First Push of the project

README.txt

+This package contains the BUCANL EEG_pipe_ASR_AMICA pipeline and all supporting documents.
+small change
+
+Code written by James A. Desjardins, supported by NSERC funding to Sidney J. Segalowitz
+at the Jack and Nora Walker Centre for Lifespan Development Research (Brock University),
+and a Dedicated Programming award from SHARCNet, Compute Ontario.
+
+This package includes the following external tools from the Matlab File Share:
+Property grid using JIDE implementation, by Levente Hunyadi
+
+System applications that work well with the Context plugin include 
+Meld 1.7 (or later), sshfs, and rsync.   
+
+
+Copyright (C) 2013 James Desjardins
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program (LICENSE.txt file in the root directory); if not, write to the Free Software
+Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA

README.txt~

+This package contains the BUCANL EEG_pipe_ASR_AMICA pipeline and all supporting documents.
+
+
+Code written by James A. Desjardins, supported by NSERC funding to Sidney J. Segalowitz
+at the Jack and Nora Walker Centre for Lifespan Development Research (Brock University),
+and a Dedicated Programming award from SHARCNet, Compute Ontario.
+
+This package includes the following external tools from the Matlab File Share:
+Property grid using JIDE implementation, by Levente Hunyadi
+
+System applications that work well with the Context plugin include 
+Meld 1.7 (or later), sshfs, and rsync.   
+
+
+Copyright (C) 2013 James Desjardins
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program (LICENSE.txt file in the root directory); if not, write to the Free Software
+Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA

analysis/data/2_preproc/ec_t1_042_eeg_sa_purge_ASR_a.param~

+files /home/jad/Documents/eye_pilot/analysis/data/2_preproc/ec_t1_042_eeg_sa_purge_ASR_purge.fdt
+outdir /home/jad/Documents/eye_pilot/analysis/data/2_preproc/ec_t1_042_eeg_sa_purge_ASR_amicaout_a
+data_dim 80
+field_dim       611000
+dble_data 0
+load_rej 0
+load_A 0
+load_c 0
+load_gm 0
+load_alpha 0
+load_mu 0
+load_beta 0
+load_rho 0
+load_comp_list 0
+num_models 1
+num_mix_comps 3
+pdftype 0
+mineig 1e-15
+pcakeep 80
+do_approx_sphere 1
+share_comps 0
+share_start 100
+comp_thresh 0.99
+share_iter 100
+do_reject 0
+numrej 5
+rejstart 1
+rejint 1
+rejsig 3.00000
+do_newton 1
+newt_start 50
+lrate 0.100000
+max_iter 2000
+do_history 0
+histstep 10
+use_grad_norm 1
+use_min_dll 1
+min_grad_norm 1.00000e-06
+min_dll 1.00000e-06
+max_threads 4
+do_opt_block 0
+block_size 256
+fix_init 0
+print_debug 0
+num_samples 1
+field_blocksize 1
+minlrate 1.00000e-08
+lratefact 0.500000
+rholrate 0.050000
+rho0 1.50000
+minrho 1.00000
+maxrho 2.00000
+rholratefact 0.500000
+kurt_start 3
+num_kurt 5
+kurt_int 1
+newt_ramp 10
+newtrate 1.00000
+writestep 10
+write_nd 1
+write_LLt 1
+decwindow 1
+max_decs 3
+update_A 1
+update_c 1
+update_gm 1
+update_alpha 1
+update_mu 1
+update_beta 1
+do_rho 1
+invsigmax 100.000
+invsigmin 1.00000e-08
+do_mean 1
+do_sphere 1
+doPCA 0
+doscaling 1
+scalestep 1
+

analysis/support/config/Script1.txt~

+file_name
+	Script1.txt
+exec_func
+	ef_sqsub
+replace_string
+    ''
+order
+	[1]
+session_init
+	'analysis/support/config/octave.sesinit'
+job_name
+	'[batch_hfn]'
+job_init
+	''
+m_init
+	''
+qsub_options
+	'-r 1m -o [batch_hfn]'
+software
+	octave
+program_options
+	'--traditional'
+

