls
bin doc License.txt Resource_JS simulator stversion.txt
code examples README.txt sequences src templates
jiasen@jiasen:/sequencetree4$ cd bin
jiasen@jiasen:/sequencetree4/bin$ ls
results_viewer simulator_executable1.exe st4 tmp
simulator simulator_executable2.exe st4controller VS
jiasen@jiasen:/sequencetree4/bin$ cd ..
jiasen@jiasen:/sequencetree4$ sudo rm bin -r
jiasen@jiasen:/sequencetree4$ ls
code examples README.txt sequences src templates
doc License.txt Resource_JS simulator stversion.txt
jiasen@jiasen:/sequencetree4$ cd src
jiasen@jiasen:/sequencetree4/src$ ls
gui Makefile results_viewer st4controller todo.txt
install.x meta shared st4.pro VS
jiasen@jiasen:/sequencetree4/src$ make
cd gui/ && make -f Makefile
make[1]: Entering directory /home/jiasen/sequencetree4/src/gui' g++ -Wl,-O1 -Wl,-rpath,/opt/Qt/5.5/gcc_64 -Wl,-rpath,/opt/Qt/5.5/gcc_64/lib -o ../../bin/st4 build/main.o build/sstring.o build/slist.o build/stresources.o build/stsimscannerblocklist.o build/sttreeview.o build/stnodeview.o build/stparametertree.o build/stmainwindow.o build/stsequenceview.o build/stringchooserdlg.o build/stsimview.o build/stsimblockview.o build/steventlist.o build/stcompilelog.o build/stclassview.o build/stglobalview.o build/stpastedialog.o build/stconfigurationdlg.o build/openfilefromwebdlg.o build/readrawdatadlg.o build/distribute_raw_data.o build/staboutbox.o build/editresourcedlg.o build/streconstructionhighlighter.o build/stmetaclass.o build/stmetanode.o build/stmetasequence.o build/stmetasequencesimulator.o build/stsourceeditor.o build/cpphighlighter.o build/haiqtextedit.o build/defaulteditorwindow.o build/haiqtexteditgroup.o build/haiqmarker.o build/exporttoscannerdlg.o build/mda.o build/complex.o build/stpreferencesdlg.o build/qrc_st4.o build/moc_sttreeview.o build/moc_stnodeview.o build/moc_stparametertree.o build/moc_stmainwindow.o build/moc_stsequenceview.o build/moc_stringchooserdlg.o build/moc_stsimview.o build/moc_stsimblockview.o build/moc_steventlist.o build/moc_stcompilelog.o build/moc_stclassview.o build/moc_stglobalview.o build/moc_openfilefromwebdlg.o build/moc_readrawdatadlg.o build/moc_staboutbox.o build/moc_stmetasequencesimulator.o build/moc_stsourceeditor.o build/moc_haiqtextedit.o build/moc_defaulteditorwindow.o build/moc_haiqtexteditgroup.o -L/opt/Qt/5.5/gcc_64/lib -lQt5Widgets -L/usr/lib64 -lQt5Gui -lQt5Network -lQt5Core -lGL -lpthread make[1]: Leaving directory/home/jiasen/sequencetree4/src/gui'
cd VS/ && make -f Makefile
make[1]: Entering directory /home/jiasen/sequencetree4/src/VS' g++ -Wl,-O1 -Wl,-rpath,/opt/Qt/5.5/gcc_64 -Wl,-rpath,/opt/Qt/5.5/gcc_64/lib -o ../../bin/VS build/vsmain.o build/vsmainwindow.o build/vssequenceview.o build/vsphantomview.o build/vspropertyeditor.o build/run_virtual_scan.o build/vsabstractscanner.o build/vsobjectstate.o build/vsobjecttransformation.o build/vsphantom.o build/vsktermlist.o build/vsktermscanner.o build/stsimscannerblocklist.o build/stmetasequencesimulator.o build/stmetasequence.o build/stmetanode.o build/stmetaclass.o build/slist.o build/sstring.o build/stresources.o build/mda.o build/complex.o build/distribute_raw_data.o build/stringchooserdlg.o build/stconfigurationdlg.o build/stglobalview.o build/stcompilelog.o build/basicphantoms.o build/kspacefunction.o build/basickspacefunctions.o build/vsbasicphantoms.o build/vsphantomplugin.o build/qrc_st4.o build/moc_vsmainwindow.o build/moc_vssequenceview.o build/moc_vsphantomview.o build/moc_vspropertyeditor.o build/moc_vsabstractscanner.o build/moc_vsphantom.o build/moc_vsktermlist.o build/moc_stmetasequencesimulator.o build/moc_stringchooserdlg.o build/moc_stglobalview.o build/moc_stcompilelog.o build/moc_basicphantoms.o build/moc_basickspacefunctions.o build/moc_vsbasicphantoms.o -L../../bin -lgsl -lgslcblas -L/opt/Qt/5.5/gcc_64/lib -lQt5Widgets -L/usr/lib64 -lQt5Gui -lQt5Core -lGL -lpthread make[1]: Leaving directory/home/jiasen/sequencetree4/src/VS'
cd results_viewer/ && make -f Makefile
make[1]: Entering directory /home/jiasen/sequencetree4/src/results_viewer' g++ -Wl,-O1 -Wl,-rpath,/opt/Qt/5.5/gcc_64 -Wl,-rpath,/opt/Qt/5.5/gcc_64/lib -o ../../bin/results_viewer build/rvmain.o build/rvmainwindow.o build/rvfileview.o build/mda.o build/complex.o build/viewmdamodel.o build/viewmdawidget2d.o build/viewmdawidget1d.o build/viewmdawidget.o build/brightnesstool.o build/fftw_library.o build/apply_fft.o build/export_to_imagej.o build/qrc_st4.o build/moc_rvmainwindow.o build/moc_rvfileview.o build/moc_viewmdamodel.o build/moc_viewmdawidget2d.o build/moc_viewmdawidget1d.o build/moc_viewmdawidget.o build/moc_brightnesstool.o -L../../bin -lfftw3 -L/opt/Qt/5.5/gcc_64/lib -lQt5Widgets -L/usr/lib64 -lQt5Gui -lQt5Core -lGL -lpthread make[1]: Leaving directory/home/jiasen/sequencetree4/src/results_viewer'
cd st4controller/ && make -f Makefile
make[1]: Entering directory /home/jiasen/sequencetree4/src/st4controller' g++ -Wl,-O1 -Wl,-rpath,/opt/Qt/5.5/gcc_64 -Wl,-rpath,/opt/Qt/5.5/gcc_64/lib -o ../../bin/st4controller build/st4controllermain.o build/stcontrollermainwindow.o build/stcontrollerconfigdlg.o build/stcontroller.o build/rawdatafiletree.o build/sequencestree.o build/mda.o build/distribute_raw_data.o build/qrc_st4.o build/moc_stcontrollermainwindow.o build/moc_stcontroller.o -L/opt/Qt/5.5/gcc_64/lib -lQt5Widgets -L/usr/lib64 -lQt5Gui -lQt5Core -lGL -lpthread make[1]: Leaving directory/home/jiasen/sequencetree4/src/st4controller'
jiasen@jiasen:/sequencetree4/src$ ls
gui Makefile results_viewer st4controller todo.txt
install.x meta shared st4.pro VS
jiasen@jiasen:/sequencetree4/src$ cd ..
jiasen@jiasen:/sequencetree4$ ls
bin doc License.txt Resource_JS simulator stversion.txt
code examples README.txt sequences src templates
jiasen@jiasen:/sequencetree4$ cd bin
jiasen@jiasen:/sequencetree4/bin$ ls
results_viewer st4 st4controller VS
jiasen@jiasen:~/sequencetree4/bin$ ./st4
libpng warning: iCCP: known incorrect sRGB profile
loadFromText
("++++++ HEADER ++++++", "STVERSION=4.1.14", "++++++ END HEADER ++++++",
"++++++ NOTES ++++++", "=== spgr.sts - Spoiled gradient echo ===", "",
"Global Parameters", " FOV [mm] - field of view", " readout_N - number of
points per readout", " PE1 - first phase encode iterator", " PE2 - second
phase encode iterator", " TE [us] - echo time", " TR [us] - repetition
time", " dwell_time [us] - readout dwell time", " RF_spoiling [0 or 1] -
turn on or off RF-spoiling (randomization of transmit/receive phase)", "
flip_angle [degrees] - flip angle", " slice_thickness [mm] - slice
thickness", " slice_gradient_amplitude [uT/mm] - amplitude of slice select
gradient", " spoiler_moment [uT/mm-us] - 3D moment of spoiler gradient at
end of each repetition", " prep_PE1 - iterator for preparation
repetetitions", "", "", "To perform 3D phase encoding", " For example, set
PE2 = -4:1:3, for 8 phase encodes", " To interchange the looping order, go
to the source code for the loop node and simply switch the order of PE1 and
PE2 iterators", "", "To switch to a non-selective pulse", " 1. set
slice_thickness=0", " 2. set slice_gradient_amplitude=(0,0,0)", " 3. If
you want a rectangular shape pulse, right click on the "RF" node and
select "promote node", then select STRF", "", "== Siemens User Interface
Directives =====",

"UIDOUBLE\tNAME=TE\t\tRANGE=1:1:100\tLABEL="TE"\t\tUNITS="ms"\tFACTOR=0.001",

"UIDOUBLE\tNAME=TR\t\tRANGE=10:10:3000\tLABEL="TR"\t\tUNITS="ms"\tFACTOR=0.001",
"UIDOUBLE\tNAME=flip_angle\tRANGE=0:5:180\tLABEL="Flip
angle"\tUNITS="deg"",
"UIDOUBLE\tNAME=slice_thickness\tRANGE=2:2:50\t\tLABEL="Slice
thickness"\tUNITS="mm"", "UICHECKBOX\tNAME=RF_spoiling\tLABEL="RF
Spoiling"", "============================", "", "++++++ END NOTES ++++++",
"++++++ GLOBAL ++++++", "FOV\t(256,256,50)\tmm", "readout_N\t256\t",
"PE1\t-128:1:127\t", "PE2\t0:1:0\t", "TE\t6000\tmicrosec",
"TR\t50000\tmicrosec", "dwell_time\t30\tmicrosec", "RF_spoiling\t1\t0 or
1", "flip_angle\t45\tdegrees", "slice_thickness\t10\tmm",
"slice_gradient_amplitude\t(0,0,10)\tuT/mm",
"spoiler_moment\t(0,0,100000)\tuT/mm-us", "prep_PE1\t1:1:10\t",
"FOV\t->\tRoot->FOV",
"readout_N\t->\tRoot->MainLoop->Block->Acquire->Readout->N",
"readout_N\t->\tRoot->PrepLoop->Block->Acquire->Readout->N",
"PE1\t->\tRoot->MainLoop->PE1", "PE2\t->\tRoot->MainLoop->PE2",
"TE\t->\tRoot->MainLoop->Block->TE", "TE\t->\tRoot->PrepLoop->Block->TE",
"TR\t->\tRoot->MainLoop->Block->TR", "TR\t->\tRoot->PrepLoop->Block->TR",
"dwell_time\t->\tRoot->MainLoop->Block->Acquire->Readout->dwell_time",
"dwell_time\t->\tRoot->PrepLoop->Block->Acquire->Readout->dwell_time",
"RF_spoiling\t->\tRoot->MainLoop->RF_spoiling",
"RF_spoiling\t->\tRoot->PrepLoop->RF_spoiling",
"flip_angle\t->\tRoot->PrepLoop->Block->Excite->RF->flip_angle",
"flip_angle\t->\tRoot->MainLoop->Block->Excite->RF->flip_angle",
"slice_thickness\t->\tRoot->MainLoop->Block->Excite->slice_thickness",
"slice_thickness\t->\tRoot->PrepLoop->Block->Excite->slice_thickness",

"slice_gradient_amplitude\t->\tRoot->MainLoop->Block->Excite->gradient_amplitude",

