Re: [Freesurfer] [Tracula] error running trac-all –path –c Configuration_file.txt
From: Francesco Siciliano Sent: Monday, August 19, 2013 12:54 PM To: Francesco Siciliano Subject: RE: [Tracula] error running trac-all –path –c Configuration_file.txt I also noticed that even on those that appeared to finish, there was no dpath folder. Any help would be greatly appreciated! Francesco Siciliano, B.A. Research Assistant Department of Child and Adolescent Psychiatry The New York State Psychiatric Institute Columbia University 1051 Riverside Drive, Unit 74 New York, NY 10032 (212) 543-6155 From: Francesco Siciliano Sent: Monday, August 19, 2013 12:13 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Tracula] error running trac-all –path –c Configuration_file.txt Hello, I received an error on several terminals running trac-all –path –c Configuration_file.txt 55 slices processed 56 slices processed 56 slices processed 57 slices processed 57 slices processed 58 slices processed 59 slices processed 60 slices processed 61 slices processed Queuing post processing stage 70 slices processed For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. /Users/jonathanposner/Desktop/MRI_Software/FSL_installer/fsl/bin/bedpostx: line 262: kill: (15849) - No such process Is this an indication that the processing did not finish? Could this have anything to do with limited computer memory? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] [Tracula] error running trac-all –path –c Configuration_file.txt
Hi Francesco - There's a list of bedpostx output files here: http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/fdt/fdt_bedpostx.html The best way to determine if bedpostx finished running properly is to check if those files were created in the dmri.bedpostX directory. a.y On Mon, 19 Aug 2013, Francesco Siciliano wrote: Hello, I received an error on several terminals running trac-all –path –c Configuration_file.txt 55 slices processed 56 slices processed 56 slices processed 57 slices processed 57 slices processed 58 slices processed 59 slices processed 60 slices processed 61 slices processed Queuing post processing stage 70 slices processed For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. /Users/jonathanposner/Desktop/MRI_Software/FSL_installer/fsl/bin/bedpostx: line 262: kill: (15849) - No such process Is this an indication that the processing did not finish? Could this have anything to do with limited computer memory? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] [Tracula] error running trac-all –path –c Configuration_file.txt
Hi Francesco - The bedpostx files are created when you run trac-all -bedp. Then you need to run trac-all -path to reconstruct the paths under dpath/... as the final step. Did you run this? a.y On Mon, 19 Aug 2013, Francesco Siciliano wrote: Thank you! Is it normal, however, not to have a dpath folder with summary statistics? I have all of the bedpostx output files, however, I seem to be missing the dpath folder as well as a script confirming that -path was completed. Thanks, Francesco From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] Sent: Monday, August 19, 2013 1:56 PM To: Francesco Siciliano Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [Tracula] error running trac-all –path –c Configuration_file.txt Hi Francesco - There's a list of bedpostx output files here: http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/fdt/fdt_bedpostx.html The best way to determine if bedpostx finished running properly is to check if those files were created in the dmri.bedpostX directory. a.y On Mon, 19 Aug 2013, Francesco Siciliano wrote: Hello, I received an error on several terminals running trac-all –path –c Configuration_file.txt 55 slices processed 56 slices processed 56 slices processed 57 slices processed 57 slices processed 58 slices processed 59 slices processed 60 slices processed 61 slices processed Queuing post processing stage 70 slices processed For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. /Users/jonathanposner/Desktop/MRI_Software/FSL_installer/fsl/bin/bedpostx: line 262: kill: (15849) - No such process Is this an indication that the processing did not finish? Could this have anything to do with limited computer memory? The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