analysis/support/config/Script2.txt~

+file_name
+	Script2.txt
+exec_func
+	ef_sqsub
+replace_string
+
+order
+	[2,1]
+session_init
+	'analysis/support/config/octave.sesinit'
+job_name
+	'[batch_hfn]'
+job_init
+	''
+m_init
+	''
+qsub_options
+	'-r 1m -o [batch_hfn]'
+software
+	octave
+program_options
+	'--traditional'
+
+

analysis/support/config/Script3.txt~

+file_name
+	Script3.txt
+exec_func
+	ef_sqsub
+replace_string
+
+order
+	[3,1]
+session_init
+	'analysis/support/config/octave.sesinit'
+job_name
+	'[batch_hfn]'
+job_init
+	''
+m_init
+	''
+qsub_options
+	'-r 1m -o [batch_hfn]'
+software
+	octave
+program_options
+	'--traditional'
+

analysis/support/config/Script4.txt~

+file_name
+	Script4.txt
+exec_func
+	ef_sqsub
+replace_string
+
+order
+	[4,2]
+session_init
+	'analysis/support/config/octave.sesinit'
+job_name
+	'[batch_hfn]'
+job_init
+	''
+m_init
+	''
+qsub_options
+	'-r 1m -o [batch_hfn]'
+software
+	octave
+program_options
+	'--traditional'
+

analysis/support/config/amica.jobinit

+LD_LIBRARY_PATH=$LD_RUN_PATH \

analysis/support/config/amica.sesinit

+OMPI_MCA_mpi_cuda_support=0
+export OMPI_MCA_mpi_cuda_support

analysis/support/config/c1_scalpart_local.txt

+file_name
+	c1_scaplart_local.txt
+exec_func
+	ef_current_base
+replace_string
+	[in_path],analysis/data/1_init
+	[recur_sec],1
+	[limit_sec],[-1 0]
+	[sd_chan_z],2.326
+	[sd_chan_p],.1
+	[sd_chan_trim],10
+	[ref_loc_file],analysis/support/misc/standard_1020_bucanl19.elc
+	[low_bound_hz],2
+	[high_bound_hz],30
+	[n_neighb_chan],3
+	[r_chan_z],2.326
+	[r_chan_p],.1
+	[r_chan_trim],10
+	[bridge_trim],40
+	[bridge_z],3
+	[n_neighb_epoch],3
+	[epoch_z],2.32
+	[epoch_p],.2
+	[epoch_trim],20
+	[out_path],analysis/data/2_preproc
+	[amica_param_file],analysis/support/misc/amica_default.param
+order
+	[1]
+session_init
+	''
+job_name
+	''
+job_init
+	''
+m_init
+	''
+qsub_options
+	''
+software
+	matlab
+program_options
+	''
+

analysis/support/config/c1_scalpart_remote.txt

+file_name
+	c1_scaplart_remote.txt
+exec_func
+	ef_sqsub
+replace_string
+	[in_path],analysis/data/1_init
+	[recur_sec],1
+	[limit_sec],[-1 0]
+	[sd_chan_z],2.326
+	[sd_chan_p],.1
+	[sd_chan_trim],10
+	[ref_loc_file],analysis/support/misc/standard_1020_bucanl19.elc
+	[low_bound_hz],2
+	[high_bound_hz],30
+	[n_neighb_chan],3
+	[r_chan_z],2.326
+	[r_chan_p],.1
+	[r_chan_trim],10
+	[bridge_trim],40
+	[bridge_z],3
+	[n_neighb_epoch],3
+	[epoch_z],2.32
+	[epoch_p],.2
+	[epoch_trim],20
+	[out_path],analysis/data/2_preproc
+	[amica_param_file],analysis/support/misc/amica_default.param
+order
+	[1]
+session_init
+	'analysis/support/config/octave.sesinit'
+job_name
+	'[batch_hfn]'
+job_init
+	'-r 4h -o [batch_hfn]'
+m_init
+	''
+qsub_options
+	''
+software
+	octave
+program_options
+	'--traditional'
+