"slice_gradient_amplitude\t->\tRoot->PrepLoop->Block->Excite->gradient_amplitude",
"spoiler_moment\t->\tRoot->PrepLoop->Block->Rewind->moment",
"spoiler_moment\t->\tRoot->MainLoop->Block->Rewind->moment",
"prep_PE1\t->\tRoot->PrepLoop->PE1", "++++++ END GLOBAL ++++++", "++++++
RECONSTRUCTION ++++++", "function reconstruction(num_channels)", "if
(nargin<1) num_channels=1; end;", "", "if (num_channels==1)",
"\tX=readmda('ADC1.mda');", "\tX=fftshift(fftn(fftshift(X)));",
"\twritemda(X,'recon.mda');", "end;", "", "++++++ END NOTES ++++++",
"++++++ LINK GROUPS ++++++", "",
"GROUP\tRoot->PrepLoop->Block\tRoot->MainLoop->Block", "", "++++++ END LINK
GROUPS ++++++", "", "", "++++++ NODES ++++++", "",
"PARAMETER\tSTVector3\tFOV\t(256,256,50)\tmm\tactive\tFOV",
"PARAMETER\tSTReal\tmaxamp\t20\tuT/mm\tactive\t",
"PARAMETER\tSTReal\tramprate\t0.1\t[uT/mm]/us\tactive\t",
"PARAMETER\tSTReal\tgamma\t42.5764\tHz/uT\tactive\t",
"PARAMETER\tSTVector3\tFOV_shift\t(0,0,0)\tmm\tactive\t",
"PARAMETER\tSTVector3\tphase_shift\t237\tdegrees\tpassive\t",
"PARAMETER\tSTVector3\tFOV_shift_offset\t(0,0,0)\tmm; used
internally\tactive\t", "CHILD\tSPGRLoop\tPrepLoop", "
PARAMETER\tSTIterator\tPE1\t1:1:10\t\tactive\tprep_PE1", "
PARAMETER\tSTIterator\tPE2\t0:1:0\t\tactive\t", "
PARAMETER\tSTVector3\treadout_dir\t(1,0,0)\t\tactive\t", "
PARAMETER\tSTVector3\tPE1_dir\t(0,0,0)\t\tactive\t", "
PARAMETER\tSTVector3\tPE2_dir\t(0,0,1)\t\tactive\t", "
PARAMETER\tSTInteger\tRF_spoiling\t1\t0 or 1\tactive\tRF_spoiling", "
CHILD\tSTGradientEchoBlock\tBlock", "
PARAMETER\tSTReal\tTE\t6000\tmicrosec\tactive\tTE", "
PARAMETER\tSTReal\tTR\t50000\tmicrosec\tactive\tTR", "
PARAMETER\tSTVector3\tkspace_dir\t(1,0,0)\t\tpassive\t", "
PARAMETER\tSTVector3\tkspace_echo\t(0,0,0)\t\tpassive\t", "
PARAMETER\tSTReal\texcite_time\t1000\tmicrosec\tactive\t", "
CHILD\tSTExcite\tExcite", "

PARAMETER\tSTVector3\tgradient_amplitude\t(0,0,10)\tuT/mm\tactive\tslice_gradient_amplitude",
"
PARAMETER\tSTReal\tslice_thickness\t10\tmm\tactive\tslice_thickness", "
PARAMETER\tSTReal\tbandwidth\t4257.64\tHz\tpassive\t", "
PARAMETER\tSTInteger\tprephase\t1\t0 or 1\tactive\t", "
CHILD\tSTGradientMom\tPrephase", "
PARAMETER\tSTVector3\tramp_times_1\t(0,0,200)\tmicrosec\tpassive\t", "

PARAMETER\tSTVector3\tplateau_times\t(0,0,210)\tmicrosec\tpassive\t", "

PARAMETER\tSTVector3\tramp_times_2\t(0,0,200)\tmicrosec\tpassive\t", "

PARAMETER\tSTVector3\tstart_times\t(0,0,0)\tmicrosec\tpassive\t", "

PARAMETER\tSTVector3\tamplitude\t(0,0,-19.7561)\tuT/mm\tpassive\t", "
PARAMETER\tSTInteger\talignment\t0\t0=left; 1=right;
2=center\tactive\t", "
PARAMETER\tSTInteger\talways_min_dur\t0\t0 or 1\tactive\t", "
PARAMETER\tSTReal\tmaxamp\t0\t[uT/mm]\tactive\t", "
PARAMETER\tSTReal\tramprate\t0\t[uT/mm]/us\tactive\t", "
END", " CHILD\tSTGradientAmp\tSliceGradient", "
PARAMETER\tSTReal\tramp_time_1\t200\tmicrosec\tactive\t", "
PARAMETER\tSTReal\tplateau_time\t1400\tmicrosec\tpassive\t", "
PARAMETER\tSTReal\tramp_time_2\t200\tmicrosec\tactive\t", "
PARAMETER\tSTVector3\tamplitude\t(0,0,10)\tuT/mm\tpassive\t", "
END", " CHILD\tSTSincRF\tRF", "
PARAMETER\tSTReal\tnum_lobes_left\t2\t\tactive\t", "
PARAMETER\tSTReal\tnum_lobes_right\t2\t\tactive\t", "
PARAMETER\tSTReal\tflip_angle\t45\tdegrees\tactive\tflip_angle", "
PARAMETER\tSTReal\tpulse_duration\t1409.23\tmicrosec\tpassive\t", "
PARAMETER\tSTReal\treference_fraction\t0.5\t\tpassive\t", "
PARAMETER\tSTReal\tbandwidth\t4257.64\tHz\tpassive\t", "
PARAMETER\tSTReal\ttime_step\t10\tmicrosec\tactive\t", "
PARAMETER\tSTReal\tphase\t0\tdegrees\tactive\t", "
PARAMETER\tSTReal\tfrequency\t0\tHz\tactive\t", "
PARAMETER\tSTInteger\tpulse_type\t1\t1=Excite; 2=Refocus\tactive\t", "
PARAMETER\tSTVector3\tgradient_amplitude\t(0,0,10)\tuT/mm; for
internal use\tpassive\t", "
PARAMETER\tSTReal\tslice_thickness\t10\tmm; for internal use\tpassive\t",
" END", " END", "
CHILD\tSTAcquire\tAcquire", "
PARAMETER\tSTVector3\techo_moment\t(0,0,0)\t[uT/mm]-us\tpassive\t", "

PARAMETER\tSTVector3\tmoment_per_point\t(91.7468,0,0)\t[uT/mm]-us\tpassive\t",
" CHILD\tSTGradientMom\tEncode", "
PARAMETER\tSTVector3\tramp_times_1\t(200,0,200)\tmicrosec\tpassive\t", "

PARAMETER\tSTVector3\tplateau_times\t(410,0,200)\tmicrosec\tpassive\t", "

PARAMETER\tSTVector3\tramp_times_2\t(200,0,200)\tmicrosec\tpassive\t", "

PARAMETER\tSTVector3\tstart_times\t(0,0,0)\tmicrosec\tpassive\t", "

PARAMETER\tSTVector3\tamplitude\t(-19.7531,0,-19.75)\tuT/mm\tpassive\t", "
PARAMETER\tSTInteger\talignment\t0\t0=left; 1=right;
2=center\tactive\t", "
PARAMETER\tSTInteger\talways_min_dur\t0\t0 or 1\tactive\t", "
PARAMETER\tSTReal\tmaxamp\t0\t[uT/mm]\tactive\t", "
PARAMETER\tSTReal\tramprate\t0\t[uT/mm]/us\tactive\t", "
END", " CHILD\tSTGradientAmp\tReadoutGradient", "
PARAMETER\tSTReal\tramp_time_1\t200\tmicrosec\tactive\t", "
PARAMETER\tSTReal\tplateau_time\t7680\tmicrosec\tpassive\t", "
PARAMETER\tSTReal\tramp_time_2\t200\tmicrosec\tactive\t", "
PARAMETER\tSTVector3\tamplitude\t(3.05823,0,0)\tuT/mm\tpassive\t", "
END", " CHILD\tSTReadout\tReadout", "
PARAMETER\tSTReal\tdwell_time\t30\tmicrosec\tactive\tdwell_time", "
PARAMETER\tSTInteger\tN\t256\t\tactive\treadout_N", "
PARAMETER\tSTReal\treference_fraction\t0.5\t\tactive\t", "
PARAMETER\tSTReal\tactual_reference_fraction\t0.5\t\tpassive\t", "
PARAMETER\tSTReal\treference_sample\t128.5\t\tpassive\t", "
PARAMETER\tSTReal\tphase\t0\tdegrees\tactive\t", "
PARAMETER\tSTReal\tfrequency\t0\tHz\tactive\t", "
PARAMETER\tSTVector3\tgradient_amplitude\t(3.05823,0,0)\tuT/mm; for
internal use\tpassive\t", "
PARAMETER\tSTInteger\tround_up_reference_time\t1\t0 or 1\tactive\t", "
END", " END", " CHILD\tSTEncode\tRewind", "

PARAMETER\tSTVector3\tmoment\t(0,0,100000)\t[uT/mm]-us\tactive\tspoiler_moment",
" PARAMETER\tSTInteger\tdo_rewind\t1\t0 or 1\tactive\t", "
CHILD\tSTGradientMom\tGradient", "
PARAMETER\tSTVector3\tramp_times_1\t(200,0,200)\tmicrosec\tpassive\t", "

PARAMETER\tSTVector3\tplateau_times\t(410,0,4800)\tmicrosec\tpassive\t", "

PARAMETER\tSTVector3\tramp_times_2\t(200,0,200)\tmicrosec\tpassive\t", "

PARAMETER\tSTVector3\tstart_times\t(0,0,0)\tmicrosec\tpassive\t", "

PARAMETER\tSTVector3\tamplitude\t(-19.7531,0,20)\tuT/mm\tpassive\t", "
PARAMETER\tSTInteger\talignment\t0\t0=left; 1=right;
2=center\tactive\t", "
PARAMETER\tSTInteger\talways_min_dur\t0\t0 or 1\tactive\t", "
PARAMETER\tSTReal\tmaxamp\t0\t[uT/mm]\tactive\t", "
PARAMETER\tSTReal\tramprate\t0\t[uT/mm]/us\tactive\t", "
END", " END", " END", " END",
"CHILD\tSPGRLoop\tMainLoop", "
PARAMETER\tSTIterator\tPE1\t-128:1:127\t\tactive\tPE1", "
PARAMETER\tSTIterator\tPE2\t0:1:0\t\tactive\tPE2", "
PARAMETER\tSTVector3\treadout_dir\t(1,0,0)\t\tactive\t", "
PARAMETER\tSTVector3\tPE1_dir\t(0,1,0)\t\tactive\t", "
PARAMETER\tSTVector3\tPE2_dir\t(0,0,1)\t\tactive\t", "
PARAMETER\tSTInteger\tRF_spoiling\t1\t0 or 1\tactive\tRF_spoiling", "
CHILD\tSTGradientEchoBlock\tBlock", "
PARAMETER\tSTReal\tTE\t6000\tmicrosec\tactive\tTE", "
PARAMETER\tSTReal\tTR\t50000\tmicrosec\tactive\tTR", "
PARAMETER\tSTVector3\tkspace_dir\t(1,0,0)\t\tpassive\t", "
PARAMETER\tSTVector3\tkspace_echo\t(0,-88,0)\t\tpassive\t", "
PARAMETER\tSTReal\texcite_time\t1000\tmicrosec\tactive\t", "
CHILD\tSTExcite\tExcite", "

PARAMETER\tSTVector3\tgradient_amplitude\t(0,0,10)\tuT/mm\tactive\tslice_gradient_amplitude",
"
PARAMETER\tSTReal\tslice_thickness\t10\tmm\tactive\tslice_thickness", "
PARAMETER\tSTReal\tbandwidth\t4257.64\tHz\tpassive\t", "
PARAMETER\tSTInteger\tprephase\t1\t0 or 1\tactive\t", "
CHILD\tSTGradientMom\tPrephase", "
PARAMETER\tSTVector3\tramp_times_1\t(0,0,200)\tmicrosec\tpassive\t", "

PARAMETER\tSTVector3\tplateau_times\t(0,0,210)\tmicrosec\tpassive\t", "

