Dual regression error (multiple files in a text file) - command-line

So I'm running into some trouble using dual_regression. The problem here is that I'm using the following command and getting the following error:
> macminngh:session_one_and_three sondosayyash$ dual_regression /Users/sondosayyash/Downloads/FIX_sNorm/40_subjects.gica/groupmelodic.ica/melodic_IC.nii.gz 1 -1 5000 dualreg_40subj_output.dr 'cat /Users/sondosayyash/Desktop/Users.txt'
/Users/sondosayyash/abin/fsl/bin/dual_regression: line 126: [: too many arguments
mkdir: dualreg_40subj_output.dr: File exists
mkdir: dualreg_40subj_output.dr/scripts+logs: File exists
creating common mask
/bin/sh: line 1: syntax error near unexpected token `dualreg_40subj_output.dr/scripts+logs/drA'
/bin/sh: line 1: `file (dualreg_40subj_output.dr/scripts+logs/drA) does not exist -T 5 -N drB -l dualreg_40subj_output.dr/scripts+logs dualreg_40subj_output.dr/scripts+logs/drB'
doing the dual regressions
sorting maps and running randomise
/bin/sh: line 1: you: command not found
I don't know where I'm going wrong.
As for the text file listed as 'Users.txt' has many different file directories to filtered_func data.
I have a feeling there is a problem with the text file but I'm not entirely sure.

Related

Running druid script for injestion spec failed - bin/post-index-task --file quickstart/tutorial/wikipedia-index.json

I am trying to follow the quickstart for running the script but it is failing with this error in druid router cli:
~ $ bin/post-index-task --file quickstart/tutorial/wikipedia-index.json
bin/post-index-task: /opt/druid/bin/post-index-task-main: /usr/bin/env: bad interpreter: No such file or directory
bin/post-index-task: line 31: /opt/druid/bin/post-index-task-main: No error information
bin/post-index-task is already present but it seem to throw an error of No such file or directory.
Please guide, thanks.

How to use bibliography in different directory when knitting rmarkdown document to beamer presentation?

I'm knitting some beamer slides in an RMarkdown script in Rstudio on a Windows 7 PC. The slides are in the directory
C:/me/slides/myslides.Rmd
I have a master bibliography that lives in
C:/me/bib/masterbib.bib
I cannot figure out how to link to the bibliography file from the RMarkdown document. Here's the YAML from my attempt:
---
title: "Slides"
author: "me"
date: "2016-12-20"
bibliography: C:/me/bib/masterbib.bib
biblio-style: "apalike"
output:
beamer_presentation:
citation_package: natbib
---
Here's the error:
! Undefined control sequence.
<write> \string \bibdata {C:\me\bib\masterbib}
l.174 \end{frame}
Error: Failed to compile Slides.tex. See Slides.log for more info.
In addition: Warning message:
running command '"pdflatex" -halt-on-error -interaction=batchmode "Slides.tex"' had status 1
Execution halted
I've tried a couple other ways to specify the directory for masterbib.bib, but none have worked. I would prefer to keep the masterbib.bib file where it is, and not make an extra copy in the C:/me/slides/ directory. Thanks for your help!
Edit
When attempting to pass the following into YAML (quoteed with forward slashes):
bibliography: "C:/LaTeXstuff/BibTexLibrary/BrianBib.bib"
I get a fatal error with log output:
! Undefined control sequence.
<write> \string \bibdata {C:\me
\bib\masterbib}
l.174 \end{frame}
Here is how much of TeX's memory you used:
18047 strings out of 494045
334241 string characters out of 3145937
424206 words of memory out of 3000000
20891 multiletter control sequences out of 15000+200000
31808 words of font info for 44 fonts, out of 3000000 for 9000
715 hyphenation exceptions out of 8191
56i,11n,55p,434b,376s stack positions out of 5000i,500n,10000p,200000b,50000s
! ==> Fatal error occurred, no output PDF file produced!
When passing the following into YAML (quoted with backslashes)
bibliography: "C:\me\bib\masterbib.bib"
I get the following error in the Rstudio console
Error in yaml::yaml.load(enc2utf8(string), ...) :
Scanner error: while parsing a quoted scalar at line 4, column 15found unknown escape character at line 4, column 29
Calls: <Anonymous> ... yaml_load_utf8 -> mark_utf8 -> <Anonymous> -> .Call
Execution halted
When passing the following into YAML (unquoted with backslashes)
bibliography: C:\me\bib\masterbib.bib
I get the following error in the Rstudio console
! Undefined control sequence.
<write> \string \bibdata {C:\me
\bib\masterbib}
l.174 \end{frame}
Error: Failed to compile BibTest.tex. See BibTest.log for more info.
In addition: Warning message:
running command '"pdflatex" -halt-on-error -interaction=batchmode "BibTest.tex"' had status 1
Execution halted
Try unquoted with two backslashes:
...
bibliography: C:\\me\\bib\\masterbib.bib
...