analysis/support/config/c1_scaplart.txt~

+file_name
+	c1_scaplart.txt
+exec_func
+	ef_current_base
+replace_string
+	[in_path],analysis/data/1_init
+	[recur_sec],1
+	[limit_sec],[-1 0]
+	[sd_chan_z],2.326
+	[sd_chan_p],.1
+	[sd_chan_trim],10
+	[ref_loc_file],analysis/support/misc/standard_1020_bucanl19.elc
+	[low_bound_hz],2
+	[high_bound_hz],30
+	[n_neighb_chan],3
+	[r_chan_z],2.326
+	[r_chan_p],.1
+	[r_chan_trim],10
+	[bridge_trim],40
+	[bridge_z],3
+	[n_neighb_epoch],3
+	[epoch_z],2.32
+	[epoch_p],.2
+	[epoch_trim],20
+	[out_path],analysis/data/2_preproc
+	[amica_param_file],analysis/support/misc/amica_default.param
+order
+	[]
+session_init
+	''
+job_name
+	''
+job_init
+	''
+m_init
+	''
+qsub_options
+	''
+software
+	matlab
+program_options
+	''
+

analysis/support/config/c2_amica_1.txt~

+file_name
+	c2_amica_1.txt
+exec_func
+	ef_current_base
+replace_string
+	[dep_path],analysis/support/dependencies/eeglab/plugins/amica
+    [in_path],analysis/data/2_preproc
+order
+	[2]
+session_init
+	''
+job_name
+	''
+job_init
+	''
+m_init
+	''
+qsub_options
+	''
+software
+	None
+program_options
+	''
+

analysis/support/config/c2_amica_1_local.txt

+file_name
+	c2_amica_1_local.txt
+exec_func
+	ef_current_base
+replace_string
+	[dep_path],analysis/support/dependencies/eeglab/plugins/amica
+    [in_path],analysis/data/2_preproc
+order
+	[2]
+session_init
+	''
+job_name
+	''
+job_init
+	''
+m_init
+	''
+qsub_options
+	''
+software
+	matlab
+program_options
+	''
+

analysis/support/config/c2_amica_1_remote.txt

+file_name
+	c2_amica_1_remote.txt
+exec_func
+	ef_sqsub
+replace_string
+	[dep_path],analysis/support/dependencies/eeglab/plugins/amica
+    [in_path],analysis/data/2_preproc
+order
+	[2 1]
+session_init
+	'analysis/support/config/octave.sesinit'
+job_name
+	'[batch_hfn]'
+job_init
+	''
+m_init
+	''
+qsub_options
+	'-r 4h -o [batch_hfn]'
+software
+	none
+program_options
+	''
+

analysis/support/config/c3_runasr.txt~

+file_name
+	c3_runasr.txt
+exec_func
+	ef_current_base
+replace_string
+	[in_path],analysis/data/1_init
+	[recur_sec],1
+	[limit_sec],[-1 0]
+	[init_recur_sec],1
+    [init_limit_sec],[-1 0]
+	[sd_chan_z],2.326
+	[sd_chan_p],.1
+	[sd_chan_trim],10
+	[ref_loc_file],analysis/support/misc/standard_1020_bucanl19.elc
+	[low_bound_hz],2
+	[high_bound_hz],30
+	[n_neighb_chan],3
+	[r_chan_z],2.326
+	[r_chan_p],.1
+	[r_chan_trim],10
+	[bridge_trim],40
+	[bridge_z],3
+	[n_neighb_epoch],3
+	[epoch_z],2.32
+	[epoch_p],.2
+	[epoch_trim],20
+	[out_path],analysis/data/2_preproc
+	[amica_param_file],analysis/support/misc/amica_default.param
+	[asr_sd_cutoff],3
+    [asr_winlen],[]
+    [asr_stepsize],[]
+    [asr_maxdims],[]
+    [asr_learningtime],60
+    [asr_reftol],[]
+    [asr_refwinlen],[]
+    [asr_useGPU],false
+order
+	[1]
+session_init
+	''
+job_name
+	''
+job_init
+	''
+m_init
+	''
+qsub_options
+	''
+software
+	matlab
+program_options
+	''
+

