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help > RE: Manually defining slice order
Dec 1, 2015 04:12 PM | Alfonso Nieto-Castanon - Boston University
RE: Manually defining slice order
Hi Andrew,
Sorry about this, you are right that when selecting the "manually-defined" slice-order option in the GUI, CONN will wait until a later time (when it is ready to process each subject and it has the info on the number of slices per volume) to ask you about the specific slice-order vector, which is not going to work for distributed jobs since those are expected to be run on a non-interactive session. I have fixed that in the attached patch (this patch is for release 15g, simply copy the file to the conn distribution folder overwriting the file with the same name there). Let me know if you run into any issues.
Of course, another alternative as Pravesh suggested is to define the preprocessing info through batch scripts/commands. If doing so please use the newer batch.Setup.preprocessing field (instead of the older batch.New field) since the latter is not compatible with distributed processing. For example, to run the slice-timing correction step in parallel for all subjects on your current conn project, you may simply use the syntax:
conn_batch('Setup.preprocessing.steps',{'functional_slicetime'},...
'Setup.preprocessing.sliceorder', mysliceordervector,...
'parallel.N', numberofjobs);
Hope this helps
Alfonso
Originally posted by Andrew OShea:
Sorry about this, you are right that when selecting the "manually-defined" slice-order option in the GUI, CONN will wait until a later time (when it is ready to process each subject and it has the info on the number of slices per volume) to ask you about the specific slice-order vector, which is not going to work for distributed jobs since those are expected to be run on a non-interactive session. I have fixed that in the attached patch (this patch is for release 15g, simply copy the file to the conn distribution folder overwriting the file with the same name there). Let me know if you run into any issues.
Of course, another alternative as Pravesh suggested is to define the preprocessing info through batch scripts/commands. If doing so please use the newer batch.Setup.preprocessing field (instead of the older batch.New field) since the latter is not compatible with distributed processing. For example, to run the slice-timing correction step in parallel for all subjects on your current conn project, you may simply use the syntax:
conn_batch('Setup.preprocessing.steps',{'functional_slicetime'},...
'Setup.preprocessing.sliceorder', mysliceordervector,...
'parallel.N', numberofjobs);
Hope this helps
Alfonso
Originally posted by Andrew OShea:
Hello,
I need to manually define the slice order for slice timing correction, however, I would like to be able to enter the order prior to the process starting. We are using a cluster environment and I am not able to interact with the jobs in a graphical way after submission. Any suggestions?
-Andrew
I need to manually define the slice order for slice timing correction, however, I would like to be able to enter the order prior to the process starting. We are using a cluster environment and I am not able to interact with the jobs in a graphical way after submission. Any suggestions?
-Andrew
Threaded View
| Title | Author | Date |
|---|---|---|
| Andrew OShea | Dec 1, 2015 | |
| Alfonso Nieto-Castanon | Dec 1, 2015 | |
| Andrew OShea | Dec 2, 2015 | |
| Alfonso Nieto-Castanon | Dec 2, 2015 | |
| Alfonso Nieto-Castanon | Dec 3, 2015 | |
| Pravesh Parekh | Dec 1, 2015 | |