PARAMETER\tSTVector3\tramp_times_2\t(0,0,200)\tmicrosec\tpassive\t", "

PARAMETER\tSTVector3\tstart_times\t(0,0,0)\tmicrosec\tpassive\t", "

PARAMETER\tSTVector3\tamplitude\t(0,0,-19.7561)\tuT/mm\tpassive\t", "
PARAMETER\tSTInteger\talignment\t0\t0=left; 1=right;
2=center\tactive\t", "
PARAMETER\tSTInteger\talways_min_dur\t0\t0 or 1\tactive\t", "
PARAMETER\tSTReal\tmaxamp\t0\t[uT/mm]\tactive\t", "
PARAMETER\tSTReal\tramprate\t0\t[uT/mm]/us\tactive\t", "
END", " CHILD\tSTGradientAmp\tSliceGradient", "
PARAMETER\tSTReal\tramp_time_1\t200\tmicrosec\tactive\t", "
PARAMETER\tSTReal\tplateau_time\t1400\tmicrosec\tpassive\t", "
PARAMETER\tSTReal\tramp_time_2\t200\tmicrosec\tactive\t", "
PARAMETER\tSTVector3\tamplitude\t(0,0,10)\tuT/mm\tpassive\t", "
END", " CHILD\tSTSincRF\tRF", "
PARAMETER\tSTReal\tnum_lobes_left\t2\t\tactive\t", "
PARAMETER\tSTReal\tnum_lobes_right\t2\t\tactive\t", "
PARAMETER\tSTReal\tflip_angle\t45\tdegrees\tactive\tflip_angle", "
PARAMETER\tSTReal\tpulse_duration\t1409.23\tmicrosec\tpassive\t", "
PARAMETER\tSTReal\treference_fraction\t0.5\t\tpassive\t", "
PARAMETER\tSTReal\tbandwidth\t4257.64\tHz\tpassive\t", "
PARAMETER\tSTReal\ttime_step\t10\tmicrosec\tactive\t", "
PARAMETER\tSTReal\tphase\t0\tdegrees\tactive\t", "
PARAMETER\tSTReal\tfrequency\t0\tHz\tactive\t", "
PARAMETER\tSTInteger\tpulse_type\t1\t1=Excite; 2=Refocus\tactive\t", "
PARAMETER\tSTVector3\tgradient_amplitude\t(0,0,10)\tuT/mm; for
internal use\tpassive\t", "
PARAMETER\tSTReal\tslice_thickness\t10\tmm; for internal use\tpassive\t",
" END", " END", "
CHILD\tSTAcquire\tAcquire", "
PARAMETER\tSTVector3\techo_moment\t(0,-8073.72,0)\t[uT/mm]-us\tpassive\t",
"

PARAMETER\tSTVector3\tmoment_per_point\t(91.7468,0,0)\t[uT/mm]-us\tpassive\t",
" CHILD\tSTGradientMom\tEncode", "
PARAMETER\tSTVector3\tramp_times_1\t(200,200,200)\tmicrosec\tpassive\t", "

PARAMETER\tSTVector3\tplateau_times\t(410,390,200)\tmicrosec\tpassive\t",
"
PARAMETER\tSTVector3\tramp_times_2\t(200,200,200)\tmicrosec\tpassive\t", "

PARAMETER\tSTVector3\tstart_times\t(0,0,0)\tmicrosec\tpassive\t", "

PARAMETER\tSTVector3\tamplitude\t(-19.7531,-13.6843,-19.75)\tuT/mm\tpassive\t",
" PARAMETER\tSTInteger\talignment\t0\t0=left; 1=right;
2=center\tactive\t", "
PARAMETER\tSTInteger\talways_min_dur\t0\t0 or 1\tactive\t", "
PARAMETER\tSTReal\tmaxamp\t0\t[uT/mm]\tactive\t", "
PARAMETER\tSTReal\tramprate\t0\t[uT/mm]/us\tactive\t", "
END", " CHILD\tSTGradientAmp\tReadoutGradient", "
PARAMETER\tSTReal\tramp_time_1\t200\tmicrosec\tactive\t", "
PARAMETER\tSTReal\tplateau_time\t7680\tmicrosec\tpassive\t", "
PARAMETER\tSTReal\tramp_time_2\t200\tmicrosec\tactive\t", "
PARAMETER\tSTVector3\tamplitude\t(3.05823,0,0)\tuT/mm\tpassive\t", "
END", " CHILD\tSTReadout\tReadout", "
PARAMETER\tSTReal\tdwell_time\t30\tmicrosec\tactive\tdwell_time", "
PARAMETER\tSTInteger\tN\t256\t\tactive\treadout_N", "
PARAMETER\tSTReal\treference_fraction\t0.5\t\tactive\t", "
PARAMETER\tSTReal\tactual_reference_fraction\t0.5\t\tpassive\t", "
PARAMETER\tSTReal\treference_sample\t128.5\t\tpassive\t", "
PARAMETER\tSTReal\tphase\t0\tdegrees\tactive\t", "
PARAMETER\tSTReal\tfrequency\t0\tHz\tactive\t", "
PARAMETER\tSTVector3\tgradient_amplitude\t(3.05823,0,0)\tuT/mm; for
internal use\tpassive\t", "
PARAMETER\tSTInteger\tround_up_reference_time\t1\t0 or 1\tactive\t", "
END", " END", " CHILD\tSTEncode\tRewind", "

PARAMETER\tSTVector3\tmoment\t(0,0,100000)\t[uT/mm]-us\tactive\tspoiler_moment",
" PARAMETER\tSTInteger\tdo_rewind\t1\t0 or 1\tactive\t", "
CHILD\tSTGradientMom\tGradient", "
PARAMETER\tSTVector3\tramp_times_1\t(200,200,200)\tmicrosec\tpassive\t", "

PARAMETER\tSTVector3\tplateau_times\t(410,390,4800)\tmicrosec\tpassive\t",
"
PARAMETER\tSTVector3\tramp_times_2\t(200,200,200)\tmicrosec\tpassive\t", "

PARAMETER\tSTVector3\tstart_times\t(0,0,0)\tmicrosec\tpassive\t", "

PARAMETER\tSTVector3\tamplitude\t(-19.7531,13.6843,20)\tuT/mm\tpassive\t",
" PARAMETER\tSTInteger\talignment\t0\t0=left; 1=right;
2=center\tactive\t", "
PARAMETER\tSTInteger\talways_min_dur\t0\t0 or 1\tactive\t", "
PARAMETER\tSTReal\tmaxamp\t0\t[uT/mm]\tactive\t", "
PARAMETER\tSTReal\tramprate\t0\t[uT/mm]/us\tactive\t", "
END", " END", " END", " END", "END", "", "++++++ END
NODES ++++++", "", "++++++ USERCLASS SPGRLoop ++++++", "", "++++++ HEADER",
"class ST_EXPORT SPGRLoop : public STLoop", "{", "public:", "\t/* BEGIN
SEQUENCETREE -- this section generated by SequenceTree -- do not edit /",
"\tSTIterator PE1;", "\tSTIterator PE2;", "\tSTVector3 readout_dir;",
"\tSTVector3 PE1_dir;", "\tSTVector3 PE2_dir;", "\tSTInteger RF_spoiling;",
"\tSTGradientEchoBlock *Block;", "\t/ END SEQUENCETREE -- this section
generated by SequenceTree -- do not edit /", "\t", "\tSPGRLoop();",
"\tbool prepare();", "\t", "\tbool loopRun();", "};", "", "", "++++++
SOURCE", "SPGRLoop::SPGRLoop() {", "\tST_CLASS(SPGRLoop,STLoop)", "\t/
ST_PARAMETERS /\t", "\tST_PARAMETER(STIterator,PE1,0:1:0,)",
"\tST_PARAMETER(STIterator,PE2,0:1:0,)",
"\tST_PARAMETER(STVector3,readout_dir,(1,0,0),)",
"\tST_PARAMETER(STVector3,PE1_dir,(0,1,0),)",
"\tST_PARAMETER(STVector3,PE2_dir,(0,0,1),)",
"\tST_PARAMETER(STInteger,RF_spoiling,0,0 or 1)", "\t/ ST_CHILDREN /",
"\tST_CHILD(STGradientEchoBlock,Block)", "}", "bool SPGRLoop::prepare() {",
"\tBlock->kspace_dir=readout_dir;", "\treturn STLoop::prepare();", "}", "",
"", "bool SPGRLoop::loopRun() {", " if (RF_spoiling) {", "
sequence()->phase_shift=rand()%360;", " }",
"\tBlock->kspace_echo=PE1_dir_PE1+PE2_dir_PE2;", "\treturn Block->run();",
"}", "", "++++++ END", "", "++++++ CLASS SPGRLoop_1 ++++++", "", "++++++
HEADER", "class ST_EXPORT SPGRLoop_1 : public STLoop", "{", "public:",
"\t/ BEGIN SEQUENCETREE -- this section generated by SequenceTree -- do
not edit /", "\tSTIterator PE1;", "\tSTIterator PE2;", "\tSTVector3
readout_dir;", "\tSTVector3 PE1_dir;", "\tSTVector3 PE2_dir;", "\tSTInteger
RF_spoiling;", "\tSTGradientEchoBlock *Block;", "\t/ END SEQUENCETREE --
this section generated by SequenceTree -- do not edit /", "\t",
"\tSPGRLoop_1();", "\tbool prepare();", "\t", "\tbool loopRun();", "};",
"", "", "++++++ SOURCE", "SPGRLoop_1::SPGRLoop_1() {",
"\tST_CLASS(SPGRLoop_1,STLoop)", "\t/ ST_PARAMETERS /\t",
"\tST_PARAMETER(STIterator,PE1,0:1:0,)",
"\tST_PARAMETER(STIterator,PE2,0:1:0,)",
"\tST_PARAMETER(STVector3,readout_dir,(1,0,0),)",
"\tST_PARAMETER(STVector3,PE1_dir,(0,1,0),)",
"\tST_PARAMETER(STVector3,PE2_dir,(0,0,1),)",
"\tST_PARAMETER(STInteger,RF_spoiling,0,0 or 1)", "\t/ ST_CHILDREN /",
"\tST_CHILD(STGradientEchoBlock,Block)", "}", "bool SPGRLoop_1::prepare()
{", "\tBlock->kspace_dir=readout_dir;", "\treturn STLoop::prepare();", "}",
"", "", "bool SPGRLoop_1::loopRun() {", " if (RF_spoiling) {", "
sequence()->phase_shift=rand()%360;", " }",
"\tBlock->kspace_echo=PE1_dir_PE1+PE2_dir_PE2;", "\treturn Block->run();",
"}", "", "++++++ END", "", "++++++ CLASS STRoot ++++++", "", "++++++
HEADER", "class STRoot : public STSequence", "{", "public:", "\t/ BEGIN
SEQUENCETREE -- this section generated by SequenceTree -- do not edit /",
"\tSPGRLoop *PrepLoop;", "\tSPGRLoop *MainLoop;", "\t/ END SEQUENCETREE --
this section generated by SequenceTree -- do not edit /", "\t",
"\tSTRoot();", "};", "", "", "++++++ SOURCE", "STRoot::STRoot() {",
"\tST_CLASS(STRoot,STSequence)", "\t/ ST_PARAMETERS /", "\t/ ST_CHILDREN
/", "\tST_CHILD(SPGRLoop,PrepLoop);", "\tST_CHILD(SPGRLoop,MainLoop);",
"}", "", "++++++ END", "", "++++++ USERCLASS SpinLockRF ++++++", "",
"++++++ HEADER", "class SpinLockRF : public STNode {", "public:", "\t/
BEGIN SEQUENCETREE -- this section generated by SequenceTree -- do not edit
/", "\tSTReal flip_angle_1;", "\tSTReal flip_angle_2;", "\tSTReal
pulse_duration_1;", "\tSTReal pulse_duration_2;", "\tSTInteger
alternating_phase;", "\tSTInteger frequency_offset;", "\tSTInteger
num_sl_pulses;", "\tSTReal inter_pulse_delay;", "\tSTReal time_step;",
"\tSTReal phase;", "\tSTReal frequency;", "\t/ END SEQUENCETREE -- this
section generated by SequenceTree -- do not edit /", "\t", "\t//events",
"\tSTScannerRFPulse *RF_bread;", "\tSTScannerRFPulse *RF_meat;",
"\t/////////////////////////////////////////////////////",
"\tSpinLockRF();", "\tvirtual ~SpinLockRF();", "\tbool initialize();",
"\tbool prepare();", "\tbool run();", "\tdouble duration();", "\tdouble
referenceTime();", "\tVector3 terminalMoment();", "\tVector3
gradientStartTimes(); ", "\tVector3 gradientEndTimes();", "\tdouble
SAR();", "private:", "\tvoid delete_events();", "};", "", "", "++++++
SOURCE", "SpinLockRF::SpinLockRF() {", "\tST_CLASS(SpinLockRF,STNode)",
"\tRF_bread=0;", "\tRF_meat=0;", "\t/ ST_PARAMETERS /",
"\tST_PARAMETER(STReal, flip_angle_1, 90, degrees)",
"\tST_PARAMETER(STReal, flip_angle_2, 360, degrees)",
"\tST_PARAMETER(STReal, pulse_duration_1, 300, microsec)",
"\tST_PARAMETER(STReal, pulse_duration_2, 1000, microsec)",
"\tST_PARAMETER(STInteger, alternating_phase, 0, 0 or 1) ",
"\tST_PARAMETER(STInteger, frequency_offset, 0, Hz)",
"\tST_PARAMETER(STInteger, num_sl_pulses, 10,)", "\tST_PARAMETER(STReal,
inter_pulse_delay, 60, microsec)", "\tST_PARAMETER(STReal, time_step, 10,
microsec)", "\tST_PARAMETER(STReal, phase, 0, degrees)",
"\tST_PARAMETER(STReal, frequency, 0, Hz)", "\t/ ST_CHILDREN _/", "}",
"SpinLockRF::~SpinLockRF() {", "\tdelete_events();", "}", "void
SpinLockRF::delete_events() {", "\tif (RF_bread) delete RF_bread;
RF_bread=0;", "\tif (RF_meat) delete RF_meat; RF_meat=0;", "}", "bool
SpinLockRF::initialize() {", "\tclearChildren();", "\tif (!scanner())
return false;", "\tdelete_events();",
"\tRF_bread=scanner()->allocateRFPulse(this);",
"\tRF_meat=scanner()->allocateRFPulse(this);", "\treturn true;", "}", "bool
SpinLockRF::prepare() {", "\tif (!RF_bread) return false;", "\tif
(!RF_meat) return false;", "\tif (time_step<=0) return false;", "\tif
(pulse_duration_1<=time_step) return false;", "\tif
(pulse_duration_2<=time_step) return false;", "\tif (!sequence()) return
false;", "\t\t", "\t\tlong N1=(long)(pulse_duration_1/time_step);",
"\t\tlong N2=(long)(pulse_duration_2/time_step);", "\t\t", "\t\tdouble
*data_mag_1=(double *)malloc(sizeof(double)_N1);", "\t\tdouble
_data_phase_1=(double *)malloc(sizeof(double)_N1);", "\t\tdouble
_data_mag_2=(double *)malloc(sizeof(double)_N2);", "\t\tdouble
_data_phase_2=(double *)malloc(sizeof(double)_N2);", "\t\tdouble
sum_re_1=0,sum_re_2=0;", "\t\tdouble sum_im_1=0,sum_im_2=0;", "\t\t{for
(long j=0; j<N1; j++) {", "\t\t\tdouble re=1,im=0;", "\t\t\tsum_re_1+=re;",
"\t\t\tsum_im_1+=im;", "\t\t\tdata_mag_1[j]=sqrt(re_re+im_im);",
"\t\t\tdata_phase_1[j]=atan2(im,re)/(2_3.1415926535)_360;", "\t\t}}",
"\t\t{for (long j=0; j<N2; j++) {", "\t\t\tdouble re=1,im=0;",
"\t\t\tsum_re_2+=re;", "\t\t\tsum_im_2+=im;",
"\t\t\tdata_mag_2[j]=sqrt(re_re+im_im);",
"\t\t\tdata_phase_2[j]=atan2(im,re)/(2_3.1415926535)_360;", "\t\t}}",
"\t\t//uT * sec * Hz/uT * degrees = degrees ", "\t\tdouble