Tesseract index >= 0 && index < size_used_:Error:Assert failed Error

I successfully wrote the traineddata file for a new tesseract language, but when I was finished, I continue to get the following error:
index >= 0 && index < size_used_:Error:Assert failed:in file ../ccutil/genericvector.h, line 657
However, this even happens when I run tesseract on an image I trained with! I am confused as to what is going on, as I would expect that the error should not occur if I run tesseract on the training set.
This error is being caused to the lack of a lang.shapetable file in your lang.traineddata file.
Make sure that you generate the shapetable:
shapeclustering -F font_properties -U unicharset lang.font.exp0.box.tr
This will create a file named shapetable. You will need to rename this to lang.shapetable before you can combine everything:
combine_tessdata lang.
That error indicates your training failed => you overlooked some error message during training.

Error in PHP code, Line // Col Non-existent?

WHen I try to run indexer for sphinx.
/usr/bin/indexer --rotate --all
I get this error...
using config file '/etc/sphinx/sphinx.conf'...
ERROR: invalid section type 'Strict' in /etc/sphinx/sphinx.conf line 1617 col 8.
ERROR: invalid section type 'Strict' in /etc/sphinx/sphinx.conf line 1617 col 1.
FATAL: failed to parse config file '/etc/sphinx/sphinx.conf'
When I check sphinx.conf there is no line 1617. The last line of code is 1373. Could someone tell this newb what I'm doing wrong and how do I debug a line that doesn't exist?
Thanks!
It sounds like you have a dynamic config file? ie contains embedded PHP code?
If so try running the config file on its own, and then inspecting that.
php /etc/sphinx/sphinx.conf > /tmp/sphinx.conf
cat -n /tmp/sphinx.conf | grep 1617 -C10
ie sphinx is finding the error in the generated output, not the raw code.

Unexpected EOF when linking Arduino project in Eclipse on OS X

I have been trying to link Arduino and Eclipse, and I feel like I'm close.
Where should I start looking for this?
Similar errors have been caused by extra/incomplete quote blocks (according to google searches). I have already dug through my AVR linker settings looking for quotes, but haven't had much luck.
Am I looking in the right place?
Which files should I check?
I have already looked in the file I have written myself (in this case, the basic Arduino blink program).
**** Build of configuration Release for project C64_Arduino1 ****
make all
Building target: C64_Arduino1.elf
Invoking: AVR C++ Linker
avr-gcc --cref -s -Os -o"C64_Arduino1.elf" ./C64_Arduino1.o ./CDC.o ./HID.o
./HardwareSerial.o ./Print.o ./Stream.o ./Tone.o ./USBCore.o ./WInterrupts.o ./WMath.o ./WString.o ./malloc.o ./wiring.o ./wiring_analog.o ./wiring_digital.o ./wiring_pulse.o
./wiring_shift.o -l"Arduino_Mega_2560_or_Mega_ADK" -lm -L/Users/Chet/Desktop/Chet's Shit/Side Projects/Programming/C64_Arduino1/Release -L"/Users/Chet/Desktop/Chet's Shit/Side
Projects/Programming/C64_Arduino1" -mmcu=atmega2560
/bin/sh: -c: line 0: unexpected EOF while looking for matching `"'
/bin/sh: -c: line 1: syntax error: unexpected end of file
make: *** [C64_Arduino1.elf] Error 2
**** Build Finished ****
EDIT:
I have commented out all of my code (including #include's) except the main (which is empty) and I still get the error. I have set up my IDE as specified Here and also Here. Still nothing.
Looking at the actual error message:
/bin/sh: -c: line 0: unexpected EOF while looking for matching `"'
/bin/sh: -c: line 1: syntax error: unexpected end of file
I can see that the problem is most likely due to some kind of Makefile syntax error.
When you write a make rule such like:
foo:
touch foo
What make does, it first checkes whether file called foo exists already, if not, then it runs command /bin/sh -c 'touch foo'. So the line where we said touch foo should have valid shell script syntax.
Looking at the command that you ended up running:
avr-gcc --cref -s -Os -o"C64_Arduino1.elf" ./C64_Arduino1.o ./CDC.o ./HID.o
./HardwareSerial.o ./Print.o ./Stream.o ./Tone.o ./USBCore.o ./WInterrupts.o ./WMath.o ./WString.o ./malloc.o ./wiring.o ./wiring_analog.o ./wiring_digital.o ./wiring_pulse.o
./wiring_shift.o -l"Arduino_Mega_2560_or_Mega_ADK" -lm -L/Users/Chet/Desktop/Chet's Shit/Side Projects/Programming/C64_Arduino1/Release -L"/Users/Chet/Desktop/Chet's Shit/Side
Projects/Programming/C64_Arduino1" -mmcu=atmega2560
I can see that the issue is with the ' character in some of the directory paths. You should either escape it (as in "/Users/Chet/Desktop/Chet\'s Shit") or, as a quick work-around symlink or move the directory.
As a general methodology tip, you should first check whether everything works in CLI, and then move on to teaching Eclipse what commands it should run.
Also, I would consider using the tool called ino instead of make, it might just work with minimum configuration. I have had some experience replacing Arduino IDE with just a Makefile, but it gets hairy when you need to use different boards and perhaps several connected at the same time. Give ino a try, it looks quite promising.