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tonev
Junior Member
USA
26 Posts |
 Posted - Jul 22 2004 : 11:03:54 AM
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In attempting to run a number of exams through the Golgi utility, I've had a problem that (I think) is similar to the one Michele brought up. Specifically, for some subjects, the process will successfully complete all steps, whereas for others, it will stop in the middle. For instance, here is an excerpt of an error log for 2 subjects I recently ran through the utility. For the first, everything went well, and I managed to TRAlign, Motion Correct, and get QAstats. For the second subject, there was a problem in the middle of the TRAlign step that caused further problems down the processing line. Note that these 2 subjects were run in the same bputil batch.
Subject 1:
SPM: spm_slice_timing (v2.6) 09:59:09 - 22/07/2004
========================================================================
Your TR is 2.5
Warning: Terminal mode only supports Renderer of Painters..
> In /usr/local/MATLAB/spm99/spm_progress_bar.m at line 89
In /usr/local/MATLAB/spm99/spm_progress_bar.m at line 37
In /usr/local/MATLAB/spm_preprocess/spm_slice_timing.m at line 217
In /usr/local/MATLAB/spm_preprocess/sincalign_spm.m at line 155
SPM: spm_slice_timing (v2.6) 09:59:54 - 22/07/2004
========================================================================
Your TR is 2.5
SPM: spm_slice_timing (v2.6) 10:00:35 - 22/07/2004
========================================================================
Your TR is 2.5
SPM: spm_slice_timing (v2.6) 10:01:19 - 22/07/2004
========================================================================
Your TR is 2.5
SPM: spm_slice_timing (v2.6) 10:02:03 - 22/07/2004
========================================================================
Your TR is 2.5
Subject 2:
SPM: spm_slice_timing (v2.6) 09:59:08 - 22/07/2004
========================================================================
Your TR is 2.5
Warning: Terminal mode only supports Renderer of Painters..
> In /usr/local/MATLAB/spm99/spm_progress_bar.m at line 89
In /usr/local/MATLAB/spm99/spm_progress_bar.m at line 37
In /usr/local/MATLAB/spm_preprocess/spm_slice_timing.m at line 217
In /usr/local/MATLAB/spm_preprocess/sincalign_spm.m at line 155
SPM: spm_slice_timing (v2.6) 09:59:55 - 22/07/2004
========================================================================
Your TR is 2.5
SPM: spm_slice_timing (v2.6) 10:00:37 - 22/07/2004
========================================================================
Your TR is 2.5
Warning: File not found or permission denied.
> In /usr/local/matlab6p5/toolbox/matlab/general/@char/delete.m at line 35
In /usr/local/MATLAB/BIAC/mr/readbxhhdr.m at line 52
In /usr/local/MATLAB/BIAC/mr/readmr.m at line 639
In /usr/local/MATLAB/spm_preprocess/sincalign_spm.m at line 105
??? Error using ==> sincalign_spm
error reading BXH header
So, somewhere in the middle of processing the 4th run, it was unable to find a certain set of files, and I didn't get any TRAligned (or Motion-Corrected) images for runs 4 or 5 for Subject 2. In contrast, I got all of my expected data for Subject 1.
Any help would be appreciated. |
Simon T. Tonev, Ph.D.
Department of Psychiatry and Behavioral Sciences
Duke University Medical Center
Durham, NC |
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jimmy.dias
BIAC Alum
USA
210 Posts |
Posted - Jul 22 2004 : 11:33:30 AM
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Hi Simon,
The error you posted above seems to suggest that there might not be a BXH file (or it might not be readable) in some run directories for your second subject. Can you verify the presence of those files? You could also try using one of the bputil options to help regenerate those headers so long as the directory structure is standard and there is a pfile header (*.pfh) in the directory.
Jimmy |
Edited by - jimmy.dias on Jul 22 2004 11:34:29 AM |
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diaz
BIAC Alum
USA
212 Posts |
Posted - Jul 22 2004 : 12:02:22 PM
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The problem that I was having was related to a matlab startup.m file that I had on Golgi. It was changing directories which made the scripts unable to find the files.
So you might try editing out lines like that (e.g., chexp mask.05), if you have a startup.m file, that is.
Michele |
Michele T. Diaz, Ph.D.
Associate Director
Brain Imaging and Analysis Center |
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tonev
Junior Member
USA
26 Posts |
Posted - Jul 22 2004 : 4:30:48 PM
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| I tried recreating the bxh files, though they had only been created from the p-file headers yesterday. When I use the bxh files to read in the images using readmr, I don't get any errors. I still have the same problem, though: some exams finishing, others ending part-way through and still others not starting. I find that it works better it if I limit it to processing 3 or 4 exams at a time, but that's still not a guarantee. Also, I find that if I re-run the analysis, it usually works on the second or third try. |
Simon T. Tonev, Ph.D.
Department of Psychiatry and Behavioral Sciences
Duke University Medical Center
Durham, NC |
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Golgi Problem