factor1=sqrt(sum_re_1_sum_re_1+sum_im_1_sum_im_1)_time_step/1.0E6_sequence()->gamma*360/90;",
"\t\tdouble

factor2=sqrt(sum_re_2_sum_re_2+sum_im_2_sum_im_2)_time_step/1.0E6_sequence()->gamma*360/90;",
"\t\t{for (long j=0; j<N1; j++) {", "\t\t\tdata_mag_1[j]/=factor1;",
"\t\t}}", "\t\t{for (long j=0; j<N2; j++) {",
"\t\t\tdata_mag_2[j]/=factor2;", "\t\t}}",

"\t\tRF_bread->setPulse(N1,data_mag_1,data_phase_1,time_step,90,pulse_duration_1/2);",

"\t\tRF_meat->setPulse(N2,data_mag_2,data_phase_2,time_step,90,pulse_duration_2/2);",
"\t\tfree(data_mag_1);", "\t\tfree(data_phase_1);",
"\t\tfree(data_mag_2);", "\t\tfree(data_phase_2);", "\t",
"\tRF_bread->setFlipAngle(flip_angle_1);",
"\tRF_meat->setFlipAngle(flip_angle_2);", "\t", "\tsetModified(false);",
"\treturn true;", "}", "bool SpinLockRF::run() {", "\tif (!RF_bread) return
false;", "\tif (!RF_meat) return false;", "\tif (!scanner()) return
false;", "\tif (!sequence()) return false;", "", "\tdouble ph=phase;",
"\tVector3 totmom=initialTotalMoment();",
"\tph+=sequence()->phaseAdjustment();",
"\tph+=(totmom.x()_sequence()->getFOVShiftX()",
"\t\t+totmom.y()_sequence()->getFOVShiftY()",
"\t\t+totmom.z()_sequence()->getFOVShiftZ())sequence()->gamma/1.0E6_360;",
"\tRF_bread->setPhase(ph);", "\tRF_meat->setPhase(ph);", "\t",
"\tRF_bread->setFrequency(frequency);",
"\tRF_meat->setFrequency(frequency);", "\t", "", "\t//The excite pulse ",
"\tdouble time_offset=0;",
"\tRF_bread->setStartTime(startTime()+time_offset);", "\tif
(RF_bread->pulseCount()) scanner()->addEvent(RF_bread);",
"\ttime_offset+=pulse_duration_1+inter_pulse_delay;", "", "\t//inner
pulses", "\tfor (int j=0; j<num_sl_pulses; j++) {", "\t\tif
(alternating_phase) {", "\t\t\tif (j%2==0) {",
"\t\t\t\tRF_meat->setPhase(ph+0);",
"\t\t\t\tRF_meat->setFrequency(frequency_offset);", "\t\t\t}", "\t\t\telse
{", "\t\t\t\tRF_meat->setPhase(ph+180);",
"\t\t\t\tRF_meat->setFrequency(frequency_offset);", "\t\t\t}", "\t\t}",
"\t\tRF_meat->setStartTime(startTime()+time_offset);", "\t\tif
(RF_meat->pulseCount()) scanner()->addEvent(RF_meat);",
"\t\ttime_offset+=pulse_duration_2+inter_pulse_delay;", "\t}", "", "\t//The
store pulse", "\tRF_bread->setStartTime(startTime()+time_offset);", "\tif
(RF_bread->pulseCount()) scanner()->addEvent(RF_bread);",
"\ttime_offset+=pulse_duration_1+inter_pulse_delay;", "\t", "\treturn
true;", "}", "double SpinLockRF::duration() {", "\tif
((!RF_meat)||(RF_bread)) return 0;", "\treturn pulse_duration_1_2 +
pulse_duration_2_num_sl_pulses + inter_pulse_delay(num_sl_pulses+1);",
"}", "double SpinLockRF::referenceTime() {", "\treturn 0;", "}", "Vector3
SpinLockRF::terminalMoment() {", "\treturn Vector3();", "}", "", "Vector3
SpinLockRF::gradientStartTimes() {", "\treturn Vector3(0,0,0);", "}",
"Vector3 SpinLockRF::gradientEndTimes() {", "\tdouble dur=duration();",
"\treturn Vector3(dur,dur,dur);", "}", "", "double SpinLockRF::SAR() {",
"\tif ((!RF_bread)||(!RF_meat)) return 0;", "\treturn RF_bread->SAR()_2 +
RF_meat->SAR()_num_sl_pulses;", "}", "", "++++++ END", "++++++ RESOURCES
++++++", "", "", "", "++++++ END RESOURCES ++++++", "", "")
"Writing
/home/jiasen/sequencetree4/bin/../simulator/foundationclasses.h..."
"Writing
/home/jiasen/sequencetree4/bin/../simulator/foundationclasses.cpp.."
"Writing /home/jiasen/sequencetree4/bin/../simulator/customclasses.h..."
"Writing /home/jiasen/sequencetree4/bin/../simulator/customclasses.cpp.."
"Writing /home/jiasen/sequencetree4/bin/../simulator/createsequence.cpp.."
"Writing
/home/jiasen/sequencetree4/bin/../simulator/loadparametersfile.cpp.."
"Running /bin/sh
"/home/jiasen/sequencetree4/bin/../simulator/compile-linux.sh".."
Running: "/home/jiasen/sequencetree4/bin/simulator_executable1.exe"
("stat",
"/home/jiasen/sequencetree4/bin/../tmp/sequence_parameters_in.txt",
"/home/jiasen/sequencetree4/bin/../tmp/sequence_parameters_out.txt",
"/home/jiasen/sequencetree4/bin/../tmp/simulation_output.dat",
"/home/jiasen/sequencetree4/bin/../tmp/results_output_stat.txt", "-1",
"-1")

Best wishes,
Jia Sen

On Wed, Oct 21, 2015 at 11:01 PM, licheng2002 [email protected]
wrote:

Did you attach the log file? Try to take a look at the simulator folder,
and delete the temporary object file, i.e. the file with extension ".o".
Then compile the sequence again.

On Wed, Oct 21, 2015 at 10:41 AM, siatjiasen [email protected]
wrote:

Thank you very much for help.

The tmp folder didn't exist.

I created it manually, then compile SPGR.sts sequence, still:

Simulation finished...
Unexpected problem in simulation, output file does not exist.

I attached the full log file recording the output of building and
running
./st4.

Thank you again.
Best wishes,
Jia Sen

—
Reply to this email directly or view it on GitHub
<
#3 (comment)

.

Regards!
Cheng Li
Email: [email protected]

—
Reply to this email directly or view it on GitHub
<
https://github.com/magland/sequencetree4/issues/3#issuecomment-149924546>
.

—
Reply to this email directly or view it on GitHub
#3 (comment)
.

Regards!

Cheng Li
Email: [email protected]

[siatjiasen]

Hi,

Thank you so much for help.

I did as what you said. Now I can compile and simulate the sequences (I
tried with both qt4 and qt5.5).

[image: Inline image 1]

Best wishes,
Jia Sen

On Fri, Oct 23, 2015 at 11:13 PM, licheng2002 [email protected]
wrote:

Hi,
I just tried a fresh compilation, it seems working fine on my PC,
Ubuntu 14.04, qmake v3.0 using Qt v5.2.1

Following the steps:

1. git clone https://github.com/magland/sequencetree4.git
2. cd sequence4/src
3. qmake
4. make
5. cd ../
6. mkdir tmp
7. cd bin
8. ./st4

Could you please try again from a fresh download? Thanks!
Cheng

On Thu, Oct 22, 2015 at 8:03 PM, siatjiasen [email protected]
wrote:

Thank you for help.

I did as you said. But I still got: Unexpected problem in simulation,
output files does not exist.