analysis/support/config/c3_runasr_local.txt

+file_name
+	c3_runasr_local.txt
+exec_func
+	ef_current_base
+replace_string
+	[in_path],analysis/data/2_preproc
+	[recur_sec],1
+	[limit_sec],[-1 0]
+	[init_recur_sec],1
+    [init_limit_sec],[-1 0]
+	[sd_chan_z],2.326
+	[sd_chan_p],.1
+	[sd_chan_trim],10
+	[ref_loc_file],analysis/support/misc/standard_1020_bucanl19.elc
+	[low_bound_hz],2
+	[high_bound_hz],30
+	[n_neighb_chan],3
+	[r_chan_z],2.326
+	[r_chan_p],.1
+	[r_chan_trim],10
+	[bridge_trim],40
+	[bridge_z],3
+	[n_neighb_epoch],3
+	[epoch_z],2.32
+	[epoch_p],.2
+	[epoch_trim],20
+	[out_path],analysis/data/2_preproc
+	[amica_param_file],analysis/support/misc/amica_default.param
+	[asr_sd_cutoff],3
+    [asr_winlen],[]
+    [asr_stepsize],[]
+    [asr_maxdims],[]
+    [asr_learningtime],60
+    [asr_reftol],[]
+    [asr_refwinlen],[]
+    [asr_useGPU],false
+order
+	[3]
+session_init
+	''
+job_name
+	''
+job_init
+	''
+m_init
+	''
+qsub_options
+	''
+software
+	matlab
+program_options
+	''
+

analysis/support/config/c3_runasr_remote.txt

+file_name
+	c3_runasr_remote.txt
+exec_func
+	ef_sqsub
+replace_string
+	[in_path],analysis/data/2_preproc
+	[recur_sec],1
+	[limit_sec],[-1 0]
+	[init_recur_sec],1
+    [init_limit_sec],[-1 0]
+	[sd_chan_z],2.326
+	[sd_chan_p],.1
+	[sd_chan_trim],10
+	[ref_loc_file],analysis/support/misc/standard_1020_bucanl19.elc
+	[low_bound_hz],2
+	[high_bound_hz],30
+	[n_neighb_chan],3
+	[r_chan_z],2.326
+	[r_chan_p],.1
+	[r_chan_trim],10
+	[bridge_trim],40
+	[bridge_z],3
+	[n_neighb_epoch],3
+	[epoch_z],2.32
+	[epoch_p],.2
+	[epoch_trim],20
+	[out_path],analysis/data/2_preproc
+	[amica_param_file],analysis/support/misc/amica_default.param
+	[asr_sd_cutoff],3
+    [asr_winlen],[]
+    [asr_stepsize],[]
+    [asr_maxdims],[]
+    [asr_learningtime],60
+    [asr_reftol],[]
+    [asr_refwinlen],[]
+    [asr_useGPU],false
+order
+	[3 2]
+session_init
+	'analysis/support/config/octave.sesinit'
+job_name
+	'[batch_hfn]'
+job_init
+	''
+m_init
+	''
+qsub_options
+	'-r 4h -o [batch_hfn]'
+software
+	octave
+program_options
+	'--traditional'
+

analysis/support/config/c4_amica_2a.txt~

+file_name
+	c4_amica_2a.txt
+exec_func
+	ef_current_base
+replace_string
+	[dep_path],analysis/support/dependencies/eeglab/plugins/amica
+    [in_path],analysis/data/2_preproc
+order
+	[4]
+session_init
+	''
+job_name
+	''
+job_init
+	''
+m_init
+	''
+qsub_options
+	''
+software
+	none
+program_options
+	''
+

analysis/support/config/c4_amica_2a_local.txt

+file_name
+	c4_amica_2a_local.txt
+exec_func
+	ef_current_base
+replace_string
+	[dep_path],analysis/support/dependencies/eeglab/plugins/amica
+    [in_path],analysis/data/2_preproc
+order
+	[4]
+session_init
+	''
+job_name
+	''
+job_init
+	''
+m_init
+	''
+qsub_options
+	''
+software
+	matlab
+program_options
+	''
+