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vinod
Average Member
USA
68 Posts |
 Posted - Jun 11 2007 : 09:32:38 AM
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Yes. It looks like it creates a whole bunch of prefiltered_func* files for MC, ST and so on. Because of a specification in the script, these files get deleted once all preprocessing steps are complete and filtered_func_data.nii.gz file is created. However, if the program crashed, I suspect some of these files should still be found in the directory and we can use the last completed step to restart analysis. So, for example, if Goldman crashed when it was running slice timing for a subject, we should see a file that is named prefiltered_func_data_mcf.nii.gz which can be input to the slice timer step again. And we can run all steps below that in the report.log file at the command line or a bash script.
Petty, given that you can pull out lines from log file and run it on command line, would it be better to script FSL using a template report.log instead of the currently popular way of doing so from template.fsf files? In other words, we save a report.log file as an executable bash script? And then use "sed" to replace subject names and directories? This way, we might even be able to choose which steps we wants to rerun if analysis crashes? I may be missing something.. |
Vinod Venkatraman
IPCN Graduate Student
Huettel Lab
"UNIX is basically a simple operating system, but you have to be a genius to understand the simplicity." - Dennis Ritchie |
Edited by - vinod on Jun 11 2007 09:33:37 AM |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Jun 11 2007 : 09:54:13 AM
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| The command-line programs in the report.log file are designed to do the particular analysis and pre-processing you have specified in the .fsf file. It would be much more difficult for anyone to create a template report.log file that is generic enough to accommodate what anyone might want to do. I think from the perspective of creating something that nearly anyone can use, I think the template .fsf file is the right approach (it is also much more compact and easier to read!) But if you already have a successful run using your particular design choices, I agree with Dharol and Chris that you would probably be able to use portions of the report.log file to restart another (failed) analysis (but I haven't tried this myself). |
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Dichter
BIAC Faculty
190 Posts |
Posted - Aug 22 2007 : 09:40:17 AM
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A number of us continue to run into this FILM memory error, and it seems to be specific to certain runs only (ie, I get the error repeatedly for a particular run, but not other runs). This is the only job on my machine, and I am running post-stats only, so I doubt this is a truly a memory issue. 3 column format files are fine as well.
The full error is:
An exception has been thrown
Logic error:- detected by Newmat: index error: requested index = 1
MatrixType = Rect # Rows = 0; # Cols = 1
Trace: Histogram::generate; AutoCorrEstimator::spatiallySmooth.
Error: FILM did not complete - it probably ran out of memory.
Thanks for any help,
-Gabriel |
Gabriel S. Dichter, PhD
UNC Departments of Psychiatry & Psychology
http://www.can.unc.edu/ |
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vinod
Average Member
USA
68 Posts |
Posted - Aug 22 2007 : 1:00:50 PM
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I am quite sure it has to do something with your design matrix. It is mostly the case that FSL does not like something about the ordering of events in these particular cases or something. Look at the design_cov.gif files from the output feat folders for these runs, especially the effect required values below and make sure they are not very large numbers. And also make sure that the only white elements are along the disagonal and every other square is black.
The request index = 1 seems to suggest that it not able to find something related to the first element of an array. So, it could just be some empty three-column files or something wrong about the filenames for the inputs or something. |
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FSL memory problems?
