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carter
BIAC Alum
USA
20 Posts |
 Posted - Jan 04 2006 : 3:22:31 PM
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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
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jamie.morris
BIAC Alum
59 Posts |
Posted - Jan 08 2006 : 10:01:58 AM
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| I am having the same problem. |
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jimmy.dias
BIAC Alum
USA
210 Posts |
Posted - Jan 09 2006 : 12:09:49 AM
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Hey all,
Hmmm. So the Itanium that holds the database table from which the instruction list came from is currently unavailable. I'm working with Redhat on getting the box back up and running. In the meanwhile, I'll try and hardcode the instruction set into bputil. I'll post here as its done and ready to accept job submissions.
Cheers,
Jimmy |
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carter
BIAC Alum
USA
20 Posts |
Posted - Jan 11 2006 : 3:18:33 PM
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Is there a way I can do the exact same preprocessing without bputil to avoid this issue for the time being? I need the last few subjects' worth of data for a grant application by the beginning of next week.
Thanks!
-Liz |
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jimmy.dias
BIAC Alum
USA
210 Posts |
Posted - Jan 11 2006 : 4:12:59 PM
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Hey Liz,
Would you email me offline Exam Number and Experiment ID and what Instruction Set you'd like to have done? I am testing bputil on Golgi (works on my machine) and would like a dataset to test everything out on.
Cheers,
Jimmy |
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jimmy.dias
BIAC Alum
USA
210 Posts |
Posted - Jan 11 2006 : 8:37:24 PM
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Hey all,
A preliminary version of bputil on Golgi is ready for those of you anxious to get processing. I have a couple more features to add back but for now, you can use bputil if
- you are happy with the default processing options for SPM99
- you know your exam number in advance (you can always look it up on the schedule)
- you have not changed the name of your BXH file from the default runXXX_XX.bxh or seriesXXX.bxh to something else
As soon as I'm done with the rest of the updates, I'll post follow ups listing all the updates/changes I've made.
Cheers,
Jimmy |
Edited by - jimmy.dias on Jan 11 2006 8:39:10 PM |
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tankersley
BIAC Alum
USA
143 Posts |
Posted - Jan 13 2006 : 5:19:15 PM
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I still can't get bputil to run. It let's me enter the experiment, instructions, exam #, functionals and anatomicals, but then when I go to submit the job it does nothing.
DHarol |
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marion
BIAC Alum
19 Posts |
Posted - Jan 17 2006 : 10:43:11 AM
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I'm having problems selecting an instruction set: I select QA from thelist, but in the main menu it doesn't actually list it, looks like this:
1) Experiment Name Selected.
Experiment Name => BIRN.20
Experiment Location => /home/marion/net/nernst/data1
2) Instruction Set Selected.
3) Exam Number Selected. 45537.
4) Functional Runs Selected.
etc.
And then when I try to submit the job, it says:
ERROR! invalid instruction
Everything else seems to be working correctly for me.
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tankersley
BIAC Alum
USA
143 Posts |
Posted - Jan 17 2006 : 10:43:50 AM
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So bputil seems to be working now but it's not very communicative about what it's doing.
1. Can you enter more than one exam at a time (e.g., enter subject 8888888 and 7777777 when it asks for exam #), or will this confuse it?
2. Once you've submitted the job, you get this prompt for the next command. I think this means the job is processing. Can you enter another job in this same window, or do you need to wait until you get a signal that the job has finsihed processing?
Dharol |
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marion
BIAC Alum
19 Posts |
Posted - Jan 17 2006 : 12:04:10 PM
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| I've tried some other stuff, it looks liek all the instruction sets other than BIAC QA are working, however it then says that there is 'not enough space in the file system' and the functional/anatomical data cannot be copied, and crashes. |
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price
BIAC Alum
USA
8 Posts |
Posted - Jan 17 2006 : 1:10:46 PM
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| Hrm, I also just started a job, and it has already successfully done the BIAC QA and the motion correction and has yet to crash. I wonder what makes the difference? |
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jamie.morris
BIAC Alum
59 Posts |
Posted - Jan 18 2006 : 10:03:06 AM
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I'm getting this....
1) Experiment Name Selected.
Experiment Name => Facemask.02
Experiment Location => /home/morris/net/goldman/data/BIAC
2) Instruction Set Selected.
SPM99 Time Slice Correction
SPM99 Motion Correction
SPM99 Coreg and Normalize
BIAC QA
3) Exam Number Selected. 20051007_45321.
4) Functional Runs Selected.
Func/20051007_45321/run004_02
Func/20051007_45321/run004_03
Func/20051007_45321/run004_04
Func/20051007_45321/run004_05
Func/20051007_45321/run004_06
Func/20051007_45321/run004_07
Func/20051007_45321/run004_08
5) Anatomical Series Selected.
Anat/20051007_45321/series002
6) Submit Processing Jobs.
7) Exit.
Enter option (1..7): 6
ERROR!! The following must be addressed before continuing
Functional Runs to process not selected
Anatomical Series not selected
Job Submitted
Why the error? It seems to have the info it is asking for. |
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diaz
BIAC Alum
USA
212 Posts |
Posted - Jan 20 2006 : 09:41:52 AM
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If you are just interested in doing QA, you can use fmriqa_biac. Here are the instructions:
[diaz@golgi: ~] $ fmriqa_biac
Usage: /usr/local/bin/fmriqa_biac <expName> <dataSubDir> <study>
Example: /usr/local/bin/fmriqa_biac Study.01 Func 20010101_12345
fmriqa_biac reads BXH files in the given study and creates an HTML
page that displays QA data.
In the example, it will look for the following BXH files:
Study.01/Data/Func/20010101_12345/run*/run???_??.bxh
and the output will go in the following experiment directory:
Study.01/Data/Func/20010101_12345/QA
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Michele T. Diaz, Ph.D.
Associate Director
Brain Imaging and Analysis Center |
Edited by - diaz on Jan 20 2006 09:43:55 AM |
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tankersley
BIAC Alum
USA
143 Posts |
Posted - Jan 20 2006 : 11:30:14 AM
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Questions about using fmriqa_biac on BPUTIL:
1. what do we put in for the first part of the command
/usr/loca/bin
2. For each folder we list to direct it to the appropriate subject folder, do we just separate each one with a space? For example
/usr/local/bin/fmriqa_biac execinfo.09 Data Func 20051103_5555555
thanks.
Dharol |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Jan 20 2006 : 11:42:09 AM
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Dharol, either the full pathname to the program /usr/local/bin/fmriqa_biac or just fmriqa_biac will work on golgi.
The three arguments after the program name are experiment name, type of data (in our case always Func), and the exam directory name. You do not have to specify any other components of the directory. So in your example, you should use:fmriqa_biac ExecInfo.09 Func 20051103_5555555 I believe correct capitalization of the experiment name is required. |
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tankersley
BIAC Alum
USA
143 Posts |
Posted - Jan 20 2006 : 11:51:18 AM
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Here's what happens:
[tankersl@golgi: ~] $ /usr/local/bin/fmriqa_biac execinfo.09 Func 20051103_31180
Use of uninitialized value in join or string at /usr/opt/perl5/lib/5.8.0/aix-thread-multi/File/Spec/Unix.pm line 82.
Experiment directory /execinfo.09 doesn't exist? at /usr/local/bin/fmriqa_biac line 95.
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bputil instructions
