Hoffman2:MATLAB:SPM - Revision history

Hwang at 18:07, 15 October 2018

2018-10-15T18:07:14Z

← Older revision		Revision as of 18:07, 15 October 2018
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	After creating a Batch file for a single subject, those individuals comfortable with MATLAB programming should be capable of reading the contents of the Batch file and understanding how to apply its settings to N subjects with a few "for" loops and directory listings. We highly recommend that you save yourself the carpal tunnel from clicking and leverage the power of scripting.		After creating a Batch file for a single subject, those individuals comfortable with MATLAB programming should be capable of reading the contents of the Batch file and understanding how to apply its settings to N subjects with a few "for" loops and directory listings. We highly recommend that you save yourself the carpal tunnel from clicking and leverage the power of scripting.



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	$ ./run_spm_job.sh		$ ./run_spm_job.sh
	</pre>		</pre>


	==Wait for the Job to Run==		==Wait for the Job to Run==

Hwang: /* Using Interactive mode */

2018-10-15T18:06:06Z

Using Interactive mode

← Older revision		Revision as of 18:06, 15 October 2018
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	==Using Interactive mode==		==Using Interactive mode==
	~~<pre>~~
	For spm8 you need this in your .bashrc file:		For spm8 you need this in your .bashrc file:
	export MATLABPATH=/u/project/CCN/apps/spm8		export MATLABPATH=/u/project/CCN/apps/spm8

	For spm12 you need this in your .bashrc file:		For spm12 you need this in your .bashrc file:
	export MATLABPATH=/u/project/CCN/apps/spm12		export MATLABPATH=/u/project/CCN/apps/spm12

			<pre>
	1. Start an interactive session via qrsh (for example):		1. Start an interactive session via qrsh (for example):
	qrsh -l h_data=4G,h_rt=8:00:00 -pe shared 2		qrsh -l h_data=4G,h_rt=8:00:00 -pe shared 2

	2. Load the MATLAB module. Use matlab/8.4 for spm8 and matlab/9.1 for spm12:		2. Load the MATLAB module. Use matlab/8.4 for spm8 and matlab/9.1 for spm12:
	module load matlab/9.1		module load matlab/9.1

	3. Set the MATLABPATH environment variable:		3. Set the MATLABPATH environment variable:
	export MATLABPATH=/u/project/CCN/apps/spm12		export MATLABPATH=/u/project/CCN/apps/spm12

	4. Start MATLAB:		4. Start MATLAB:
	matlab		matlab

	5. Start spm from the MATLAB prompt:		5. Start spm from the MATLAB prompt:
	>> spm		>> spm

Hwang at 18:05, 15 October 2018

2018-10-15T18:05:26Z

← Older revision		Revision as of 18:05, 15 October 2018
Line 80:		Line 80:

	==Using Interactive mode==		==Using Interactive mode==
			<pre>
	For spm8 you need this in your .bashrc file:		For spm8 you need this in your .bashrc file:
	export MATLABPATH=/u/project/CCN/apps/spm8		export MATLABPATH=/u/project/CCN/apps/spm8
Line 94:		Line 95:
	5. Start spm from the MATLAB prompt:		5. Start spm from the MATLAB prompt:
	>> spm		>> spm
			</pre>

	==View the Results==		==View the Results==

Hwang at 18:03, 15 October 2018

2018-10-15T18:03:19Z

Hwang at 18:02, 15 October 2018

2018-10-15T18:02:16Z

← Older revision		Revision as of 18:02, 15 October 2018
Line 80:		Line 80:

	==Using Interactive mode==		==Using Interactive mode==
	For spm8 you need this in your .bashrc file:		For spm8 you need this in your .bashrc file:
	export MATLABPATH=/u/project/CCN/apps/spm8		export MATLABPATH=/u/project/CCN/apps/spm8

	For spm12 you need this in your .bashrc file:		For spm12 you need this in your .bashrc file:
	export MATLABPATH=/u/project/CCN/apps/spm12		export MATLABPATH=/u/project/CCN/apps/spm12

	1. Start an interactive session via qrsh (for example):		1. Start an interactive session via qrsh (for example):

	qrsh -l h_data=4G,h_rt=8:00:00 -pe shared 2		qrsh -l h_data=4G,h_rt=8:00:00 -pe shared 2