The log file was:

jiasen@jiasen:$ cd sequencetree4/
jiasen@jiasen:/sequencetree4$ cd simulator/
jiasen@jiasen:/sequencetree4/simulator$ cd build
jiasen@jiasen:/sequencetree4/simulator/build$ ls
createsequence.o foundationclasses.o main.o stsimscannerblocklist.o
customclasses.o loadparametersfile.o st4.o stsimscanner.o
jiasen@jiasen:/sequencetree4/simulator/build$ sudo rm *.o
[sudo] password for jiasen:
jiasen@jiasen:/sequencetree4/simulator/build$ ls
jiasen@jiasen:/sequencetree4/simulator/build$ cd ..
jiasen@jiasen:/sequencetree4/simulator$ cd ..
jiasen@jiasen:/sequencetree4$ ls
bin doc License.txt Resource_JS simulator stversion.txt
code examples README.txt sequences src templates
jiasen@jiasen:/sequencetree4$ cd bin
jiasen@jiasen:/sequencetree4/bin$ ls
results_viewer simulator_executable1.exe st4 tmp
simulator simulator_executable2.exe st4controller VS
jiasen@jiasen:/sequencetree4/bin$ cd ..
jiasen@jiasen:/sequencetree4$ sudo rm bin -r
jiasen@jiasen:/sequencetree4$ ls
code examples README.txt sequences src templates
doc License.txt Resource_JS simulator stversion.txt
jiasen@jiasen:/sequencetree4$ cd src
jiasen@jiasen:/sequencetree4/src$ ls
gui Makefile results_viewer st4controller todo.txt
install.x meta shared st4.pro VS
jiasen@jiasen:/sequencetree4/src$ make
cd gui/ && make -f Makefile
make[1]: Entering directory /home/jiasen/sequencetree4/src/gui' g++ -Wl,-O1 -Wl,-rpath,/opt/Qt/5.5/gcc_64 -Wl,-rpath,/opt/Qt/5.5/gcc_64/lib -o ../../bin/st4 build/main.o build/sstring.o build/slist.o build/stresources.o build/stsimscannerblocklist.o build/sttreeview.o build/stnodeview.o build/stparametertree.o build/stmainwindow.o build/stsequenceview.o build/stringchooserdlg.o build/stsimview.o build/stsimblockview.o build/steventlist.o build/stcompilelog.o build/stclassview.o build/stglobalview.o build/stpastedialog.o build/stconfigurationdlg.o build/openfilefromwebdlg.o build/readrawdatadlg.o build/distribute_raw_data.o build/staboutbox.o build/editresourcedlg.o build/streconstructionhighlighter.o build/stmetaclass.o build/stmetanode.o build/stmetasequence.o build/stmetasequencesimulator.o build/stsourceeditor.o build/cpphighlighter.o build/haiqtextedit.o build/defaulteditorwindow.o build/haiqtexteditgroup.o build/haiqmarker.o build/exporttoscannerdlg.o build/mda.o build/complex.o build/stpreferencesdlg.o build/qrc_st4.o build/moc_sttreeview.o build/moc_stnodeview.o build/moc_stparametertree.o build/moc_stmainwindow.o build/moc_stsequenceview.o build/moc_stringchooserdlg.o build/moc_stsimview.o build/moc_stsimblockview.o build/moc_steventlist.o build/moc_stcompilelog.o build/moc_stclassview.o build/moc_stglobalview.o build/moc_openfilefromwebdlg.o build/moc_readrawdatadlg.o build/moc_staboutbox.o build/moc_stmetasequencesimulator.o build/moc_stsourceeditor.o build/moc_haiqtextedit.o build/moc_defaulteditorwindow.o build/moc_haiqtexteditgroup.o -L/opt/Qt/5.5/gcc_64/lib -lQt5Widgets -L/usr/lib64 -lQt5Gui -lQt5Network -lQt5Core -lGL -lpthread make[1]: Leaving directory/home/jiasen/sequencetree4/src/gui'
cd VS/ && make -f Makefile
make[1]: Entering directory /home/jiasen/sequencetree4/src/VS' g++ -Wl,-O1 -Wl,-rpath,/opt/Qt/5.5/gcc_64 -Wl,-rpath,/opt/Qt/5.5/gcc_64/lib -o ../../bin/VS build/vsmain.o build/vsmainwindow.o build/vssequenceview.o build/vsphantomview.o build/vspropertyeditor.o build/run_virtual_scan.o build/vsabstractscanner.o build/vsobjectstate.o build/vsobjecttransformation.o build/vsphantom.o build/vsktermlist.o build/vsktermscanner.o build/stsimscannerblocklist.o build/stmetasequencesimulator.o build/stmetasequence.o build/stmetanode.o build/stmetaclass.o build/slist.o build/sstring.o build/stresources.o build/mda.o build/complex.o build/distribute_raw_data.o build/stringchooserdlg.o build/stconfigurationdlg.o build/stglobalview.o build/stcompilelog.o build/basicphantoms.o build/kspacefunction.o build/basickspacefunctions.o build/vsbasicphantoms.o build/vsphantomplugin.o build/qrc_st4.o build/moc_vsmainwindow.o build/moc_vssequenceview.o build/moc_vsphantomview.o build/moc_vspropertyeditor.o build/moc_vsabstractscanner.o build/moc_vsphantom.o build/moc_vsktermlist.o build/moc_stmetasequencesimulator.o build/moc_stringchooserdlg.o build/moc_stglobalview.o build/moc_stcompilelog.o build/moc_basicphantoms.o build/moc_basickspacefunctions.o build/moc_vsbasicphantoms.o -L../../bin -lgsl -lgslcblas -L/opt/Qt/5.5/gcc_64/lib -lQt5Widgets -L/usr/lib64 -lQt5Gui -lQt5Core -lGL -lpthread make[1]: Leaving directory/home/jiasen/sequencetree4/src/VS'
cd results_viewer/ && make -f Makefile
make[1]: Entering directory
/home/jiasen/sequencetree4/src/results_viewer' g++ -Wl,-O1 -Wl,-rpath,/opt/Qt/5.5/gcc_64 -Wl,-rpath,/opt/Qt/5.5/gcc_64/lib -o ../../bin/results_viewer build/rvmain.o build/rvmainwindow.o build/rvfileview.o build/mda.o build/complex.o build/viewmdamodel.o build/viewmdawidget2d.o build/viewmdawidget1d.o build/viewmdawidget.o build/brightnesstool.o build/fftw_library.o build/apply_fft.o build/export_to_imagej.o build/qrc_st4.o build/moc_rvmainwindow.o build/moc_rvfileview.o build/moc_viewmdamodel.o build/moc_viewmdawidget2d.o build/moc_viewmdawidget1d.o build/moc_viewmdawidget.o build/moc_brightnesstool.o -L../../bin -lfftw3 -L/opt/Qt/5.5/gcc_64/lib -lQt5Widgets -L/usr/lib64 -lQt5Gui -lQt5Core -lGL -lpthread make[1]: Leaving directory /home/jiasen/sequencetree4/src/results_viewer'
cd st4controller/ && make -f Makefile
make[1]: Entering directory
/home/jiasen/sequencetree4/src/st4controller' g++ -Wl,-O1 -Wl,-rpath,/opt/Qt/5.5/gcc_64 -Wl,-rpath,/opt/Qt/5.5/gcc_64/lib -o ../../bin/st4controller build/st4controllermain.o build/stcontrollermainwindow.o build/stcontrollerconfigdlg.o build/stcontroller.o build/rawdatafiletree.o build/sequencestree.o build/mda.o build/distribute_raw_data.o build/qrc_st4.o build/moc_stcontrollermainwindow.o build/moc_stcontroller.o -L/opt/Qt/5.5/gcc_64/lib -lQt5Widgets -L/usr/lib64 -lQt5Gui -lQt5Core -lGL -lpthread make[1]: Leaving directory/home/jiasen/sequencetree4/src/st4controller'
jiasen@jiasen:/sequencetree4/src$ ls
gui Makefile results_viewer st4controller todo.txt
install.x meta shared st4.pro VS
jiasen@jiasen:/sequencetree4/src$ cd ..
jiasen@jiasen:/sequencetree4$ ls
bin doc License.txt Resource_JS simulator stversion.txt
code examples README.txt sequences src templates
jiasen@jiasen:/sequencetree4$ cd bin
jiasen@jiasen:/sequencetree4/bin$ ls
results_viewer st4 st4controller VS
jiasen@jiasen:~/sequencetree4/bin$ ./st4
libpng warning: iCCP: known incorrect sRGB profile
loadFromText
("++++++ HEADER ++++++", "STVERSION=4.1.14", "++++++ END HEADER ++++++",
"++++++ NOTES ++++++", "=== spgr.sts - Spoiled gradient echo ===", "",
"Global Parameters", " FOV [mm] - field of view", " readout_N - number of
points per readout", " PE1 - first phase encode iterator", " PE2 - second
phase encode iterator", " TE [us] - echo time", " TR [us] - repetition
time", " dwell_time [us] - readout dwell time", " RF_spoiling [0 or 1] -
turn on or off RF-spoiling (randomization of transmit/receive phase)", "
flip_angle [degrees] - flip angle", " slice_thickness [mm] - slice
thickness", " slice_gradient_amplitude [uT/mm] - amplitude of slice
select
gradient", " spoiler_moment [uT/mm-us] - 3D moment of spoiler gradient at
end of each repetition", " prep_PE1 - iterator for preparation
repetetitions", "", "", "To perform 3D phase encoding", " For example,
set
PE2 = -4:1:3, for 8 phase encodes", " To interchange the looping order,
go
to the source code for the loop node and simply switch the order of PE1
and
PE2 iterators", "", "To switch to a non-selective pulse", " 1. set
slice_thickness=0", " 2. set slice_gradient_amplitude=(0,0,0)", " 3. If
you want a rectangular shape pulse, right click on the "RF" node and
select "promote node", then select STRF", "", "== Siemens User
Interface
Directives =====",

"UIDOUBLE\tNAME=TE\t\tRANGE=1:1:100\tLABEL="TE"\t\tUNITS="ms"\tFACTOR=0.001",

"UIDOUBLE\tNAME=TR\t\tRANGE=10:10:3000\tLABEL="TR"\t\tUNITS="ms"\tFACTOR=0.001",
"UIDOUBLE\tNAME=flip_angle\tRANGE=0:5:180\tLABEL="Flip
angle"\tUNITS="deg"",
"UIDOUBLE\tNAME=slice_thickness\tRANGE=2:2:50\t\tLABEL="Slice
thickness"\tUNITS="mm"", "UICHECKBOX\tNAME=RF_spoiling\tLABEL="RF
Spoiling"", "============================", "", "++++++ END NOTES
++++++",
"++++++ GLOBAL ++++++", "FOV\t(256,256,50)\tmm", "readout_N\t256\t",
"PE1\t-128:1:127\t", "PE2\t0:1:0\t", "TE\t6000\tmicrosec",
"TR\t50000\tmicrosec", "dwell_time\t30\tmicrosec", "RF_spoiling\t1\t0 or
1", "flip_angle\t45\tdegrees", "slice_thickness\t10\tmm",
"slice_gradient_amplitude\t(0,0,10)\tuT/mm",
"spoiler_moment\t(0,0,100000)\tuT/mm-us", "prep_PE1\t1:1:10\t",
"FOV\t->\tRoot->FOV",
"readout_N\t->\tRoot->MainLoop->Block->Acquire->Readout->N",
"readout_N\t->\tRoot->PrepLoop->Block->Acquire->Readout->N",
"PE1\t->\tRoot->MainLoop->PE1", "PE2\t->\tRoot->MainLoop->PE2",
"TE\t->\tRoot->MainLoop->Block->TE", "TE\t->\tRoot->PrepLoop->Block->TE",
"TR\t->\tRoot->MainLoop->Block->TR", "TR\t->\tRoot->PrepLoop->Block->TR",
"dwell_time\t->\tRoot->MainLoop->Block->Acquire->Readout->dwell_time",
"dwell_time\t->\tRoot->PrepLoop->Block->Acquire->Readout->dwell_time",
"RF_spoiling\t->\tRoot->MainLoop->RF_spoiling",
"RF_spoiling\t->\tRoot->PrepLoop->RF_spoiling",
"flip_angle\t->\tRoot->PrepLoop->Block->Excite->RF->flip_angle",
"flip_angle\t->\tRoot->MainLoop->Block->Excite->RF->flip_angle",
"slice_thickness\t->\tRoot->MainLoop->Block->Excite->slice_thickness",
"slice_thickness\t->\tRoot->PrepLoop->Block->Excite->slice_thickness",

