Difference between revisions of "FSL"

Revision as of 18:56, 12 August 2022

Description

fsl website

FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.

Environment Modules

Run module spider fsl to find out what environment modules are available for this application.

System Variables

HPC_FSL_DIR - installation directory
HPC_FSL_BIN - executable directory

Additional Information

Running bedpostx

Log into dev1 or dev2.
Run 'screen' and turn the screen log onto monitor the run

ctrl+a shift+h

The name of the log file will be displayed in your terminal.

Load the fsl module

module load fsl

Run bedpostx, a typical minimal command should look like

bedpostx datadir -M emailaddr

You may detach the screen at any time and then use screen -r to reattach at a later time.
Once the bedpostx script has finished running turn the screen log off with

ctrl+a shift+h

Look at the bedpostx output in the screen log and in your email for job warning or error notifications.

Available bedpostx options

The bedpostx script has been modified to work with Moab/Torque for job submissions. In addition to the standard bedpostx command line options, the following Moab/Torque options have been added:

Option	Default Value	Description
-m	abe	see qsub. Note: slice job mail options are set to 'a' to avoid email overload
-M		see qsub. Note: you must provide an email address (REQUIRED)
-N	pbx	job name prefix. Note: this is followed by _pre, _slice, and _post
-ws	4:00:00	see qsub -l walltime. Applies to all slice processing jobs
-wp	1:00:00	see qsub -l walltime. Applies to pre and post processing jobs
-ms	1gb	see qsub -l pmem. Applies to all slice processing jobs
-mp	gb	see qsub -l pmem. Applies to all pre and post processing jobs
-v		turns on verbose option, i.e. displays additional information

How bedpostx is run

A directory will be created for the output data. It will be named using the original data folder name followed by '.bedpostX'.
Only one bedpostx script at a time can be run for a given data directory otherwise the output data will be unreliable.
If you run bedpostx and the output directory already exists, beedpostx will look to see if any slices need to be processed. It will then run jobs for all the unprocessed slices and post-process all the slice data.
There are 3 stages in the execution of bedpostx:

pre-processing. To view job status use: qstat -u yourusername
slice processing. A job is posted for each individual slice as part of a job array. To view individual job status use: 'qstat -t -u yourusername'.
post-processing. To view job status use: 'qstat -u yourusername'

Notes

If you are sure that the terminal will not be disconnected at any time while running the bedpostx script then you don't need to use screen. You can not allow the terminal from which you run bedpostx to get disconnected while the script is running. If the terminal is disconnected, it will cause the job array completion detection to fail and the post processing will run before the slice processing is finished. This is why using screen is recommended.
If you need to cancel an on-going bedpostx run you can execute the 'cancel' command from the created output data directory by typing ./cancel or by using the full path to the command. You must execute cancel from the same server where you originally started bedpostx. The cancel command will display the bedpostx PID in case you want to run 'ps aux | grep yourusername' and make sure that the PID matches your bedpostx process. It may take up to 30 seconds for bedpostx to handle the request. If you run bedpostx after previously cancelling it, you may either leave the existing output data directory in place or manually delete it to start from scratch. If you do not delete the directory and there are some slices that were previously processed, they will not be processed again. The cancel command will delete itself once it's executed.
Be aware that the job array numbers do not match the sub-directory numbers in the diff_slices directory. The jobs are always numbered 1-n and the directory numbers 0-(n-1) the first time you run bedpostx. If you were to rerun bedpostx again with some slices already processed in a prior run, then the only way to match job numbers with sub-directory numbers is via the job control file commands.txt.