	2. Load the MATLAB module. Use matlab/8.4 for spm8 and matlab/9.1 for spm12:		2. Load the MATLAB module. Use matlab/8.4 for spm8 and matlab/9.1 for spm12:

	module load matlab/9.1		module load matlab/9.1

	3. Set the MATLABPATH environment variable:		3. Set the MATLABPATH environment variable:

	export MATLABPATH=/u/project/CCN/apps/spm12		export MATLABPATH=/u/project/CCN/apps/spm12

	4. Start MATLAB:		4. Start MATLAB:

	matlab		matlab

	5. Start spm from the MATLAB prompt:		5. Start spm from the MATLAB prompt:

	>> spm		>> spm

Hwang at 18:00, 15 October 2018

2018-10-15T18:00:53Z

@@ Line 73: / Line 73: @@
   $ ./run_spm_job.sh
 </pre>
@@ Line 79: / Line 78: @@
 Remember how to [[Hoffman2:Monitoring_Jobs | check on job status?]]

Dmargolis: /* Create the Wrapper Script */

2017-05-26T20:08:49Z

Create the Wrapper Script

← Older revision		Revision as of 20:08, 26 May 2017
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	==Create the Wrapper Script==		==Create the Wrapper Script==
	SPM is a wonderful tool because it is capable of being compiled into an executable using SPM8's own "make_exec" script. On Hoffman2, we have compiled it and placed it at		SPM is a wonderful tool because it is capable of being compiled into an executable using SPM8's own "make_exec" script. On Hoffman2, we have compiled it and placed it at
	/u/~~home~~/~~FMRI~~/apps/spm_exec/spm8		/u/project/CCN/apps/spm_exec/spm8
	Now you need to create a wrapper script that will call this executable properly. The example shown below may be found at		Now you need to create a wrapper script that will call this executable properly. The example shown below may be found at
	/u/~~home~~/~~FMRI~~/apps/examples/spm/run_spm_job.sh		/u/project/CCN/apps/examples/spm/run_spm_job.sh

	<pre>		<pre>
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	# Run the compiled version of SPM8 on your batch file		# Run the compiled version of SPM8 on your batch file
	/u/~~home~~/~~FMRI~~/apps/spm_exec/spm8 "batch" "PATH_TO_YOUR_BATCH_FILE"		/u/project/CCN/apps/spm_exec/spm8 "batch" "PATH_TO_YOUR_BATCH_FILE"

	CMD		CMD
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	$ chmod 750 /path/to/your/wrapper/script		$ chmod 750 /path/to/your/wrapper/script
	filling in the appropriate path to your script.		filling in the appropriate path to your script.



	==Submit the Job==		==Submit the Job==

Dmargolis at 23:44, 22 May 2017

2017-05-22T23:44:38Z

← Older revision		Revision as of 23:44, 22 May 2017
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	'''Make this wrapper script executable''' using the command		'''Make this wrapper script executable''' using the command
	$ chmod ~~755~~ /path/to/your/wrapper/script		$ chmod 750 /path/to/your/wrapper/script
	filling in the appropriate path to your script.		filling in the appropriate path to your script.

Elau: SPM jobs

2014-03-22T00:59:03Z

SPM jobs

New page

[[Hoffman2|Back to all things Hoffman2]]

[[Hoffman2:MATLAB|Back to all things MATLAB]]

If you have a bunch of subjects that need to be processed through SPM, why waste your laptop using the GUI interface to slowly process each subject? And '''why waste a MATLAB license''' doing rote work that can be accomplished with compiled MATLAB code that works without a license?

Use Hoffman2's strengths and run that processing as one (or more!) jobs to get it done quickly and efficiently.

==Create the Batch File(s)==
#Launch SPM
#Click on the "Batch" button (to the left of "Quit").
#In the new window, go "File" > "New batch" to start with a new batch file.
#Using the "SPM" menu at the top of the window, add and modify the appropriate steps you would like to take and specify which data should be worked with.
#When you are satisfied with how things are set up, click "File" > "Save batch" and give your batch file a name (ending with ".mat").
#This is the basis for your SPM job.

