From f1d0f2d03f656e95b0020433260374ba6c9e48e8 Mon Sep 17 00:00:00 2001 From: Mike Cichonski Date: Wed, 20 Mar 2019 13:48:17 -0400 Subject: [PATCH 1/5] qc_init.htb fix to work for data without ch_s_sd flag --- derivatives/lossless/code/scripts/qc_init.htb | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/derivatives/lossless/code/scripts/qc_init.htb b/derivatives/lossless/code/scripts/qc_init.htb index 81632f6..3d8cbd5 100644 --- a/derivatives/lossless/code/scripts/qc_init.htb +++ b/derivatives/lossless/code/scripts/qc_init.htb @@ -1,5 +1,10 @@ %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; -- GitLab From 9992667acd3c6bad11d549b7dc253a809419fd85 Mon Sep 17 00:00:00 2001 From: Mike Cichonski Date: Wed, 20 Mar 2019 14:16:52 -0400 Subject: [PATCH 2/5] added warning messages to vised_marks deprecated functions --- derivatives/lossless/code/dependencies/eeglab_asr_amica | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/derivatives/lossless/code/dependencies/eeglab_asr_amica b/derivatives/lossless/code/dependencies/eeglab_asr_amica index 669715c..37e0637 160000 --- a/derivatives/lossless/code/dependencies/eeglab_asr_amica +++ b/derivatives/lossless/code/dependencies/eeglab_asr_amica @@ -1 +1 @@ -Subproject commit 669715cba56a6f164971de89e79f7a152eff1040 +Subproject commit 37e06371c320cbc0c71e67dc8a3287005651542f -- GitLab From c4cfb7729c459175a6c576af5b4a0fbec45e72e1 Mon Sep 17 00:00:00 2001 From: Mike Cichonski Date: Wed, 20 Mar 2019 15:07:19 -0400 Subject: [PATCH 3/5] setup_remote.sh fix for installing Octave signal package --- derivatives/lossless/code/config/octave.sesinit | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/derivatives/lossless/code/config/octave.sesinit b/derivatives/lossless/code/config/octave.sesinit index db1b8ff..f4f0e3c 100644 --- a/derivatives/lossless/code/config/octave.sesinit +++ b/derivatives/lossless/code/config/octave.sesinit @@ -1,2 +1,2 @@ +module load gcc; module load octave; - -- GitLab From 016206cff0e395c7733f672a1709ef7c19184da8 Mon Sep 17 00:00:00 2001 From: Mike Cichonski Date: Wed, 20 Mar 2019 15:47:15 -0400 Subject: [PATCH 4/5] removed --account from submit_options fields in face13_sbatch configs --- .../lossless/code/config/face13_sbatch/c01_scalpart_remote.cfg | 2 +- .../code/config/face13_sbatch/c02_amica_init_remote.cfg | 2 +- .../code/config/face13_sbatch/c03_compart_data_remote.cfg | 2 +- .../lossless/code/config/face13_sbatch/c04a_amica_remote.cfg | 2 +- .../lossless/code/config/face13_sbatch/c04b_amica_remote.cfg | 2 +- .../lossless/code/config/face13_sbatch/c04c_amica_remote.cfg | 2 +- .../lossless/code/config/face13_sbatch/c05_concat_data.cfg | 2 +- 7 files changed, 7 insertions(+), 7 deletions(-) diff --git a/derivatives/lossless/code/config/face13_sbatch/c01_scalpart_remote.cfg b/derivatives/lossless/code/config/face13_sbatch/c01_scalpart_remote.cfg index e7bfbf2..9804fe1 100644 --- a/derivatives/lossless/code/config/face13_sbatch/c01_scalpart_remote.cfg +++ b/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 diff --git a/derivatives/lossless/code/config/face13_sbatch/c02_amica_init_remote.cfg b/derivatives/lossless/code/config/face13_sbatch/c02_amica_init_remote.cfg index 8cb286a..afe4685 100644 --- a/derivatives/lossless/code/config/face13_sbatch/c02_amica_init_remote.cfg +++ b/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 diff --git a/derivatives/lossless/code/config/face13_sbatch/c03_compart_data_remote.cfg b/derivatives/lossless/code/config/face13_sbatch/c03_compart_data_remote.cfg index 55a08bc..abf3887 100644 --- a/derivatives/lossless/code/config/face13_sbatch/c03_compart_data_remote.cfg +++ b/derivatives/lossless/code/config/face13_sbatch/c03_compart_data_remote.cfg @@ -29,7 +29,7 @@ job_init m_init derivatives/lossless/code/config/octave.minit submit_options - --account=def-jdesjard + memory 16g time_limit diff --git a/derivatives/lossless/code/config/face13_sbatch/c04a_amica_remote.cfg b/derivatives/lossless/code/config/face13_sbatch/c04a_amica_remote.cfg index ae46a01..b53115b 100644 --- a/derivatives/lossless/code/config/face13_sbatch/c04a_amica_remote.cfg +++ b/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 diff --git a/derivatives/lossless/code/config/face13_sbatch/c04b_amica_remote.cfg b/derivatives/lossless/code/config/face13_sbatch/c04b_amica_remote.cfg index 5b75071..01bec04 100644 --- a/derivatives/lossless/code/config/face13_sbatch/c04b_amica_remote.cfg +++ b/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 diff --git a/derivatives/lossless/code/config/face13_sbatch/c04c_amica_remote.cfg b/derivatives/lossless/code/config/face13_sbatch/c04c_amica_remote.cfg index b1f0f17..01bea69 100644 --- a/derivatives/lossless/code/config/face13_sbatch/c04c_amica_remote.cfg +++ b/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 diff --git a/derivatives/lossless/code/config/face13_sbatch/c05_concat_data.cfg b/derivatives/lossless/code/config/face13_sbatch/c05_concat_data.cfg index 506bfa0..8aa256e 100644 --- a/derivatives/lossless/code/config/face13_sbatch/c05_concat_data.cfg +++ b/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 -- GitLab From 4676f0375e119687058ad58de1fa658f41b4bb24 Mon Sep 17 00:00:00 2001 From: Mike Cichonski Date: Thu, 21 Mar 2019 13:29:16 -0400 Subject: [PATCH 5/5] face_13 config fix for c04_amica --- .../code/config/face13_sbatch/c03_compart_data_remote.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/derivatives/lossless/code/config/face13_sbatch/c03_compart_data_remote.cfg b/derivatives/lossless/code/config/face13_sbatch/c03_compart_data_remote.cfg index abf3887..62100bd 100644 --- a/derivatives/lossless/code/config/face13_sbatch/c03_compart_data_remote.cfg +++ b/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 -- GitLab