I am new to FSL, using version 4.1.8. I am trying to run a script that reads and generates *.nii files, which format is normally supported by FSL. I am calling an FSL function, probtrackx from within Matlab. However, I get the following error message seemingly unable to generate or recognize *.nii files:
** ERROR (nifti_image_read): failed to find header file for '~/Documents/fMRI_data/../DTI/fsl_dti/masks/target_mask_001'
** ERROR: nifti_image_open(~/Documents/fMRI_data/../DTI/fsl_dti/masks/target_mask_001): bad header info
ERROR: failed to open file ~/Documents/fMRI_data/../DTI/fsl_dti/masks/target_mask_001
ERROR: Could not open image ~/Documents/fMRI_data/../DTI/fsl_dti/masks/target_mask_001
The files do exist but FSL fails to recognize them. Any help as to how to correct the issue and get FSL to work properly would be most appreciated. I suspect it's a Linux settings issue, just not sure how to fix it. A solution to a related problem in a previous posting suggested adding ls='ls --color=auto'. I've tried it to on avail.
Some FSL tools assume that the $FSLDIR unix unvironment variable is set, which might not be the case in your MATLAB environment. You can fix that with something like setenv('FSLDIR', '/usr/local/fsl') (modified of course if your FSL installation is in a different place). Some also need the regular FSL setup script to be executed as well: system('. ${FSLDIR}/etc/fslconf/fsl.sh'). See also: http://www.fmrib.ox.ac.uk/fsl/fsl/downloading.html.
Instead of the more complicated probtrackx script, another thing to try first is simply:
system('fslhd ~/Documents/fMRI_data/../DTI/fsl_dti/masks/target_mask_001')
If this fails with the same error, then you know that you entered the path to the data incorrectly. For example, do you mean to have the .. in there?
Also, in the future, the best place to get FSL support is on their mailing list at: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=fsl
Does MATLAB have access to run other fsl commands? If you are able to run a command from the command line but not through MATLAB, the MATLAB user may not have access to run fsl or may be looking for some FSL variables.
You might have to do the equivalent of this for a linux system
Related
First, take note that I am using the Xilinx SDK 2018.2 on Kubuntu 22.04 because of my companies policy. I know from research, that the command I'm using is deprecated in newer versions, but in the version I am using, it works flawlessly - kind of... But read for yourself:
My task is to automate all steps in the FPGA build to create a pipeline which automatically builds and tests the FPGAs. To achieve this, I need to build the code - this works flawlessly in XSDK. For automation, this also has to work in the command line, so what I did is following the manual to find out how this is achieved. Everything works as expected if I write it in the interactive prompt like shown here:
user#ubuntuvm:~$ xsct
****** Xilinx Software Commandline Tool (XSCT) v2018.2
**** Build date : Jun 14 2018-20:18:43
** Copyright 1986-2018 Xilinx, Inc. All Rights Reserved.
xsct%
Then I can enter the commands I need to import all needed files and projects (hw, bsp, main project). With this toolset, everything works as expected.
Because I want to automate it via a pipeline, I decided to pack this into a script for easier access. The script contains exactly the commands I entered in the interactive shell and therefore looks like this:
user#ubuntuvm:~/gitrepos/repository$ cat ../autoBuildScript.tcl
setws /home/user/gitrepos/repository
openhw ./hps_packages/system.hdf
openbsp ./bsp_packages/system.mss
importprojects ./sources/mainApp
importprojects ./bsp_packages
importprojects ./hps_packages
regenbsp -bsp ./bsp_packages/system.mss
projects –clean
projects -build
The commands are identical to the ones entered via the interactive CLI tool, the only difference is that this is now packed into a script. The difference is, that this now does not build completely anymore. I get the following error:
user#ubuntuvm:~/gitrepos/repository$ xsct ../autoBuildScript.tcl
INFO: [Hsi 55-1698] elapsed time for repository loading 1 seconds
Starting xsdk. This could take few seconds... done
'mainApp' will not be imported... [ALREADY EXIST]
'bsp_packages' will not be imported... [ALREADY EXIST]
'hps_packages' will not be imported... [ALREADY EXIST]
/opt/Xilinx/SDK/2018.2/gnu/microblaze/lin
unexpected arguments: –clean
while executing
"error "unexpected arguments: $arglist""
(procedure "::xsdb::get_options" line 69)
invoked from within
"::xsdb::get_options args $options"
(procedure "projects" line 12)
invoked from within
"projects –clean"
(file "../autoBuildScript.tcl" line 8)
I've inserted projects -clean only, because I got the error before with projects -build and wanted to check, if this also happens with another argument.
In the internet I didn't really find anything according to my specific problem. Also I strictly held on to the official manual, in which the command is also used just as I use it - but with the result of it being working.
Also, I've checked the line endings (set to UNIX) because I suspected xsct to read maybe a newline character or something similar, with no result. This error also occurs, when I create the bsp and hardware from sketch. Also, to me the error looks like an internal one from Xilinx, but let me know what you think.
So, it appears that I just fixed the problem on my own. Thanks on everyone reading for being my rubber ducky.
Apparently, the version 2018.2 of XSDK has a few bugs, including inconsistency with their command interpretation. For some reason the command works in the interactive shell, but not in the script - because the command is in its short form. I just learned from a Xilinx tutorial, that projects -build is - even though it works - apparently not the full command. You usually need to clarify, that this command should come from the SDK like this: sdk projects -build. The interactive shell seems to ignore this fact for a reason - and so does the script for any command except projects. Therefore, I added the "sdk" prefix to all commands which I used from the SDK, just to be safe.