After creating a Batch file for a single subject, those individuals comfortable with MATLAB programming should be capable of reading the contents of the Batch file and understanding how to apply its settings to N subjects with a few "for" loops and directory listings. We highly recommend that you save yourself the carpal tunnel from clicking and leverage the power of scripting.

==Create the Wrapper Script==
SPM is a wonderful tool because it is capable of being compiled into an executable using SPM8's own "make_exec" script. On Hoffman2, we have compiled it and placed it at
/u/home/FMRI/apps/spm_exec/spm8
Now you need to create a wrapper script that will call this executable properly. The example shown below may be found at
/u/home/FMRI/apps/examples/spm/run_spm_job.sh

<pre>
qsub <<CMD
#!/bin/bash
# No spaces before each pound (#) sign
# Use current working directory
#$ -cwd
# Error stream is merged with the standard output
#$ -j y
# Use the bash shell for job execution
#$ -S /bin/bash
# Use your normal environment variables in the job
#$ -V
# Use 1GB of RAM and the main queue, estimating 2 hours for completion
#$ -l h_data=1G,h_rt=2:00:00
# Only email on abort
#$ -m a
# Name the job "spm"
#$ -N spm
#

# Load the module environment
. /u/local/Modules/default/init/modules.sh

# Load the newest MATLAB
module load matlab

# Run the compiled version of SPM8 on your batch file
/u/home/FMRI/apps/spm_exec/spm8 "batch" "PATH_TO_YOUR_BATCH_FILE"

CMD
</pre>

As always, normal [[Hoffman2:Submitting_Jobs | job submission guidelines]] should be followed when creating this file. Such as setting the time and memory limits appropriately.

The words "PATH_TO_YOUR_BATCH_FILE" should also be replaced with the actual full path to the .mat batch file you saved previously and want processed.

'''Make this wrapper script executable''' using the command
$ chmod 755 /path/to/your/wrapper/script
filling in the appropriate path to your script.

==Submit the Job==
Now just execute the wrapper script to submit the job. If we were running our example, we would do
<pre>
$ cd /u/home/FMRI/apps/examples/spm
$ ./run_spm_job.sh
</pre>

==Wait for the Job to Run==
Remember how to [[Hoffman2:Monitoring_Jobs | check on job status?]]

==View the Results==
Use SPM or whichever tool is appropriate to view the results.

==Going Further==
If you created a single batch file to process 100 subjects, that would be fine and dandy, but it would take a very long time to go through each one in sequence.

But if you created 10 batch files with 10 subjects in each, and ran 10 separate jobs (since the compiled version of SPM does not use MATLAB licenses), the processing would be finished 10 times as quickly.

Consider parallelising your jobs when working at scale.

← Older revision		Revision as of 18:03, 15 October 2018
Line 82:		Line 82:
	For spm8 you need this in your .bashrc file:		For spm8 you need this in your .bashrc file:
	export MATLABPATH=/u/project/CCN/apps/spm8		export MATLABPATH=/u/project/CCN/apps/spm8

	For spm12 you need this in your .bashrc file:		For spm12 you need this in your .bashrc file:
	export MATLABPATH=/u/project/CCN/apps/spm12		export MATLABPATH=/u/project/CCN/apps/spm12

	1. Start an interactive session via qrsh (for example):		1. Start an interactive session via qrsh (for example):

	qrsh -l h_data=4G,h_rt=8:00:00 -pe shared 2		qrsh -l h_data=4G,h_rt=8:00:00 -pe shared 2

	2. Load the MATLAB module. Use matlab/8.4 for spm8 and matlab/9.1 for spm12:		2. Load the MATLAB module. Use matlab/8.4 for spm8 and matlab/9.1 for spm12:

	module load matlab/9.1		module load matlab/9.1

	3. Set the MATLABPATH environment variable:		3. Set the MATLABPATH environment variable:

	export MATLABPATH=/u/project/CCN/apps/spm12		export MATLABPATH=/u/project/CCN/apps/spm12

	4. Start MATLAB:		4. Start MATLAB:

	matlab		matlab

	5. Start spm from the MATLAB prompt:		5. Start spm from the MATLAB prompt:

	>> spm		>> spm