general-discussion > perl in t1_preprocessing
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Oct 6, 2014  05:10 PM | Kangjoo Lee
perl in t1_preprocessing
Hi, 
I'm trying niak-boss-0.12.15 on Guillimin, (/sb/project/gsf-624-aa/quarantaine/niak-boss-0.12.15) for fMRI preprocessing.
I only copied niak-boss-0.12.15 directory to mine (to change psom options), while I'm using all the other packages such as minc and gnuplot located in /sb/project/gsf-624-aa/quarantaine/.
In t1-preprocess, after masking the brain, I have this error:

******************************************
Linear coregistration to stereotaxic space
******************************************
Running BESTLINREG with the following command:
/sb/project/ixx-903-aa/kangjoo/Matlab_code/niak-boss-0.12.15/commands/t1_processing/niak_bestlinreg.pl -clobber -source_mask /tmp/niak_tmp_t1_preprocess_subject1_506036198_babtain_fawzi_20090714_095643_7_mrit1_preprocess/babtain_fawzi_20090714_095643_7_mri_mask_native.mnc -target_mask /sb/project/ixx-903-aa/kangjoo/Matlab_code/niak-boss-0.12.15/template/mni-models_icbm152-nl-2009-1.0/mni_icbm152_t1_tal_nlin_sym_09a_mask.mnc.gz /gs/scratch/kangjoo/Data/control/Danser_Control_24/controls_newprotocol_2/01_fmri_preprocess_con24_141006/anat/subject1/anat_subject1_nuc_nativet1.mnc /sb/project/ixx-903-aa/kangjoo/Matlab_code/niak-boss-0.12.15/template/mni-models_icbm152-nl-2009-1.0/mni_icbm152_t1_tal_nlin_sym_09a.mnc.gz /gs/scratch/kangjoo/Data/control/Danser_Control_24/controls_newprotocol_2/01_fmri_preprocess_con24_141006/anat/subject1/transf_subject1_nativet1_to_stereolin.xfm /tmp/niak_tmp_t1_preprocess_subject1_506036198_babtain_fawzi_20090714_095643_7_mrit1_preprocess/babtain_fawzi_20090714_095643_7_mri_raw_stereolin.mnc

sh: /sb/project/ixx-903-aa/kangjoo/Matlab_code/niak-boss-0.12.15/commands/t1_processing/niak_bestlinreg.pl: Permission denied
ans = 126
Done !

*****************************************
Non-uniformity correction on an MR volume
*****************************************
Running NU_CORRECT with the following command:
nu_correct -clobber -tmpdir /tmp/niak_tmp_t1_preprocess_subject1_898630958_gb_niak_omitted/ -distance 200 -mask /sb/project/ixx-903-aa/kangjoo/Matlab_code/niak-boss-0.12.15/template/mni-models_icbm152-nl-2009-1.0/mni_icbm152_t1_tal_nlin_sym_09a_mask_eroded5mm.mnc.gz /tmp/niak_tmp_t1_preprocess_subject1_506036198_babtain_fawzi_20090714_095643_7_mrit1_preprocess/babtain_fawzi_20090714_095643_7_mri_raw_stereolin.mnc /tmp/niak_tmp_t1_preprocess_subject1_898630958_gb_niak_omitted/vol_nu.mnc

