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Oct 18, 2012  01:10 PM | Kangjoo Lee
PIPE_history.txt
Hello,

I downloaded niak-0.6.4.1 with psom-0.8.8 equipped in its extensions folder.
I just tried to run 'niak_template_frmi_preprocess.m' using demo dataset but an error occurs, indicating that there's no PIPE_history.txt file.

At line 97 in (1) 'niak_template_frmi_preprocess.m', it goes to (2) 'niak_pipeline_preprocess.m'

At line 570 in (2), it goes to (3) 'psom_run_pipeline.m'.

In the guideline of (3), which starts from line 119, 'PIPE_history.txt' is generated as an output of (3).

When I look at (3), there is (4) 'psom_pipeline_init.m' in line 324, (5) 'psom_pipeline_process.m' in line 351 and (6) 'psom_pipeline_visu.m' in line 364.

----> By running (4), a directory 'fmri_preprocess' is generated and log files are also generated in this folder as following; PIPE.mat, PIPE_jobs.mat, PIPE_jobs_backup.mat, PIPE_logs.mat, PIPE_logs_backup.mat, PIPE_status.mat, and PIPE_status_backup.mat.

----> By running (5), a directory 'tmp' is generated and other files are also generated as following; PIPE.lock, PIPE_manager_opt.mat, and pipeline_manager.sh in tmp.

----> 'PIPE_history.txt' should be generated between (4) and (6)

----> The error occurs in (6) when it tries to check whether 'PIPE_history.txt' exists or not at line 213. 



How can I solve this problem?

Thank you in advance.

Kangjoo
Oct 18, 2012  01:10 PM | Pierre Bellec
RE: PIPE_history.txt
Dear Kangjoo,

As indicated in the documentation, NIAK_DEMO_FMRI_PREPROCESS can be used to run a preprocessing pipeline on a small example dataset (which have to be downloaded independently, see the wiki). The file NIAK_TEMPLATE_FMRI_PREPROCESS is not meant to run. It's meant as a starting point to write a new script for running the fMRI preprocessing pipeline.

I hope this helps,

Pierre
Oct 18, 2012  03:10 PM | Kangjoo Lee
RE: PIPE_history.txt
Dear Pierre

Thank you for your response. Unfortunately, the same error occurs when I run NIAK_DEMO_FMRI_PREPROCESS.

In the line 193 of NIAC_DEMO_FMRI_PREPROCESS, it goes to NIAK_PIPELINE_FMRI_PREPROCESS.

In the line 570 of NIAK_PIPELINE_FMRI_PREPROCESS, it goes to PSOM_RUN_PIPELINE.

and I see the exactly same error messeage that PIPE_HISTORY.TXT does not exist.
=====================================================
I could not find any log file. This pipeline has not been started (yet?). Press CTRL-C to cancel.
??? Operation terminated by user during ==>
psom_pipeline_visu at 213

In ==> psom_run_pipeline at 364
                psom_pipeline_visu(path_logs,'monitor');

In ==> niak_pipeline_fmri_preprocess at 570
    psom_run_pipeline(pipeline,opt.psom);

In ==> niak_demo_fmri_preprocess at 193
[pipeline,opt] =
niak_pipeline_fmri_preprocess(files_in,opt);
==================================================

Did I miss something?

Thank you so much.

Kangjoo
Nov 9, 2012  11:11 PM | Kangjoo Lee
RE: PIPE_history.txt
Actually, this seems like a matter of configuration.
when I changed some options in psom_gb_vars.m, this problem has been solved.