| T O P I C R E V I E W |
| carter |
Posted - Jan 04 2006 : 3:22:31 PM
I'm getting weirdness from bputil when trying to preprocess data, and I'm not sure why. It won't show me the instruction set (and apparently won't let me try to enter things anyway). Please see below.
Thanks!
Liz
1) Select Experiment
Name: CogDev.01
Location: /home/pelphrey/net/hodgkin/data/NDRC
2) Select Instruction Set
--- no instructions selected ---
3) Select exams to be processed
--- no exams selected ---
4) Update Exam Database for BIAC studies
5) Change configuration file (default)
6) Select processing script options
Debug Level: 1
Force (Overwrite existing files?): true
Save Analyze Headers?: true
Background Submitted Jobs?: false
12) Cleanup temporary directories
/data/users/pelphrey/bputil/20051130_45455_1133465804
/data/users/pelphrey/bputil/20051130_45456_1133470153
/data/users/pelphrey/bputil/20051215_45508_1134702667
13) Reset menu and clear profile
14) Submit 0 Processing Job(s)
15) Exit Menu
Enter option (1..15): 2
-- INFO Enter comma delimited set of numbers (e.g. 4,5,6) --
Select Instructions in Order of Execution [-1 to cancel]: 1,2,3,4,5
USER SELECTIONS: 1,2,3,4,5
-- INFO Enter comma delimited set of numbers (e.g. 4,5,6) --
Select Instructions in Order of Execution [-1 to cancel]: -1
user aborted instruction selection
|
| 15 L A T E S T R E P L I E S (Newest First) |
| jimmy.dias |
Posted - May 18 2006 : 3:24:30 PM
http://www.ee.surrey.ac.uk/Teaching/Unix/ should help. Tutorials One and Two should give you enough information to navigate to the file and list its contents.
You'll want to change to directory /data/users/tankersl/bputil/scripts and open up the script you last submitted (date and time is in the filename).
Jimmy |
| tankersley |
Posted - May 18 2006 : 3:18:47 PM
Jimmy:
I have only interacted with the interface you created for the newest version of bputil.
I have no idea how to do anything in UNIX. I'm willing to learn if you want to point me to a UNIX tutorial or explain how to open this script. ??
Sorry.
Dharol |
| jimmy.dias |
Posted - May 18 2006 : 3:15:14 PM
Hi Dharol,
Does the script you looked at to try and debug this issue contain the 'smooth' command?
Jimmy |
| tankersley |
Posted - May 18 2006 : 3:02:58 PM
I am continuing to have the same problem with bputil that I posted on back in February:
I will ask bputil to perform the following processes:
6. QA
1. Time correction
2. Motion correction
3. Normalization and coregistration
5. Smoothing.
bputil will run 6,1,2, and 3 and produce
QA files
arun files
rarun files
ncrarun files
But it FAILS TO PRODUCE sncrarun files.
Then I go back and ask bputil only to perform the smoothing, but it just produces files called 'srun'.
QUESTION 1: How come I'm not getting the sncrarun files?
QUESTION 2: Is there a way to go back and get bputil to smooth over processed files without rerunning all the steps again?
Any help is much appreciated!
Thanks.
Dharol |
| syam.gadde |
Posted - Mar 31 2006 : 11:25:37 AM
I don't know what your disk quota is exactly
(Francis or perhaps your PI would know).
But you can tell how much disk space the
experiment is using in Windows by right-clicking
on the experiment directory, and selecting
Properties. It will start counting and eventually
should show you the amount of disk space used.
I don't know that this is the issue, it's just
one thing to check. Another thing is to look
through the bputil logs in question (located in
/data/users/LOGIN/bputil/logs) to see if there
are any funny things in there. |
| tankersley |
Posted - Mar 31 2006 : 11:19:12 AM
Sam:
How can I tell if I'm over disk quota?
Dharol |
| syam.gadde |
Posted - Mar 31 2006 : 11:17:36 AM
I was wondering more about the disk quota on
ExecInfo.09. It looks like there should be
plenty of space in /data/users.
|
| tankersley |
Posted - Mar 31 2006 : 11:10:54 AM
I'm on \\Katz\Data\ExecInfo.09
I ran rm -fr /data/users/tankersl/bputil/jobs/exam
on almost every single one of my subjects last night.
The output from fmriqa_biac is an empty index.html file, but it produces about half of the .png files that also go into the QA folder. |
| syam.gadde |
Posted - Mar 31 2006 : 11:06:17 AM
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? |
| tankersley |
Posted - Mar 31 2006 : 10:49:18 AM
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
|
| tankersley |
Posted - Feb 22 2006 : 12:43:16 PM
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
|
| syam.gadde |
Posted - Feb 03 2006 : 3:18:47 PM
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. |
| syam.gadde |
Posted - Feb 03 2006 : 3:03:08 PM
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.
|
| jcarter |
Posted - Feb 03 2006 : 2:29:24 PM
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?
|
| tankersley |
Posted - Feb 01 2006 : 3:27:03 PM
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 |