Citation

If you publish research that uses fsl you have to cite it as follows:

M. Jenkinson, C.F. Beckmann, T.E. Behrens, M.W. Woolrich, S.M. Smith. FSL. NeuroImage, 62:782-90, 2012
M.W. Woolrich, S. Jbabdi, B. Patenaude, M. Chappell, S. Makni, T. Behrens, C. Beckmann, M. Jenkinson, S.M. Smith. Bayesian analysis of neuroimaging data in FSL. NeuroImage, 45:S173-86, 2009
S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady, and P.M. Matthews. Advances in functional and structural MR image analysis and implementation as FSL. NeuroImage, 23(S1):208-19, 2004

@@ Line 1: / Line 1: @@
-[[Category:Software]][[Category:Bioinformatics]][[Category:Neurology]]
+[[Category:Software]][[Category:Neuroscience]][[Category:Biology]][[Category:Imaging]]
 {|<!--CONFIGURATION: REQUIRED-->
 |{{#vardefine:app|fsl}}
@@ Line 20: / Line 20: @@
 FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.
 <!--Modules-->
-==Required Modules==
+==Environment Modules==
-===Serial===
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
-* {{#var:app}}
-<!--
-===Parallel (OpenMP)===
-* intel
-* {{#var:app}}
-===Parallel (MPI)===
-* intel
-* openmpi
-* {{#var:app}}
--->
 ==System Variables==
-* HPC_{{#uppercase:{{#var:app}}}}_DIR
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
+* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
 <!--Configuration-->
 {{#if: {{#var: conf}}|==Configuration==
@@ Line 42: / Line 33: @@
 |}}
 ===Running bedpostx===
+* Log into dev1 or dev2.
+* Run '<code>screen</code>' and turn the screen log onto monitor the run
+ ctrl+a shift+h
+The name of the log file will be displayed in your terminal.
+* Load the fsl module
+ module load fsl
+* Run <code>bedpostx</code>, a typical minimal command should look like
+ bedpostx datadir -M emailaddr
+* You may detach the screen at any time and then use screen -r to reattach at a later time.
+* Once the <code>bedpostx</code> script has finished running turn the screen log off with
+ ctrl+a shift+h
+* Look at the bedpostx output in the screen log and in your email for job warning or error notifications.
+;Available bedpostx options
 The bedpostx script has been modified to work with Moab/Torque for job submissions. In addition to the standard bedpostx command line options, the following Moab/Torque options have been added:
@@ Line 48: / Line 53: @@
 ! Option !! Default Value !! Description
 |-
-| &nbsp;-m || &nbsp;abe || &nbsp;see qsub. Note: slice job mail options are set to 'a' to avoid email overload &nbsp;
+| -m || abe || see qsub. Note: slice job mail options are set to 'a' to avoid email overload
 |-
-| &nbsp;-M || || &nbsp;see qsub. Note: you must provide an email address (REQUIRED) &nbsp;
+| -M || || see qsub. Note: you must provide an email address (REQUIRED)
 |-
-| &nbsp;-N || &nbsp;pbx || &nbsp;job name prefix. Note: this is followed by _pre, _slice, and _post &nbsp;
+| -N || pbx || job name prefix. Note: this is followed by _pre, _slice, and _post
 |-
-| &nbsp;-ws || &nbsp;4:00:00 || &nbsp;see qsub -l walltime. Applies to all slice processing jobs &nbsp;
+| -ws || 4:00:00 || see qsub -l walltime. Applies to all slice processing jobs
 |-
-| &nbsp;-wp || &nbsp;1:00:00 || &nbsp;see qsub -l walltime. Applies to pre and post processing jobs &nbsp;
+| -wp || 1:00:00 || see qsub -l walltime. Applies to pre and post processing jobs
 |-
-| &nbsp;-ms || &nbsp;1gb || &nbsp;see qsub -l pmem. Applies to all slice processing jobs &nbsp;
+| -ms || 1gb || see qsub -l pmem. Applies to all slice processing jobs
 |-
-| &nbsp;-mp || &nbsp;1gb || &nbsp;see qsub -l pmem. Applies to all pre and post processing jobs &nbsp;
+| -mp || gb || see qsub -l pmem. Applies to all pre and post processing jobs
 |-
-| &nbsp;-v || || &nbsp;turns on verbose option, i.e. displays additional information &nbsp;
+| -v || || &nbsp;turns on verbose option, i.e. displays additional information
 |}
+;How bedpostx is run:
+* A directory will be created for the output data. It will be named using the original data folder name followed by '<code>.bedpostX</code>'.
+* Only one bedpostx script at a time can be run for a given data directory otherwise the output data will be unreliable.
+* If you run bedpostx and the output directory already exists, beedpostx will look to see if any slices need to be processed. It will then run jobs for all the unprocessed slices and post-process all the slice data.
