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Dichter
BIAC Faculty
190 Posts |
 Posted - Oct 04 2006 : 11:43:24 AM
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Preprocessing doesn't seem to be working right now. The log file contains a lot of errors like the following:
Can't locate loadable object for module XML::Parser::Expat in @INC (@INC contains: /usr/opt/perl5/lib/5.8.0/aix-thread-multi /usr/opt/perl5/lib/5.8.0 /usr/opt/perl5/lib/site_perl/5.8.0/aix-thread-multi /usr/opt/perl5/lib/site_perl/5.8.0 /usr/opt/perl5/lib/site_perl .) at /usr/opt/perl5/lib/site_perl/5.8.0/aix-thread-multi/XML/Parser.pm line 14
Compilation failed in require at /usr/opt/perl5/lib/site_perl/5.8.0/aix-thread-multi/XML/Parser.pm line 14.
BEGIN failed--compilation aborted at /usr/opt/perl5/lib/site_perl/5.8.0/aix-thread-multi/XML/Parser.pm line 18.
...ect. |
Gabriel S. Dichter, PhD
UNC Departments of Psychiatry & Psychology
http://www.can.unc.edu/ |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Oct 04 2006 : 12:17:54 PM
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| Oops. I think this was my fault. I think I accidentally deleted some files while installing something else completely unrelated. I will work with Jimmy to fix this and will post here when fixed. |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Oct 04 2006 : 12:36:30 PM
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| I think I have fixed the modules that bputil requires. Can you try again and report back whether this resolves this issue? Sorry for the inconvenience. |
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Dichter
BIAC Faculty
190 Posts |
Posted - Feb 09 2007 : 2:09:32 PM
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When I try to run QA, I get the following error:
Didn't find executable 3dFWHMx!
Warning: cannot find program 3dFWHMx, so will not generate smoothness data
Error running /usr/local/bin/fmriqa_mean
NOT OK
But it looks like QA is proceeding after that.
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Gabriel S. Dichter, PhD
UNC Departments of Psychiatry & Psychology
http://www.can.unc.edu/ |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Feb 09 2007 : 2:18:06 PM
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The warning is harmless. It is due to extra functionality (that we are not currently taking advantage of, because the latest version of AFNI is not installed).
However, the error (which is independent of this warning) is maybe something to be concerned about. "NOT OK" is probably something bputil generates -- is the QA really continuing from that point? (or is preprocessing continuing) |
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Dichter
BIAC Faculty
190 Posts |
Posted - Feb 09 2007 : 2:26:04 PM
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| Sorry - QA looked like it was continuing, but actually crashed a few moments later. So no. |
Gabriel S. Dichter, PhD
UNC Departments of Psychiatry & Psychology
http://www.can.unc.edu/ |
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cascio
Starting Member
6 Posts |
Posted - Mar 02 2007 : 2:06:46 PM
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Hi,
I'm running bputil on a recent scan, and am getting this error:
junk after document element at line 124, column 1, byte 4035:
</history>
</bxh>
fScan version 1.36.7
^
Quit with status 0
at /usr/opt/perl5/lib/site_perl/5.8.0/aix-thread-multi/XML/Parser.pm line 187 NOT OK
Can anyone tell me what that is?
Thanks,
Carissa
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Mar 02 2007 : 4:00:50 PM
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Looks like your input .bxh files have junk at the end of them?
Not sure where that is coming from. |
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cascio
Starting Member
6 Posts |
Posted - Mar 04 2007 : 08:04:17 AM
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Hi Syam,
I went into the bxh file and manually deleted the junk at the end, tried to re-run bputil, and got this error:
Sizes of frags (278528) and dimensions (33423360) don't match!
Creating raw datarec failed.
Error running /usr/local/bin/fmriqa_mean
NOT OK
Can you help?
Thanks! |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Mar 05 2007 : 10:02:54 AM
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| I took a look at your input files. They seem to be pointing to only one volume, but describe a 4-D time series. Did you process these files after getting them from the scanner, and before sending them to bputil, or are they as you received them? (they show evidence of being written by fscan, but I don't know if that was due to the pipeline or if it was executed manually) |
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cascio
Starting Member
6 Posts |
Posted - Mar 06 2007 : 08:21:06 AM
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| The files weren't processed before sending to bputil, but while we were at the scanner during the acquisition, we tried to use fscan to look at motion artifact in the first run. |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Mar 06 2007 : 09:37:23 AM
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quote:
Originally posted by cascio
The files weren't processed before sending to bputil, but while we were at the scanner during the acquisition, we tried to use fscan to look at motion artifact in the first run.
In that case I suggest renaming the old .bxh file, and regenerating the .bxh file from the Pfile and .img files using pfile2bxh on golgi:
cd /my/data/dir/exam/series
mv run003_01.bxh run003_01.bxh_old
pfile2bxh run003_01.pfh V*.img run003_01.bxh
Alternatively you could also copy the .bxh file from another run if the spatial dimensions and number of time points are the same, but regenerating the .bxh file is better. |
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dvsmith
Advanced Member
USA
218 Posts |
Posted - May 12 2007 : 11:57:59 AM
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Hi,
I'm getting the following error when I run the BIAC QA with bputil:
Empty compile time value given to use lib at /usr/local/bin/fmriqa_generate.pl line 13
Can't locate fmriqa_utils.pm in @INC (@INC contains: /usr/opt/perl5/lib/5.8.0/aix-thread-multi /usr/opt/perl5/lib/5.8.0 /usr/opt/perl5/lib/site_perl/5.8.0/aix-thread-multi /usr/opt/perl5/lib/site_perl/5.8.0 /usr/opt/perl5/lib/site_perl .) at /usr/local/bin/fmriqa_generate.pl line 25.
BEGIN failed--compilation aborted at /usr/local/bin/fmriqa_generate.pl line 25.
NOT OK
copying Functionals (run005_02) to job directory...pwd: There is an input or output error.
Use of uninitialized value in chdir at /usr/opt/perl5/lib/5.8.0/File/Find.pm line 716, <STDIN> line 12.
Use of chdir('') or chdir(undef) as chdir() is deprecated at /usr/opt/perl5/lib/5.8.0/File/Find.pm line 716, <STDIN> line 12.
Any ideas about what's causing this? There does not seems to be any obvious problems like missing files or anything like that...
Thanks!
David |
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clithero
Junior Member
37 Posts |
Posted - Dec 13 2007 : 09:26:05 AM
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Hi,
I followed cifslogin for both goldman and huxley, but am getting the following error for bputil:
[clithero@golgi: ~] $ bputil
$VAR1 = '/home/clithero/net/huxley/data';
warn! ExperimentFileName does not exist
warn! InactiveFileName does not exist
warn! ExperimentUsers does not exist
ERROR! The following configuration file errors must be addressed:
Doesn't look like //Huxley/Data is mounted
What have I missed?
Thanks,
John |
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jimmy.dias
BIAC Alum
USA
210 Posts |
Posted - Dec 13 2007 : 11:05:08 AM
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Hi John,
We are no longer support direct NFS mounts from Golgi to the Netapp boxes so everyone's symbolic links will have to be fixed. Please see this topic for instructions on how to do so.
http://www.biac.duke.edu/forums/topic.asp?TOPIC_ID=1113
Jimmy |
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Topic |
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BPUTIL Problems?