"slice_gradient_amplitude\t->\tRoot->MainLoop->Block->Excite->gradient_amplitude",

"slice_gradient_amplitude\t->\tRoot->PrepLoop->Block->Excite->gradient_amplitude",
"spoiler_moment\t->\tRoot->PrepLoop->Block->Rewind->moment",
"spoiler_moment\t->\tRoot->MainLoop->Block->Rewind->moment",
"prep_PE1\t->\tRoot->PrepLoop->PE1", "++++++ END GLOBAL ++++++", "++++++
RECONSTRUCTION ++++++", "function reconstruction(num_channels)", "if
(nargin<1) num_channels=1; end;", "", "if (num_channels==1)",
"\tX=readmda('ADC1.mda');", "\tX=fftshift(fftn(fftshift(X)));",
"\twritemda(X,'recon.mda');", "end;", "", "++++++ END NOTES ++++++",
"++++++ LINK GROUPS ++++++", "",
"GROUP\tRoot->PrepLoop->Block\tRoot->MainLoop->Block", "", "++++++ END
LINK
GROUPS ++++++", "", "", "++++++ NODES ++++++", "",
"PARAMETER\tSTVector3\tFOV\t(256,256,50)\tmm\tactive\tFOV",
"PARAMETER\tSTReal\tmaxamp\t20\tuT/mm\tactive\t",
"PARAMETER\tSTReal\tramprate\t0.1\t[uT/mm]/us\tactive\t",
"PARAMETER\tSTReal\tgamma\t42.5764\tHz/uT\tactive\t",
"PARAMETER\tSTVector3\tFOV_shift\t(0,0,0)\tmm\tactive\t",
"PARAMETER\tSTVector3\tphase_shift\t237\tdegrees\tpassive\t",
"PARAMETER\tSTVector3\tFOV_shift_offset\t(0,0,0)\tmm; used
internally\tactive\t", "CHILD\tSPGRLoop\tPrepLoop", "
PARAMETER\tSTIterator\tPE1\t1:1:10\t\tactive\tprep_PE1", "
PARAMETER\tSTIterator\tPE2\t0:1:0\t\tactive\t", "
PARAMETER\tSTVector3\treadout_dir\t(1,0,0)\t\tactive\t", "
PARAMETER\tSTVector3\tPE1_dir\t(0,0,0)\t\tactive\t", "
PARAMETER\tSTVector3\tPE2_dir\t(0,0,1)\t\tactive\t", "
PARAMETER\tSTInteger\tRF_spoiling\t1\t0 or 1\tactive\tRF_spoiling", "
CHILD\tSTGradientEchoBlock\tBlock", "
PARAMETER\tSTReal\tTE\t6000\tmicrosec\tactive\tTE", "
PARAMETER\tSTReal\tTR\t50000\tmicrosec\tactive\tTR", "
PARAMETER\tSTVector3\tkspace_dir\t(1,0,0)\t\tpassive\t", "
PARAMETER\tSTVector3\tkspace_echo\t(0,0,0)\t\tpassive\t", "
PARAMETER\tSTReal\texcite_time\t1000\tmicrosec\tactive\t", "
CHILD\tSTExcite\tExcite", "

PARAMETER\tSTVector3\tgradient_amplitude\t(0,0,10)\tuT/mm\tactive\tslice_gradient_amplitude",
"
PARAMETER\tSTReal\tslice_thickness\t10\tmm\tactive\tslice_thickness", "
PARAMETER\tSTReal\tbandwidth\t4257.64\tHz\tpassive\t", "
PARAMETER\tSTInteger\tprephase\t1\t0 or 1\tactive\t", "
CHILD\tSTGradientMom\tPrephase", "
PARAMETER\tSTVector3\tramp_times_1\t(0,0,200)\tmicrosec\tpassive\t", "

PARAMETER\tSTVector3\tplateau_times\t(0,0,210)\tmicrosec\tpassive\t", "

PARAMETER\tSTVector3\tramp_times_2\t(0,0,200)\tmicrosec\tpassive\t", "

PARAMETER\tSTVector3\tstart_times\t(0,0,0)\tmicrosec\tpassive\t", "

PARAMETER\tSTVector3\tamplitude\t(0,0,-19.7561)\tuT/mm\tpassive\t", "
PARAMETER\tSTInteger\talignment\t0\t0=left; 1=right;
2=center\tactive\t", "
PARAMETER\tSTInteger\talways_min_dur\t0\t0 or 1\tactive\t", "
PARAMETER\tSTReal\tmaxamp\t0\t[uT/mm]\tactive\t", "
PARAMETER\tSTReal\tramprate\t0\t[uT/mm]/us\tactive\t", "
END", " CHILD\tSTGradientAmp\tSliceGradient", "
PARAMETER\tSTReal\tramp_time_1\t200\tmicrosec\tactive\t", "
PARAMETER\tSTReal\tplateau_time\t1400\tmicrosec\tpassive\t", "
PARAMETER\tSTReal\tramp_time_2\t200\tmicrosec\tactive\t", "
PARAMETER\tSTVector3\tamplitude\t(0,0,10)\tuT/mm\tpassive\t", "
END", " CHILD\tSTSincRF\tRF", "
PARAMETER\tSTReal\tnum_lobes_left\t2\t\tactive\t", "
PARAMETER\tSTReal\tnum_lobes_right\t2\t\tactive\t", "
PARAMETER\tSTReal\tflip_angle\t45\tdegrees\tactive\tflip_angle", "
PARAMETER\tSTReal\tpulse_duration\t1409.23\tmicrosec\tpassive\t", "
PARAMETER\tSTReal\treference_fraction\t0.5\t\tpassive\t", "
PARAMETER\tSTReal\tbandwidth\t4257.64\tHz\tpassive\t", "
PARAMETER\tSTReal\ttime_step\t10\tmicrosec\tactive\t", "
PARAMETER\tSTReal\tphase\t0\tdegrees\tactive\t", "
PARAMETER\tSTReal\tfrequency\t0\tHz\tactive\t", "
PARAMETER\tSTInteger\tpulse_type\t1\t1=Excite; 2=Refocus\tactive\t", "
PARAMETER\tSTVector3\tgradient_amplitude\t(0,0,10)\tuT/mm; for
internal use\tpassive\t", "
PARAMETER\tSTReal\tslice_thickness\t10\tmm; for internal use\tpassive\t",
" END", " END", "
CHILD\tSTAcquire\tAcquire", "
PARAMETER\tSTVector3\techo_moment\t(0,0,0)\t[uT/mm]-us\tpassive\t", "

PARAMETER\tSTVector3\tmoment_per_point\t(91.7468,0,0)\t[uT/mm]-us\tpassive\t",
" CHILD\tSTGradientMom\tEncode", "
PARAMETER\tSTVector3\tramp_times_1\t(200,0,200)\tmicrosec\tpassive\t", "

PARAMETER\tSTVector3\tplateau_times\t(410,0,200)\tmicrosec\tpassive\t", "

PARAMETER\tSTVector3\tramp_times_2\t(200,0,200)\tmicrosec\tpassive\t", "

PARAMETER\tSTVector3\tstart_times\t(0,0,0)\tmicrosec\tpassive\t", "

PARAMETER\tSTVector3\tamplitude\t(-19.7531,0,-19.75)\tuT/mm\tpassive\t",
"
PARAMETER\tSTInteger\talignment\t0\t0=left; 1=right;
2=center\tactive\t", "
PARAMETER\tSTInteger\talways_min_dur\t0\t0 or 1\tactive\t", "
PARAMETER\tSTReal\tmaxamp\t0\t[uT/mm]\tactive\t", "
PARAMETER\tSTReal\tramprate\t0\t[uT/mm]/us\tactive\t", "
END", " CHILD\tSTGradientAmp\tReadoutGradient", "
PARAMETER\tSTReal\tramp_time_1\t200\tmicrosec\tactive\t", "
PARAMETER\tSTReal\tplateau_time\t7680\tmicrosec\tpassive\t", "
PARAMETER\tSTReal\tramp_time_2\t200\tmicrosec\tactive\t", "
PARAMETER\tSTVector3\tamplitude\t(3.05823,0,0)\tuT/mm\tpassive\t", "
END", " CHILD\tSTReadout\tReadout", "
PARAMETER\tSTReal\tdwell_time\t30\tmicrosec\tactive\tdwell_time", "
PARAMETER\tSTInteger\tN\t256\t\tactive\treadout_N", "
PARAMETER\tSTReal\treference_fraction\t0.5\t\tactive\t", "
PARAMETER\tSTReal\tactual_reference_fraction\t0.5\t\tpassive\t", "
PARAMETER\tSTReal\treference_sample\t128.5\t\tpassive\t", "
PARAMETER\tSTReal\tphase\t0\tdegrees\tactive\t", "
PARAMETER\tSTReal\tfrequency\t0\tHz\tactive\t", "
PARAMETER\tSTVector3\tgradient_amplitude\t(3.05823,0,0)\tuT/mm; for
internal use\tpassive\t", "
PARAMETER\tSTInteger\tround_up_reference_time\t1\t0 or 1\tactive\t", "
END", " END", " CHILD\tSTEncode\tRewind", "

PARAMETER\tSTVector3\tmoment\t(0,0,100000)\t[uT/mm]-us\tactive\tspoiler_moment",
" PARAMETER\tSTInteger\tdo_rewind\t1\t0 or 1\tactive\t", "
CHILD\tSTGradientMom\tGradient", "
PARAMETER\tSTVector3\tramp_times_1\t(200,0,200)\tmicrosec\tpassive\t", "

PARAMETER\tSTVector3\tplateau_times\t(410,0,4800)\tmicrosec\tpassive\t",
"

PARAMETER\tSTVector3\tramp_times_2\t(200,0,200)\tmicrosec\tpassive\t", "

PARAMETER\tSTVector3\tstart_times\t(0,0,0)\tmicrosec\tpassive\t", "

PARAMETER\tSTVector3\tamplitude\t(-19.7531,0,20)\tuT/mm\tpassive\t", "
PARAMETER\tSTInteger\talignment\t0\t0=left; 1=right;
2=center\tactive\t", "
PARAMETER\tSTInteger\talways_min_dur\t0\t0 or 1\tactive\t", "
PARAMETER\tSTReal\tmaxamp\t0\t[uT/mm]\tactive\t", "
PARAMETER\tSTReal\tramprate\t0\t[uT/mm]/us\tactive\t", "
END", " END", " END", " END",
"CHILD\tSPGRLoop\tMainLoop", "
PARAMETER\tSTIterator\tPE1\t-128:1:127\t\tactive\tPE1", "
PARAMETER\tSTIterator\tPE2\t0:1:0\t\tactive\tPE2", "
PARAMETER\tSTVector3\treadout_dir\t(1,0,0)\t\tactive\t", "
PARAMETER\tSTVector3\tPE1_dir\t(0,1,0)\t\tactive\t", "
PARAMETER\tSTVector3\tPE2_dir\t(0,0,1)\t\tactive\t", "
PARAMETER\tSTInteger\tRF_spoiling\t1\t0 or 1\tactive\tRF_spoiling", "
CHILD\tSTGradientEchoBlock\tBlock", "
PARAMETER\tSTReal\tTE\t6000\tmicrosec\tactive\tTE", "
PARAMETER\tSTReal\tTR\t50000\tmicrosec\tactive\tTR", "
PARAMETER\tSTVector3\tkspace_dir\t(1,0,0)\t\tpassive\t", "
PARAMETER\tSTVector3\tkspace_echo\t(0,-88,0)\t\tpassive\t", "
PARAMETER\tSTReal\texcite_time\t1000\tmicrosec\tactive\t", "
CHILD\tSTExcite\tExcite", "

