Merge branch 'master' of https://git.sharcnet.ca/bucanl_pipelines/bids_lossless_eeg

derivatives/lossless/code/config/face13_sbatch/c01_scalpart_remote.cfg

@@ -59,7 +59,7 @@ job_init
 m_init
 	derivatives/lossless/code/config/octave.minit
 submit_options
-	--account=def-jdesjard
+
 memory
 	16g
 time_limit

derivatives/lossless/code/config/face13_sbatch/c02_amica_init_remote.cfg

@@ -19,7 +19,7 @@ job_init
 m_init
 	
 submit_options
-	--account=def-jdesjard
+
 memory
 	2G
 time_limit

derivatives/lossless/code/config/face13_sbatch/c03_compart_data_remote.cfg

@@ -15,7 +15,7 @@ replace_string
 	[min_gap_ms],2000
 	[out_path],derivatives/lossless
 	[amica_param_file],derivatives/lossless/code/misc/amica_default.param
-	[amica_threads_s07_08_09],8
+	[amica_threads_s04],8
 order
 	[3 2]
 session_init
@@ -29,7 +29,7 @@ job_init
 m_init
 	derivatives/lossless/code/config/octave.minit
 submit_options
-	--account=def-jdesjard
+
 memory
 	16g
 time_limit

derivatives/lossless/code/config/face13_sbatch/c04a_amica_remote.cfg

@@ -19,7 +19,7 @@ job_init
 m_init
 	
 submit_options
-	--account=def-jdesjard
+
 memory
 	2G
 time_limit

derivatives/lossless/code/config/face13_sbatch/c04b_amica_remote.cfg

@@ -19,7 +19,7 @@ job_init
 m_init
 	
 submit_options
-	--account=def-jdesjard
+
 memory
 	2G
 time_limit

derivatives/lossless/code/config/face13_sbatch/c04c_amica_remote.cfg

@@ -19,7 +19,7 @@ job_init
 m_init
 	
 submit_options
-	--account=def-jdesjard
+
 memory
 	2G
 time_limit

derivatives/lossless/code/config/face13_sbatch/c05_concat_data.cfg

@@ -35,7 +35,7 @@ job_init
 m_init
 	derivatives/lossless/code/config/octave.minit
 submit_options
-	--account=def-jdesjard
+
 memory
 	8g
 time_limit

derivatives/lossless/code/config/octave.sesinit

+module load gcc;
 module load octave;
-

eeglab_asr_amica @ 37e06371

-Subproject commit 669715cba56a6f164971de89e79f7a152eff1040
+Subproject commit 37e06371c320cbc0c71e67dc8a3287005651542f

derivatives/lossless/code/scripts/qc_init.htb

 %LOAD DATASET FILE...
 EEG = pop_loadset('filename','[batch_dfn]','filepath','[batch_dfp]');
+
+if ~find(strcmpi({EEG.marks.chan_info.label},'ch_s_sd'));
+    EEG.marks=marks_add_label(EEG.marks,'chan_info',{'ch_s_sd',[1,0,0],[]});
+end;
+
 EEG = eeg_checkset(EEG);
 
 % CHECK FOR IC CLASSIFICATION MARKS
@@ -92,7 +97,6 @@ manual_ind=find(strcmp('manual',{EEG.marks.chan_info.label}));
 
 %RESET/INITIATE IC MARKS...
 EEG.marks=marks_add_label(EEG.marks,'comp_info',{'ambig',[.3,.3,1],[.3,.3,1],3,zeros(min(size(EEG.icaweights)),1)});
-
 manual_ind=find(strcmp('manual',{EEG.marks.comp_info.label}));
 ch_s_sd_ind=find(strcmp('ch_s_sd',{EEG.marks.chan_info.label}));
 ch_sd_ind=find(strcmp('ch_sd',{EEG.marks.chan_info.label}));
@@ -110,7 +114,9 @@ other_ind=find(strcmp('other',{EEG.marks.comp_info.label}));
 ambig_ind=find(strcmp('ambig',{EEG.marks.comp_info.label}));
 
 EEG.marks.comp_info(manual_ind).order=1;
-EEG.marks.comp_info(ch_s_sd_ind).order=2;
+if ~isempty(ch_s_sd_ind); % skip study-wide criteria if not used
+    EEG.marks.comp_info(ch_s_sd_ind).order=2;
+end;
 EEG.marks.comp_info(ch_sd_ind).order=2;
 EEG.marks.comp_info(low_r_ind).order=2;
 EEG.marks.comp_info(bridge_ind).order=2;