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syam.gadde
BIAC Staff
USA
421 Posts |
 Posted - Jan 20 2006 : 12:12:34 PM
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As mentioned previously, correct capitalization of the experiment name is required. Use ExecInfo.09:
fmriqa_biac ExecInfo.09 Func 20051103_31180 |
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petty
BIAC Staff
USA
453 Posts |
Posted - Jan 20 2006 : 12:19:51 PM
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| its case sensitive, so you need to type your experiment exactly the same as it appears in the storage server |
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marion
BIAC Alum
19 Posts |
Posted - Jan 20 2006 : 12:51:19 PM
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The program in general is working ok for me now, but there is no menu option to select a confirguration file. I need to use the BIRN.20 configuration file for my analysis, is tehre any way to get it to do this without using the menu option?
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price
BIAC Alum
USA
8 Posts |
Posted - Jan 23 2006 : 5:49:58 PM
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I'm assuming the jobs are automatically submitted to background?
Earlier when I said it was working for me, I lied--it didn't do smoothing. This time around it only got through time-slice correciton. Just making sure it goes to background--otherwise that miiight explain my problems... |
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tankersley
BIAC Alum
USA
143 Posts |
Posted - Jan 24 2006 : 2:39:23 PM
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When running bputil, I enter exam # 0051212_31252 for experiment execinfo.09.
The menu lists all five of my runs, but will not allow me to select runs #1 and #3. All the files look like they're in the folder for this run, so I don't understand why I cannot select them.
Dharol |
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jimmy.dias
BIAC Alum
USA
210 Posts |
Posted - Jan 24 2006 : 3:03:28 PM
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The error that you glanced over was 'ERROR! multiple BXH files found in <directory>'.
List the contents of the relevant directory using ls.
ls ~/net/katz/data/ExecInfo.09/Data/Func/20051212_31252/run005_03/
This will reveal multiple BXH files. Remove the extra BXH file (V.bxh) and re-run bputil.
Jimmy
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tankersley
BIAC Alum
USA
143 Posts |
Posted - Feb 01 2006 : 12:36:45 PM
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I'm getting the following error message from bputil on subject #31385:
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/ExecInfo.09/Data/Func/20060130_3...','/data/users/tankersl/bputil/jobs/31385_Exam_20060201_115135') called at /usr/local/bin/bputil line 713
main::opt8_callback('Opt8','HASH(0x2072c9a4)','HASH(0x20731048)') called at /usr/local/bin/bputil line 132
ERROR! checksums for V0230.img and /data/users/tankersl/bputil/jobs/31385_Exam_20060201_115135/run005_05/V0230.img do not match
NOT OK
ERROR! Could not copy Functionals to Job Directory!!
*************************
What should I do?
Dharol
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petty
BIAC Staff
USA
453 Posts |
Posted - Feb 01 2006 : 3:22:11 PM
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| try cleaning up your directory, you could be over the limit. |
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tankersley
BIAC Alum
USA
143 Posts |
Posted - Feb 01 2006 : 3:27:03 PM
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How do I clean up my directory? The new version of bputil doesn't have the "clean directory" option that the old one had.
Or do you mean I need to clean up files within my experiment folder on Katz?
In the latter case, which files should i be deleting?
The other concern i have is that bputil will process other exam numbers, just not 31385 or 31387.???????????????
THanks.
Dharol |
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jcarter
BIAC
USA
5 Posts |
Posted - Feb 03 2006 : 2:29:24 PM
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Can someone please help with the following. I submitted a job in BPUtil to process 9 functional runs. When the batch script was finished only the first 6 runs had been analysed and the following message was displayed in Golgi
Sizes of frags (278528) and dimensions (31752192) don't match!
Creating raw datarec failed.
Sizes of frags (278528) and dimensions (31752192) don't match!
Creating raw datarec failed.
Error preparing data read for '/home/jcarter/net/hodgkin/data/UNCConte/Conte.05/Data/Func/20060202_31405/run005_07/run005_07.bxh'.
Error running bxh_brainmask
NOT OK
After cleaning up my job directory with what I believe to be the correct command to do so (rm -fr /data/users/jcarter/bputil/jobs/*)
I tried to process the final 3 runs but was still unsuccessful.
Any suggestions?
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Feb 03 2006 : 3:03:08 PM
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James, are any of those problematic directories missing image files? Or does the .bxh file point to fewer image files than the dimensions would suggest need to be there? That would cause the errors you're seeing.
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Feb 03 2006 : 3:18:47 PM
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| Just to close out on James' issue -- the .bxh file was indeed incomplete so I referred him to Jimmy to get the .bxh file regenerated for that run. |
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tankersley
BIAC Alum
USA
143 Posts |
Posted - Feb 22 2006 : 12:43:16 PM
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Has anyone else encountered the following problem:
When running an exam number through bputil, bputil only performs some of the instructions selected? I selected
2) Instruction Set Selected.
BIAC QA
SPM99 Time Slice Correction
SPM99 Motion Correction
SPM99 Coreg and Normalize
SPM99 Smoothing
But for output in my FUNC folder for the exam number, I only get arun files and rarun files.
Dharol
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tankersley
BIAC Alum
USA
143 Posts |
Posted - Mar 31 2006 : 10:49:18 AM
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I'm still having the same problem I reported on the last post, made February 22. When I run bputil, sometimes it will go through all the processing steps I select, and sometimes it won't. For example, some times it will create arun and rarun files, but not do the normalizing and coregistration for the ANATs or the FUNCs.
A second problem is that sometimes bputil will not create the html document of the QA (or rather, it creates an empty document). This will happen sometimes even if bputil does run all the processing steps I select and has created all the corresponding files.
Third, I've tried to run fmriqa_biac ExecInfo.09 Func Examnumber, and this produced an empty document for me, too.
Any advice?
Thanks. Dharol
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Mar 31 2006 : 11:06:17 AM
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quote:
Originally posted by tankersley
Third, I've tried to run fmriqa_biac ExecInfo.09 Func Examnumber, and this produced an empty document for me, too.
I have run fmriqa_biac on an exam from QA.04 (residing on
katz), and it seemed to run successfully, with a non-empty
index.html file. What experiment directory are you using?
Is it possible that you are running into your disk quota?
What is the output from frmiqa_biac? |
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Topic |
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bputil instructions
