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CVNRneuroimaging / infrastructure

Issue tracking, system documentation and configs for operations side of the neuroimaging core @ Atlanta VA CVNR / Emory University
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FIX on qball2 #168

Open J-Drucker opened 8 years ago

J-Drucker commented 8 years ago

FSL's FIX requires MATLAB.

Alternatively (and this may be a better solution in terms of portability), it can use Octave (which is free!) instead of Matlab.

In order to use Octave, the file /opt/fix/settings.sh needs to be changed (there's a variable that tells FIX to use Octave instead of Matlab). Problem is, I don't have permissions to edit that file.

I'm cool with whatever solution you guys think preserves the integrity of our infrastructure.

Many thanks, Jonathan

rrmm commented 8 years ago

Keith,

can you put matlab on qball2?

Jonathan,

I tend to prefer octave myself, but i think the decision was to keep everyone on the same set of tools to ensure consistent results.

rob

FSL's FIX requires MATLAB.

Alternatively (and this may be a better solution in terms of portability), it can use Octave (which is free!) instead of Matlab.

In order to use Octave, the file /opt/fix/settings.sh needs to be changed (there's a variable that tells FIX to use Octave instead of Matlab). Problem is, I don't have permissions to edit that file.

I'm cool with whatever solution you guys think preserves the integrity of our infrastructure.

Many thanks, Jonathan

You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/CVNRneuroimaging/infrastructure/issues/168

kmcgregor123456 commented 8 years ago

Matlab is already on qball2 in /usr/local/MATLAB/r2015b

Keith M. McGregor, PhD VA RR&D Atlanta CVNR Emory University, Department of Neurology 352.359.8084 http://www.varrd.emory.edu

From: rrmm notifications@github.com Sent: Friday, April 22, 2016 3:58:25 PM To: CVNRneuroimaging/infrastructure Subject: Re: [CVNRneuroimaging/infrastructure] FIX on qball2 (#168)

Keith,

can you put matlab on qball2?

Jonathan,

I tend to prefer octave myself, but i think the decision was to keep everyone on the same set of tools to ensure consistent results.

rob

FSL's FIX requires MATLAB.

Alternatively (and this may be a better solution in terms of portability), it can use Octave (which is free!) instead of Matlab.

In order to use Octave, the file /opt/fix/settings.sh needs to be changed (there's a variable that tells FIX to use Octave instead of Matlab). Problem is, I don't have permissions to edit that file.

I'm cool with whatever solution you guys think preserves the integrity of our infrastructure.

Many thanks, Jonathan

You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/CVNRneuroimaging/infrastructure/issues/168

You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHubhttps://github.com/CVNRneuroimaging/infrastructure/issues/168#issuecomment-213569135

This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited.

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J-Drucker commented 8 years ago

Oh. Could be a path issue? Should I update my bash profile?

On Apr 22, 2016, at 16:34, Keith McGregor notifications@github.com wrote:

Matlab is already on qball2 in /usr/local/MATLAB/r2015b

Keith M. McGregor, PhD VA RR&D Atlanta CVNR Emory University, Department of Neurology 352.359.8084 http://www.varrd.emory.edu

From: rrmm notifications@github.com Sent: Friday, April 22, 2016 3:58:25 PM To: CVNRneuroimaging/infrastructure Subject: Re: [CVNRneuroimaging/infrastructure] FIX on qball2 (#168)

Keith,

can you put matlab on qball2?

Jonathan,

I tend to prefer octave myself, but i think the decision was to keep everyone on the same set of tools to ensure consistent results.

rob

FSL's FIX requires MATLAB.

Alternatively (and this may be a better solution in terms of portability), it can use Octave (which is free!) instead of Matlab.

In order to use Octave, the file /opt/fix/settings.sh needs to be changed (there's a variable that tells FIX to use Octave instead of Matlab). Problem is, I don't have permissions to edit that file.

I'm cool with whatever solution you guys think preserves the integrity of our infrastructure.

Many thanks, Jonathan

You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/CVNRneuroimaging/infrastructure/issues/168

You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHubhttps://github.com/CVNRneuroimaging/infrastructure/issues/168#issuecomment-213569135

This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited.

If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). — You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub

J-Drucker commented 8 years ago

Guys, I found the problem!

FIX uses the file settings.sh to set a bunch of environmental variables. One of those variables is the location of MATLAB. Line 21 looks like this:

   FSL_FIX_MATLAB_ROOT=/opt/fmrib/matlab

See the problem? That's not where MATLAB is! I can't fix the code, because I don't have permissions.

kmcgregor123456 commented 8 years ago

I changed the settings.sh file. it should work now.

Keith M. McGregor, PhD VA RR&D Atlanta CVNR Emory University, Department of Neurology 352.359.8084 http://www.varrd.emory.edu

From: J. Drucker notifications@github.com Sent: Sunday, April 24, 2016 12:13:47 AM To: CVNRneuroimaging/infrastructure Cc: Keith McGregor; Comment Subject: Re: [CVNRneuroimaging/infrastructure] FIX on qball2 (#168)

Guys, I found the problem!

FIX uses the file settings.sh to set a bunch of environmental variables. One of those variables is the location of MATLAB. Line 21 looks like this:

FSL_FIX_MATLAB_ROOT=/opt/fmrib/matlab

See the problem? That's not where MATLAB is! I can't fix the code, because I don't have permissions.

You are receiving this because you commented. Reply to this email directly or view it on GitHubhttps://github.com/CVNRneuroimaging/infrastructure/issues/168#issuecomment-213881584

This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited.

If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

J-Drucker commented 8 years ago

Still crashing. The file /opt/fix/settings.sh looks unchanged:

FSL_FIX_MATLAB_ROOT=/opt/fmrib/matlab

J-Drucker commented 8 years ago

My mistake, sort of; qball2 looks good. I'll try running it soon.

I was on lens. That settings file should probably be the same on all of the machines we'll be using, though, so maybe my mistake was fortuitous?