PARAMETER\tSTVector3\tgradient_amplitude\t(0,0,10)\tuT/mm\tactive\tslice_gradient_amplitude",
"
PARAMETER\tSTReal\tslice_thickness\t10\tmm\tactive\tslice_thickness", "
PARAMETER\tSTReal\tbandwidth\t4257.64\tHz\tpassive\t", "
PARAMETER\tSTInteger\tprephase\t1\t0 or 1\tactive\t", "
CHILD\tSTGradientMom\tPrephase", "
PARAMETER\tSTVector3\tramp_times_1\t(0,0,200)\tmicrosec\tpassive\t", "

PARAMETER\tSTVector3\tplateau_times\t(0,0,210)\tmicrosec\tpassive\t", "

PARAMETER\tSTVector3\tramp_times_2\t(0,0,200)\tmicrosec\tpassive\t", "

PARAMETER\tSTVector3\tstart_times\t(0,0,0)\tmicrosec\tpassive\t", "

PARAMETER\tSTVector3\tamplitude\t(0,0,-19.7561)\tuT/mm\tpassive\t", "
PARAMETER\tSTInteger\talignment\t0\t0=left; 1=right;
2=center\tactive\t", "
PARAMETER\tSTInteger\talways_min_dur\t0\t0 or 1\tactive\t", "
PARAMETER\tSTReal\tmaxamp\t0\t[uT/mm]\tactive\t", "
PARAMETER\tSTReal\tramprate\t0\t[uT/mm]/us\tactive\t", "
END", " CHILD\tSTGradientAmp\tSliceGradient", "
PARAMETER\tSTReal\tramp_time_1\t200\tmicrosec\tactive\t", "
PARAMETER\tSTReal\tplateau_time\t1400\tmicrosec\tpassive\t", "
PARAMETER\tSTReal\tramp_time_2\t200\tmicrosec\tactive\t", "
PARAMETER\tSTVector3\tamplitude\t(0,0,10)\tuT/mm\tpassive\t", "
END", " CHILD\tSTSincRF\tRF", "
PARAMETER\tSTReal\tnum_lobes_left\t2\t\tactive\t", "
PARAMETER\tSTReal\tnum_lobes_right\t2\t\tactive\t", "
PARAMETER\tSTReal\tflip_angle\t45\tdegrees\tactive\tflip_angle", "
PARAMETER\tSTReal\tpulse_duration\t1409.23\tmicrosec\tpassive\t", "
PARAMETER\tSTReal\treference_fraction\t0.5\t\tpassive\t", "
PARAMETER\tSTReal\tbandwidth\t4257.64\tHz\tpassive\t", "
PARAMETER\tSTReal\ttime_step\t10\tmicrosec\tactive\t", "
PARAMETER\tSTReal\tphase\t0\tdegrees\tactive\t", "
PARAMETER\tSTReal\tfrequency\t0\tHz\tactive\t", "
PARAMETER\tSTInteger\tpulse_type\t1\t1=Excite; 2=Refocus\tactive\t", "
PARAMETER\tSTVector3\tgradient_amplitude\t(0,0,10)\tuT/mm; for
internal use\tpassive\t", "
PARAMETER\tSTReal\tslice_thickness\t10\tmm; for internal use\tpassive\t",
" END", " END", "
CHILD\tSTAcquire\tAcquire", "

PARAMETER\tSTVector3\techo_moment\t(0,-8073.72,0)\t[uT/mm]-us\tpassive\t",
"

PARAMETER\tSTVector3\tmoment_per_point\t(91.7468,0,0)\t[uT/mm]-us\tpassive\t",
" CHILD\tSTGradientMom\tEncode", "
PARAMETER\tSTVector3\tramp_times_1\t(200,200,200)\tmicrosec\tpassive\t",
"

PARAMETER\tSTVector3\tplateau_times\t(410,390,200)\tmicrosec\tpassive\t",
"
PARAMETER\tSTVector3\tramp_times_2\t(200,200,200)\tmicrosec\tpassive\t",
"

PARAMETER\tSTVector3\tstart_times\t(0,0,0)\tmicrosec\tpassive\t", "

PARAMETER\tSTVector3\tamplitude\t(-19.7531,-13.6843,-19.75)\tuT/mm\tpassive\t",
" PARAMETER\tSTInteger\talignment\t0\t0=left; 1=right;
2=center\tactive\t", "
PARAMETER\tSTInteger\talways_min_dur\t0\t0 or 1\tactive\t", "
PARAMETER\tSTReal\tmaxamp\t0\t[uT/mm]\tactive\t", "
PARAMETER\tSTReal\tramprate\t0\t[uT/mm]/us\tactive\t", "
END", " CHILD\tSTGradientAmp\tReadoutGradient", "
PARAMETER\tSTReal\tramp_time_1\t200\tmicrosec\tactive\t", "
PARAMETER\tSTReal\tplateau_time\t7680\tmicrosec\tpassive\t", "
PARAMETER\tSTReal\tramp_time_2\t200\tmicrosec\tactive\t", "
PARAMETER\tSTVector3\tamplitude\t(3.05823,0,0)\tuT/mm\tpassive\t", "
END", " CHILD\tSTReadout\tReadout", "
PARAMETER\tSTReal\tdwell_time\t30\tmicrosec\tactive\tdwell_time", "
PARAMETER\tSTInteger\tN\t256\t\tactive\treadout_N", "
PARAMETER\tSTReal\treference_fraction\t0.5\t\tactive\t", "
PARAMETER\tSTReal\tactual_reference_fraction\t0.5\t\tpassive\t", "
PARAMETER\tSTReal\treference_sample\t128.5\t\tpassive\t", "
PARAMETER\tSTReal\tphase\t0\tdegrees\tactive\t", "
PARAMETER\tSTReal\tfrequency\t0\tHz\tactive\t", "
PARAMETER\tSTVector3\tgradient_amplitude\t(3.05823,0,0)\tuT/mm; for
internal use\tpassive\t", "
PARAMETER\tSTInteger\tround_up_reference_time\t1\t0 or 1\tactive\t", "
END", " END", " CHILD\tSTEncode\tRewind", "

PARAMETER\tSTVector3\tmoment\t(0,0,100000)\t[uT/mm]-us\tactive\tspoiler_moment",
" PARAMETER\tSTInteger\tdo_rewind\t1\t0 or 1\tactive\t", "
CHILD\tSTGradientMom\tGradient", "
PARAMETER\tSTVector3\tramp_times_1\t(200,200,200)\tmicrosec\tpassive\t",
"

PARAMETER\tSTVector3\tplateau_times\t(410,390,4800)\tmicrosec\tpassive\t",
"
PARAMETER\tSTVector3\tramp_times_2\t(200,200,200)\tmicrosec\tpassive\t",
"

PARAMETER\tSTVector3\tstart_times\t(0,0,0)\tmicrosec\tpassive\t", "

PARAMETER\tSTVector3\tamplitude\t(-19.7531,13.6843,20)\tuT/mm\tpassive\t",
" PARAMETER\tSTInteger\talignment\t0\t0=left; 1=right;
2=center\tactive\t", "
PARAMETER\tSTInteger\talways_min_dur\t0\t0 or 1\tactive\t", "
PARAMETER\tSTReal\tmaxamp\t0\t[uT/mm]\tactive\t", "
PARAMETER\tSTReal\tramprate\t0\t[uT/mm]/us\tactive\t", "
END", " END", " END", " END", "END", "", "++++++ END
NODES ++++++", "", "++++++ USERCLASS SPGRLoop ++++++", "", "++++++
HEADER",
"class ST_EXPORT SPGRLoop : public STLoop", "{", "public:", "\t/* BEGIN
SEQUENCETREE -- this section generated by SequenceTree -- do not edit
/",
"\tSTIterator PE1;", "\tSTIterator PE2;", "\tSTVector3 readout_dir;",
"\tSTVector3 PE1_dir;", "\tSTVector3 PE2_dir;", "\tSTInteger
RF_spoiling;",
"\tSTGradientEchoBlock *Block;", "\t/ END SEQUENCETREE -- this section
generated by SequenceTree -- do not edit /", "\t", "\tSPGRLoop();",
"\tbool prepare();", "\t", "\tbool loopRun();", "};", "", "", "++++++
SOURCE", "SPGRLoop::SPGRLoop() {", "\tST_CLASS(SPGRLoop,STLoop)", "\t/
ST_PARAMETERS /\t", "\tST_PARAMETER(STIterator,PE1,0:1:0,)",
"\tST_PARAMETER(STIterator,PE2,0:1:0,)",
"\tST_PARAMETER(STVector3,readout_dir,(1,0,0),)",
"\tST_PARAMETER(STVector3,PE1_dir,(0,1,0),)",
"\tST_PARAMETER(STVector3,PE2_dir,(0,0,1),)",
"\tST_PARAMETER(STInteger,RF_spoiling,0,0 or 1)", "\t/ ST_CHILDREN /",
"\tST_CHILD(STGradientEchoBlock,Block)", "}", "bool SPGRLoop::prepare()
{",
"\tBlock->kspace_dir=readout_dir;", "\treturn STLoop::prepare();", "}",
"",
"", "bool SPGRLoop::loopRun() {", " if (RF_spoiling) {", "
sequence()->phase_shift=rand()%360;", " }",
"\tBlock->kspace_echo=PE1_dir_PE1+PE2_dir_PE2;", "\treturn
Block->run();",
"}", "", "++++++ END", "", "++++++ CLASS SPGRLoop_1 ++++++", "", "++++++
HEADER", "class ST_EXPORT SPGRLoop_1 : public STLoop", "{", "public:",
"\t/ BEGIN SEQUENCETREE -- this section generated by SequenceTree -- do
not edit /", "\tSTIterator PE1;", "\tSTIterator PE2;", "\tSTVector3
readout_dir;", "\tSTVector3 PE1_dir;", "\tSTVector3 PE2_dir;",
"\tSTInteger
RF_spoiling;", "\tSTGradientEchoBlock *Block;", "\t/ END SEQUENCETREE --
this section generated by SequenceTree -- do not edit /", "\t",
"\tSPGRLoop_1();", "\tbool prepare();", "\t", "\tbool loopRun();", "};",
"", "", "++++++ SOURCE", "SPGRLoop_1::SPGRLoop_1() {",
"\tST_CLASS(SPGRLoop_1,STLoop)", "\t/ ST_PARAMETERS /\t",
"\tST_PARAMETER(STIterator,PE1,0:1:0,)",
"\tST_PARAMETER(STIterator,PE2,0:1:0,)",
"\tST_PARAMETER(STVector3,readout_dir,(1,0,0),)",
"\tST_PARAMETER(STVector3,PE1_dir,(0,1,0),)",
"\tST_PARAMETER(STVector3,PE2_dir,(0,0,1),)",
"\tST_PARAMETER(STInteger,RF_spoiling,0,0 or 1)", "\t/ ST_CHILDREN /",
"\tST_CHILD(STGradientEchoBlock,Block)", "}", "bool SPGRLoop_1::prepare()
{", "\tBlock->kspace_dir=readout_dir;", "\treturn STLoop::prepare();",
"}",
"", "", "bool SPGRLoop_1::loopRun() {", " if (RF_spoiling) {", "
sequence()->phase_shift=rand()%360;", " }",
"\tBlock->kspace_echo=PE1_dir_PE1+PE2_dir_PE2;", "\treturn
Block->run();",
"}", "", "++++++ END", "", "++++++ CLASS STRoot ++++++", "", "++++++
HEADER", "class STRoot : public STSequence", "{", "public:", "\t/ BEGIN
SEQUENCETREE -- this section generated by SequenceTree -- do not edit
*/",