+* There are 3 stages in the execution of bedpostx:
+#pre-processing. To view job status use: qstat -u yourusername
+#slice processing. A job is posted for each individual slice as part of a job array. To view individual job status use: '<code>qstat -t -u yourusername</code>'.
+#post-processing. To view job status use: '<code>qstat -u yourusername</code>'
-Sequence for running bedpostx:
+;Notes:
+* If you are sure that the terminal will not be disconnected at any time while running the bedpostx script then you don't need to use screen. You can not allow the terminal from which you run bedpostx to get disconnected while the script is running. If the terminal is disconnected, it will cause the job array completion detection to fail and the post processing will run before the slice processing is finished. This is why using screen is recommended.
-* log into DEV1 or DEV2
+* If you need to cancel an on-going bedpostx run you can execute the '<code>cancel</code>' command from the created output data directory by typing ./cancel or by using the full path to the command. You must execute cancel from the same server where you originally started bedpostx. The cancel command will display the bedpostx PID in case you want to run '<code>ps aux | grep yourusername</code>' and make sure that the PID matches your bedpostx process. It may take up to 30 seconds for bedpostx to handle the request. If you run bedpostx after previously cancelling it, you may either leave the existing output data directory in place or manually delete it to start from scratch. If you do not delete the directory and there are some slices that were previously processed, they will not be processed again. The cancel command will delete itself once it's executed.
-* cd into the directory that contains your bedpostx data directory
-* run screen and turn the log on (ctl-a shift-h)
-* run module load fsl
-* run bedpostx, a typical command should look like: bedpostx datadir -M emailaddr
-* you may detach the screen at any time and then use screen -r to reattach at a later time
-* once the script has finished running you may turn the log off
-* use the log file to view the script output and also check your emails for any error notifications
-Note: If you can make sure that the terminal is not disconnected at any time while running the bedpostx script then you don't need to use screen.
-What you should know about running bedpostx:
-* a directory will be created for the output data. It will be named using the original data folder name followed by .bedpostX
-* only one bedpostx script at a time can be run for a given data directory otherwise the output data will be unreliable.
-* if you run bedpostx and the output directory already exists, it will look to see if any slices need to be processed. It will then run jobs for all the unprocessed slices and post process all the slice data.
-* there are 3 stages in the execution of bedpostx:
-. pre-processing   - to view job status use: qstat -u youruserid
-. slice processing - a job is posted for each individual slice as part of a job array,
-                         to view individual job status use: qstat -t -u youruserid
-. post-processing  - to view job status use: qstat -u youruserid
-Notes:
-* Because of issues with job arrays and qstat, the job array is not considered completed until all the individual jobs stop showing up in qstat - about 5 minutes after completion.
-* You can not allow the terminal from which you run bedpostx to get disconnected while the script is running. If the terminal is disconnected, it will cause the job array completion detection to fail and the post processing will run before the slice processing is finished. This is why using screen is recommended.
 * Be aware that the job array numbers do not match the sub-directory numbers in the diff_slices directory. The jobs are always numbered 1-n and the directory numbers 0-(n-1) the first time you run bedpostx. If you were to rerun bedpostx again with some slices already processed in a prior run, then the only way to match job numbers with sub-directory numbers is via the job control file commands.txt.
-* using qstat -u youruserid for a job array is not reliable. It will sometimes consider the job array done and gone, i.e. it will not display an entry for it, even though one or more of the individual jobs are still running.
 <!--PBS scripts-->