Cannot read input file: /tmp/niak_tmp_t1_preprocess_subject1_506036198_babtain_fawzi_20090714_095643_7_mrit1_preprocess/babtain_fawzi_20090714_095643_7_mri_raw_stereolin.mnc
nu_correct: crashed while running nu_estimate_np_and_em (termination status=512)
ans = 2
mv: cannot stat '/tmp/niak_tmp_t1_preprocess_subject1_898630958_gb_niak_omitted/vol_nu.mnc': No such file or directory
*****************
Masking the brain
*****************
Reading T1 image /tmp/niak_tmp_t1_preprocess_subject1_506036198_babtain_fawzi_20090714_095643_7_mrit1_preprocess/babtain_fawzi_20090714_095643_7_mri_nu_stereolin.mnc ...
********************
Something went bad ... the job has FAILED !
The last error message occured was :
Couldn't find any file fitting the description /tmp/niak_tmp_t1_preprocess_subject1_506036198_babtain_fawzi_20090714_095643_7_mrit1_preprocess/babtain_fawzi_20090714_095643_7_mri_nu_stereolin.mnc
File /sb/project/ixx-903-aa/kangjoo/Matlab_code/niak-boss-0.12.15/commands/read_write/niak_read_vol.m at line 188
File /sb/project/ixx-903-aa/kangjoo/Matlab_code/niak-boss-0.12.15/bricks/t1_processing/niak_brick_mask_brain_t1.m at line 230
File /sb/project/ixx-903-aa/kangjoo/Matlab_code/niak-boss-0.12.15/bricks/t1_processing/niak_brick_t1_preprocess.m at line 497
File /sb/project/ixx-903-aa/kangjoo/Matlab_code/niak-boss-0.12.15/extensions/psom-1.0.2/psom_run_job.m at line 214
File /sb/project/ixx-903-aa/kangjoo/Matlab_code/niak-boss-0.12.15/extensions/psom-1.0.2/psom_run_job.m at line 128
File /sb/project/ixx-903-aa/kangjoo/Matlab_code/niak-boss-0.12.15/extensions/psom-1.0.2/psom_run_script.m at line 437
File /sb/project/ixx-903-aa/kangjoo/Matlab_code/niak-boss-0.12.15/extensions/psom-1.0.2/psom_run_script.m at line 323
File /sb/project/ixx-903-aa/kangjoo/Matlab_code/niak-boss-0.12.15/extensions/psom-1.0.2/psom_pipeline_process.m at line 591
File /sb/project/ixx-903-aa/kangjoo/Matlab_code/niak-boss-0.12.15/extensions/psom-1.0.2/psom_run_pipeline.m at line 417
File /sb/project/ixx-903-aa/kangjoo/Matlab_code/niak-boss-0.12.15/pipeline/niak_pipeline_fmri_preprocess.m at line 808
File /sb/project/ixx-903-aa/kangjoo/Matlab_code/niak-boss-0.12.15/template/niak_template_fmri_preprocess.m at line 279


So it seems like there's something I've done wrong with minc configuration?
In my home directory, my .bashrc file is set like below:


# .bashrc

# Source global definitions
if [ -f /etc/bashrc ]; then
. /etc/bashrc
fi
# User specific aliases and functions
alias qstat="showq | grep kangjoo"
export PATH=$PATH:/software/applications/matlab-2012a/bin
export LC_ALL="en_US.utf8"
# minc-toolkit configuration parameters for 0.3.18-20130531
module add octave/3.6.1
export SVN_EDITOR=nano
export PATH=/sb/project/gsf-624-aa/quarantaine/progs/gnuplot-4.4.4/bin:$PATH
export PATH=/sb/project/gsf-624-aa/quarantaine/ghostscript-9.02/bin:$PATH
export PATH=/sb/project/gsf-624-aa/quarantaine/pstoedit-3.60/bin:$PATH
export GNUPLOT_PS_DIR=/sb/project/gsf-624-aa/quarantaine/gnuplot-4.4.4/share/gnuplot/4.4/PostScript
umask 002
export MINC_TOOLKIT_VERSION="0.3.18-20130531"
export PATH=/sb/project/gsf-624-aa/quarantaine/minc-toolkit-0.3.18/bin:/sb/project/gsf-624-aa/quarantaine/minc-toolkit-0.3.18/pipeline:${PATH}
export PERL5LIB=/sb/project/gsf-624-aa/quarantaine/minc-toolkit-0.3.18/perl:/sb/project/gsf-624-aa/quarantaine/minc-toolkit-0.3.18/pipeline:${PERL5LIB}
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/sb/project/gsf-624-aa/quarantaine/minc-toolkit-0.3.18/lib:/sb/project/gsf-624-aa/quarantaine/minc-toolkit-0.3.18/lib/InsightToolkit
export MNI_DATAPATH=/sb/project/gsf-624-aa/quarantaine/minc-toolkit-0.3.18/share
export MINC_FORCE_V2=0
export MINC_COMPRESS=4
export VOLUME_CACHE_THRESHOLD=-1
===================================================


Thanks in advance!

Best,
Kangjoo
Oct 7, 2014  04:10 PM | Pierre Bellec
RE: perl in t1_preprocessing
Hi Kangjoo,

I keep running into problems when people from outside the lab use NIAK on guillimin. I'll have to find a better way. In the meantime, did you check the permissions of the file:
/sb/project/ixx-903-aa/kangjoo/Matlab_code/niak-boss-0.12.15/commands/t1_processing/niak_bestlinreg.pl

you should have the right to read and execute it. 

Best,

Pierre
Oct 14, 2014  09:10 PM | Kangjoo Lee
RE: perl in t1_preprocessing
Hi Pierre, 

It's a bit late response but problem was solved as soon as I simply give permission following your comment.
Thank you! 

Best regards,
Kangjoo