"\tSPGRLoop PrepLoop;", "\tSPGRLoop *MainLoop;", "\t/ END SEQUENCETREE

this section generated by SequenceTree -- do not edit /", "\t",
"\tSTRoot();", "};", "", "", "++++++ SOURCE", "STRoot::STRoot() {",
"\tST_CLASS(STRoot,STSequence)", "\t/ ST_PARAMETERS /", "\t/
ST_CHILDREN
/", "\tST_CHILD(SPGRLoop,PrepLoop);", "\tST_CHILD(SPGRLoop,MainLoop);",
"}", "", "++++++ END", "", "++++++ USERCLASS SpinLockRF ++++++", "",
"++++++ HEADER", "class SpinLockRF : public STNode {", "public:", "\t/
BEGIN SEQUENCETREE -- this section generated by SequenceTree -- do not
edit
/", "\tSTReal flip_angle_1;", "\tSTReal flip_angle_2;", "\tSTReal
pulse_duration_1;", "\tSTReal pulse_duration_2;", "\tSTInteger
alternating_phase;", "\tSTInteger frequency_offset;", "\tSTInteger
num_sl_pulses;", "\tSTReal inter_pulse_delay;", "\tSTReal time_step;",
"\tSTReal phase;", "\tSTReal frequency;", "\t/ END SEQUENCETREE -- this
section generated by SequenceTree -- do not edit /", "\t", "\t//events",
"\tSTScannerRFPulse *RF_bread;", "\tSTScannerRFPulse *RF_meat;",
"\t/////////////////////////////////////////////////////",
"\tSpinLockRF();", "\tvirtual ~SpinLockRF();", "\tbool initialize();",
"\tbool prepare();", "\tbool run();", "\tdouble duration();", "\tdouble
referenceTime();", "\tVector3 terminalMoment();", "\tVector3
gradientStartTimes(); ", "\tVector3 gradientEndTimes();", "\tdouble
SAR();", "private:", "\tvoid delete_events();", "};", "", "", "++++++
SOURCE", "SpinLockRF::SpinLockRF() {", "\tST_CLASS(SpinLockRF,STNode)",
"\tRF_bread=0;", "\tRF_meat=0;", "\t/ ST_PARAMETERS /",
"\tST_PARAMETER(STReal, flip_angle_1, 90, degrees)",
"\tST_PARAMETER(STReal, flip_angle_2, 360, degrees)",
"\tST_PARAMETER(STReal, pulse_duration_1, 300, microsec)",
"\tST_PARAMETER(STReal, pulse_duration_2, 1000, microsec)",
"\tST_PARAMETER(STInteger, alternating_phase, 0, 0 or 1) ",
"\tST_PARAMETER(STInteger, frequency_offset, 0, Hz)",
"\tST_PARAMETER(STInteger, num_sl_pulses, 10,)", "\tST_PARAMETER(STReal,
inter_pulse_delay, 60, microsec)", "\tST_PARAMETER(STReal, time_step, 10,
microsec)", "\tST_PARAMETER(STReal, phase, 0, degrees)",
"\tST_PARAMETER(STReal, frequency, 0, Hz)", "\t/ ST_CHILDREN _/", "}",
"SpinLockRF::~SpinLockRF() {", "\tdelete_events();", "}", "void
SpinLockRF::delete_events() {", "\tif (RF_bread) delete RF_bread;
RF_bread=0;", "\tif (RF_meat) delete RF_meat; RF_meat=0;", "}", "bool
SpinLockRF::initialize() {", "\tclearChildren();", "\tif (!scanner())
return false;", "\tdelete_events();",
"\tRF_bread=scanner()->allocateRFPulse(this);",
"\tRF_meat=scanner()->allocateRFPulse(this);", "\treturn true;", "}",
"bool
SpinLockRF::prepare() {", "\tif (!RF_bread) return false;", "\tif
(!RF_meat) return false;", "\tif (time_step<=0) return false;", "\tif
(pulse_duration_1<=time_step) return false;", "\tif
(pulse_duration_2<=time_step) return false;", "\tif (!sequence()) return
false;", "\t\t", "\t\tlong N1=(long)(pulse_duration_1/time_step);",
"\t\tlong N2=(long)(pulse_duration_2/time_step);", "\t\t", "\t\tdouble
*data_mag_1=(double *)malloc(sizeof(double)_N1);", "\t\tdouble
_data_phase_1=(double *)malloc(sizeof(double)_N1);", "\t\tdouble
_data_mag_2=(double *)malloc(sizeof(double)_N2);", "\t\tdouble
_data_phase_2=(double *)malloc(sizeof(double)_N2);", "\t\tdouble
sum_re_1=0,sum_re_2=0;", "\t\tdouble sum_im_1=0,sum_im_2=0;", "\t\t{for
(long j=0; j<N1; j++) {", "\t\t\tdouble re=1,im=0;",
"\t\t\tsum_re_1+=re;",
"\t\t\tsum_im_1+=im;", "\t\t\tdata_mag_1[j]=sqrt(re_re+im_im);",
"\t\t\tdata_phase_1[j]=atan2(im,re)/(2_3.1415926535)_360;", "\t\t}}",
"\t\t{for (long j=0; j<N2; j++) {", "\t\t\tdouble re=1,im=0;",
"\t\t\tsum_re_2+=re;", "\t\t\tsum_im_2+=im;",
"\t\t\tdata_mag_2[j]=sqrt(re_re+im_im);",
"\t\t\tdata_phase_2[j]=atan2(im,re)/(2_3.1415926535)_360;", "\t\t}}",
"\t\t//uT * sec * Hz/uT * degrees = degrees ", "\t\tdouble

factor1=sqrt(sum_re_1_sum_re_1+sum_im_1_sum_im_1)_time_step/1.0E6_sequence()->gamma*360/90;",
"\t\tdouble

factor2=sqrt(sum_re_2_sum_re_2+sum_im_2_sum_im_2)_time_step/1.0E6_sequence()->gamma*360/90;",
"\t\t{for (long j=0; j<N1; j++) {", "\t\t\tdata_mag_1[j]/=factor1;",
"\t\t}}", "\t\t{for (long j=0; j<N2; j++) {",
"\t\t\tdata_mag_2[j]/=factor2;", "\t\t}}",

"\t\tRF_bread->setPulse(N1,data_mag_1,data_phase_1,time_step,90,pulse_duration_1/2);",

"\t\tRF_meat->setPulse(N2,data_mag_2,data_phase_2,time_step,90,pulse_duration_2/2);",
"\t\tfree(data_mag_1);", "\t\tfree(data_phase_1);",
"\t\tfree(data_mag_2);", "\t\tfree(data_phase_2);", "\t",
"\tRF_bread->setFlipAngle(flip_angle_1);",
"\tRF_meat->setFlipAngle(flip_angle_2);", "\t", "\tsetModified(false);",
"\treturn true;", "}", "bool SpinLockRF::run() {", "\tif (!RF_bread)
return
false;", "\tif (!RF_meat) return false;", "\tif (!scanner()) return
false;", "\tif (!sequence()) return false;", "", "\tdouble ph=phase;",
"\tVector3 totmom=initialTotalMoment();",
"\tph+=sequence()->phaseAdjustment();",
"\tph+=(totmom.x()_sequence()->getFOVShiftX()",
"\t\t+totmom.y()_sequence()->getFOVShiftY()",

"\t\t+totmom.z()_sequence()->getFOVShiftZ())sequence()->gamma/1.0E6_360;",
"\tRF_bread->setPhase(ph);", "\tRF_meat->setPhase(ph);", "\t",
"\tRF_bread->setFrequency(frequency);",
"\tRF_meat->setFrequency(frequency);", "\t", "", "\t//The excite pulse ",
"\tdouble time_offset=0;",
"\tRF_bread->setStartTime(startTime()+time_offset);", "\tif
(RF_bread->pulseCount()) scanner()->addEvent(RF_bread);",
"\ttime_offset+=pulse_duration_1+inter_pulse_delay;", "", "\t//inner
pulses", "\tfor (int j=0; j<num_sl_pulses; j++) {", "\t\tif
(alternating_phase) {", "\t\t\tif (j%2==0) {",
"\t\t\t\tRF_meat->setPhase(ph+0);",
"\t\t\t\tRF_meat->setFrequency(frequency_offset);", "\t\t\t}",
"\t\t\telse
{", "\t\t\t\tRF_meat->setPhase(ph+180);",
"\t\t\t\tRF_meat->setFrequency(frequency_offset);", "\t\t\t}", "\t\t}",
"\t\tRF_meat->setStartTime(startTime()+time_offset);", "\t\tif
(RF_meat->pulseCount()) scanner()->addEvent(RF_meat);",
"\t\ttime_offset+=pulse_duration_2+inter_pulse_delay;", "\t}", "",
"\t//The
store pulse", "\tRF_bread->setStartTime(startTime()+time_offset);", "\tif
(RF_bread->pulseCount()) scanner()->addEvent(RF_bread);",
"\ttime_offset+=pulse_duration_1+inter_pulse_delay;", "\t", "\treturn
true;", "}", "double SpinLockRF::duration() {", "\tif
((!RF_meat)||(RF_bread)) return 0;", "\treturn pulse_duration_1_2 +
pulse_duration_2_num_sl_pulses + inter_pulse_delay(num_sl_pulses+1);",
"}", "double SpinLockRF::referenceTime() {", "\treturn 0;", "}", "Vector3
SpinLockRF::terminalMoment() {", "\treturn Vector3();", "}", "", "Vector3
SpinLockRF::gradientStartTimes() {", "\treturn Vector3(0,0,0);", "}",
"Vector3 SpinLockRF::gradientEndTimes() {", "\tdouble dur=duration();",
"\treturn Vector3(dur,dur,dur);", "}", "", "double SpinLockRF::SAR() {",
"\tif ((!RF_bread)||(!RF_meat)) return 0;", "\treturn RF_bread->SAR()_2 +
RF_meat->SAR()_num_sl_pulses;", "}", "", "++++++ END", "++++++ RESOURCES
++++++", "", "", "", "++++++ END RESOURCES ++++++", "", "")
"Writing
/home/jiasen/sequencetree4/bin/../simulator/foundationclasses.h..."
"Writing
/home/jiasen/sequencetree4/bin/../simulator/foundationclasses.cpp.."
"Writing /home/jiasen/sequencetree4/bin/../simulator/customclasses.h..."
"Writing /home/jiasen/sequencetree4/bin/../simulator/customclasses.cpp.."
"Writing
/home/jiasen/sequencetree4/bin/../simulator/createsequence.cpp.."
"Writing
/home/jiasen/sequencetree4/bin/../simulator/loadparametersfile.cpp.."
"Running /bin/sh
"/home/jiasen/sequencetree4/bin/../simulator/compile-linux.sh".."
Running: "/home/jiasen/sequencetree4/bin/simulator_executable1.exe"
("stat",
"/home/jiasen/sequencetree4/bin/../tmp/sequence_parameters_in.txt",
"/home/jiasen/sequencetree4/bin/../tmp/sequence_parameters_out.txt",
"/home/jiasen/sequencetree4/bin/../tmp/simulation_output.dat",
"/home/jiasen/sequencetree4/bin/../tmp/results_output_stat.txt", "-1",
"-1")

Best wishes,
Jia Sen

On Wed, Oct 21, 2015 at 11:01 PM, licheng2002 [email protected]
wrote:

Did you attach the log file? Try to take a look at the simulator
folder,
and delete the temporary object file, i.e. the file with extension
".o".
Then compile the sequence again.

On Wed, Oct 21, 2015 at 10:41 AM, siatjiasen <[email protected]

wrote:

Thank you very much for help.

The tmp folder didn't exist.

I created it manually, then compile SPGR.sts sequence, still:

Simulation finished...
Unexpected problem in simulation, output file does not exist.

I attached the full log file recording the output of building and
running
./st4.

Thank you again.
Best wishes,
Jia Sen

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Reply to this email directly or view it on GitHub
<

#3 (comment)

.

Regards!
Cheng Li
Email: [email protected]

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<
#3 (comment)

.

—
Reply to this email directly or view it on GitHub
<
https://github.com/magland/sequencetree4/issues/3#issuecomment-150391446>
.

Regards!
Cheng Li
Email: [email protected]

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Reply to this email directly or view it on GitHub
#3 (comment)
.

[siatjiasen]

Hi,

May I suggest to update the install instructions in "Readme.txt" file? The following steps you provided really help me:
Following the steps:

1. git clone https://github.com/magland/sequencetree4.git
2. cd sequence4/src
3. qmake
4. make
5. cd ../
6. mkdir tmp
7. cd bin
8. ./st4

Thank you.
Best wishes,
Jia Sen