I cannot believe, that I just debugged 2 days for an error whose fix only contains 3 (+1 whitespace) letters.
Thanks everybody for reading and have a nice day
Repo for all code I've been using is updated here . When I run the requestor script it exits with a runtime error 2 (File not found). I am not sure how to further debug this or fix it. So far I've converted my code over to a python slim docker image to better mirror the example. It also works for me when I spin up a docker image that typing and running "/golem/work/imageclassifier.py --trainmodel" works from root. I switched all my code to use absolute paths. I also did make sure the shebang (#!) uses linux end of file characters rather than windows before which was giving me errors. Fixed a bug where my script returns error code 2 when called with no args to now pass.
clf.fit(trainDataGlobal, trainLabelsGlobal)
pkl_file = "classifier.pkl"
with open(pkl_file, 'wb') as file:
pickle.dump(clf, file)
is the only piece I could think of that causes the issue, but as far as I can tell this is the proper way to pickle something in python. Requestor script is also heavily based on the simple service example and I tried to mirror my design to that. I just need help in getting more information while debugging, or guidance on how to move forward from here
I am new in Geant4. i installed and build GEANT4 using cmake and visual stdio 17 on windlows 10 and now i am trying to practice its given basic exapmles, So, I build first example using cmake by following the toturial given here. The example build successfully and created the exampleB1.exe file. I have set up all environment variables to data installed as given in screen shot
but facing the problem of still relating to environment vairiable is the screenshots of error
I looked this ENSDFSTATE.dat file but could not be able to solve the problem. Any suggestions/ support is highly appreciated.
It looks like your "G4ENSDFSTATEDATA" environmental variable is pointing to the wrong data set. Edit this variable to point to G4ENSDFSTATE2.2 location (i.e. D:\GEANT4\share\Geant4-10.5.1\data\G4ENSDFSTATE2.2 instead of D:\GEANT4\share\Geant4-10.5.1\data\G4PARTICLEXS1.1) and should work fine for that one. Double check your other environmental variables are correct also. Looks like G4ABLADATA should be G4ABLA3.1 for example.
Here is the list of all variables from the getting started manual (http://geant4-userdoc.web.cern.ch/geant4-userdoc/UsersGuides/InstallationGuide/html/postinstall.html):
Good luck!
I am trying to make this slack bot run : https://github.com/lmammino/norrisbot
I am not very skilled with npm and node yet, but I follow his instructions and try to run the bot with the help of the npm start command.
Here's the output I get :
F:\norrisbot>npm start
> norrisbot#1.0.5 start F:\norrisbot
> node bin/bot.js
F:\norrisbot>
No error, but nothing happens either in the console or the slack general channel...
By the way I set up my BOT_API_KEY variable correctly (with the token.js method)
By your command prompt it's clear you're running in Windows. The operations for running Node properly in Windows are different in several ways from Mac/Linux, and a LOT (most?) of developers don't address these because they're on Mac/Linux themselves. Path formats, file locations, how you expose environment variables, and all sorts of things are different in Win.
Try hand-editing bin/bot.js in your locally cloned copy of the repo. Find this line at the end of the file:
norrisbot.run();
Change it to read as follows:
console.log('Running Norris Bot');
norrisbot.run();
console.log('Ran Norris Bot');
I bet you will find that either NEITHER of these lines gets printed, or only one does.
If NEITHER line gets printed, the issue is with the npm command improperly formatting the path to the executable script for Windows users. In that case, try running it as (make sure NodeJS is in your PATH):
node bin/bot.js
If only the FIRST line gets printed, there is almost certainly a bug elsewhere in the module itself. I didn't evaluate all of its code, and I'm not on Windows myself at the moment - I just use it often enough to be aware of its differences. But either way it will get you started on finding the issue, and if it's truly a bug, you can pursue the bug report I see you've already filed in Github.
When I am trying to make executable files of my .m-files on a Linux machine, some of the the .m-files are working absolutely fine.
However, one file which has camera input inside the .m-file is giving me this error:
Depfun error: 'Unexpected Standard exception from MEX file. What() is: ..' Error using mcc Error executing mcc, return status = 1 (0x1).
But when I use the same .m-file on Windows and R2012a it is working properly without any error.
I found a bug report here - is this a similar problem?
How do I solve it?
Here is the simple code of my .m-file:
function yuv()
vid1 = videoinput('linuxvideo', 1, 'YUYV_1280x960');
set(vid1,'FramesPerTrigger',1);
start(vid1);
imageData1=getdata(vid1,1);
imageData=ycbcr2rgb(imageData1);
imagesc(imageData(:,:,:,1));
end
I was getting the same Depfun error, "What() is: ..", under R2013a on Linux but no errors when using a different OS or an older MATLAB version to compile my code. Following the bug report you linked to fixed it for me.
In the zip file linked to in the bug report you'll find a depfun.opts file. Rename or move your original depfun.opts file that's located in [matlabroot]/toolbox/compiler and copy the new one in its place.
Putting the new depfun.opts file in place is all it took for me to be able to compile using R2013a on Linux.
Also note, the bug report says that it could be caused by the importdata function or the Parallel Computing Toolbox but I'm not using either of those.