From f3cf85cf7c63249a901be0e4767655ba29b8ad52 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Sat, 20 Oct 2018 11:50:15 -0700 Subject: [PATCH 1/7] ENH: Add models for ds003, ds114 --- ds003/models/model-001_smdl.json | 77 ++++++++++++++++++ ds114/models/model-1_smdl.json | 130 +++++++++++++++++++++++++++++++ 2 files changed, 207 insertions(+) create mode 100644 ds003/models/model-001_smdl.json create mode 100644 ds114/models/model-1_smdl.json diff --git a/ds003/models/model-001_smdl.json b/ds003/models/model-001_smdl.json new file mode 100644 index 000000000..618659f96 --- /dev/null +++ b/ds003/models/model-001_smdl.json @@ -0,0 +1,77 @@ +{ + "name": "ds003_model001", + "description": "", + "input": { + "task": "rhymejudgment" + }, + "blocks": [ + { + "level": "run", + "transformations": [ + { + "name": "factor", + "input": [ + "trial_type" + ] + } + ], + "model": { + "HRF_variables": [ + "trial_type.word", + "trial_type.pseudoword" + ], + "variables": [ + "trial_type.word", + "trial_type.pseudoword", + "FramewiseDisplacement", + "X", + "Y", + "Z", + "RotX", + "RotY", + "RotZ", + "aCompCor00", + "aCompCor01", + "aCompCor02", + "aCompCor03", + "aCompCor04", + "aCompCor05" + ] + }, + "contrasts": [ + { + "name": "word_gt_pseudo", + "condition_list": [ + "trial_type.word", + "trial_type.pseudoword" + ], + "weights": [ + 1, + -1 + ], + "type": "T" + } + ] + }, + { + "level": "dataset", + "model": { + "variables": [ + "word_gt_pseudo" + ] + }, + "contrasts": [ + { + "name": "group_word_gt_pseudo", + "condition_list": [ + "word_gt_pseudo" + ], + "weights": [ + 1 + ], + "type": "T" + } + ] + } + ] +} diff --git a/ds114/models/model-1_smdl.json b/ds114/models/model-1_smdl.json new file mode 100644 index 000000000..6acd2c3f8 --- /dev/null +++ b/ds114/models/model-1_smdl.json @@ -0,0 +1,130 @@ +{ + "name": "ds114_model1", + "description": "sample model for ds114", + "input": { + "task": "fingerfootlips" + }, + "blocks": [ + { + "level": "run", + "transformations": [ + { + "name": "factor", + "input": [ + "trial_type" + ] + } + ], + "model": { + "HRF_variables": [ + "trial_type.Finger", + "trial_type.Foot", + "trial_type.Lips" + ], + "variables": [ + "trial_type.Finger", + "trial_type.Foot", + "trial_type.Lips", + "FramewiseDisplacement", + "X", + "Y", + "Z", + "RotX", + "RotY", + "RotZ", + "aCompCor00", + "aCompCor01", + "aCompCor02", + "aCompCor03", + "aCompCor04", + "aCompCor05" + ] + }, + "contrasts": [ + { + "name": "finger_vs_others", + "condition_list": [ + "trial_type.Finger", + "trial_type.Foot", + "trial_type.Lips" + ], + "weights": [ + 1, + -0.5, + -0.5 + ], + "type": "T" + }, + { + "name": "lips_vs_others", + "condition_list": [ + "trial_type.Finger", + "trial_type.Foot", + "trial_type.Lips" + ], + "weights": [ + -0.5, + -0.5, + 1 + ], + "type": "T" + } + ] + }, + { + "level": "session", + "transformations": [ + { + "name": "split", + "input": [ + "finger_vs_others" + ], + "by": "session" + } + ] + }, + { + "level": "subject", + "model": { + "variables": [ + "finger_vs_others.test", + "finger_vs_others.retest" + ] + }, + "contrasts": [ + { + "name": "session_diff", + "condition_list": [ + "finger_vs_others.test", + "finger_vs_others.retest" + ], + "weights": [ + 1, + -1 + ], + "type": "T" + } + ] + }, + { + "level": "dataset", + "model": { + "variables": [ + "session_diff" + ] + }, + "contrasts": [ + { + "name": "session_diff_finger_vs_others", + "condition_list": [ + "session_diff" + ], + "weights": [ + 1 + ], + "type": "T" + } + ] + } + ] +} From 9aa6525adc4640bc20adf6cc7624aa630f17abca Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Thu, 1 Nov 2018 09:43:55 -0400 Subject: [PATCH 2/7] ENH: Conform DS003 model to updated spec * Initial capitals in JSON keys * snake_case for variables * AutoContrasts for dataset-level analysis * High-pass filter cutoff --- ds003/models/model-001_smdl.json | 81 ++++++++++---------------------- 1 file changed, 25 insertions(+), 56 deletions(-) diff --git a/ds003/models/model-001_smdl.json b/ds003/models/model-001_smdl.json index 618659f96..50491c4eb 100644 --- a/ds003/models/model-001_smdl.json +++ b/ds003/models/model-001_smdl.json @@ -1,77 +1,46 @@ { - "name": "ds003_model001", - "description": "", - "input": { + "Name": "ds003_model001", + "Description": "", + "Input": { "task": "rhymejudgment" }, - "blocks": [ + "Steps": [ { - "level": "run", - "transformations": [ + "Level": "run", + "Transformations": [ { - "name": "factor", - "input": [ - "trial_type" - ] + "Name": "Factor", + "Input": ["trial_type"] } ], - "model": { - "HRF_variables": [ - "trial_type.word", - "trial_type.pseudoword" - ], - "variables": [ + "Model": { + "X": [ "trial_type.word", "trial_type.pseudoword", - "FramewiseDisplacement", - "X", - "Y", - "Z", - "RotX", - "RotY", - "RotZ", - "aCompCor00", - "aCompCor01", - "aCompCor02", - "aCompCor03", - "aCompCor04", - "aCompCor05" - ] + "framewise_displacement", + "trans_x", "trans_y", "trans_z", "rot_x", "rot_y", "rot_z", + "a_comp_cor_00", "a_comp_cor_01", "a_comp_cor_02", + "a_comp_cor_03", "a_comp_cor_04", "a_comp_cor_05" + ], + "Options": { + "high_pass_filter_cutoff_secs": 128 + }, }, - "contrasts": [ + "Contrasts": [ { - "name": "word_gt_pseudo", - "condition_list": [ + "Name": "wordness", + "ConditionList": [ "trial_type.word", "trial_type.pseudoword" ], - "weights": [ - 1, - -1 - ], - "type": "T" + "Weights": [1, -1], + "Type": "t" } ] }, { - "level": "dataset", - "model": { - "variables": [ - "word_gt_pseudo" - ] - }, - "contrasts": [ - { - "name": "group_word_gt_pseudo", - "condition_list": [ - "word_gt_pseudo" - ], - "weights": [ - 1 - ], - "type": "T" - } - ] + "Level": "dataset", + "AutoContrasts": true } ] } From 8bad9be1be5a14b8cc5c6fd9c534f836558f5326 Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Thu, 1 Nov 2018 10:00:41 -0400 Subject: [PATCH 3/7] ENH: Conform DS114 model to updated spec * Initial capitals in JSON keys * snake_case for variables * AutoContrasts for dataset-level analysis * High-pass filter cutoff Additionally, moved Split transformation to subject level, eliminating session-level step --- ds114/models/model-1_smdl.json | 128 ++++++++++----------------------- 1 file changed, 36 insertions(+), 92 deletions(-) diff --git a/ds114/models/model-1_smdl.json b/ds114/models/model-1_smdl.json index 6acd2c3f8..05173420b 100644 --- a/ds114/models/model-1_smdl.json +++ b/ds114/models/model-1_smdl.json @@ -1,130 +1,74 @@ { - "name": "ds114_model1", - "description": "sample model for ds114", - "input": { + "Name": "ds114_model1", + "Description": "sample model for ds114", + "Input": { "task": "fingerfootlips" }, - "blocks": [ + "Steps": [ { - "level": "run", - "transformations": [ + "Level": "run", + "Transformations": [ { - "name": "factor", - "input": [ - "trial_type" - ] + "Name": "Factor", + "Input": ["trial_type"] } ], - "model": { - "HRF_variables": [ - "trial_type.Finger", - "trial_type.Foot", - "trial_type.Lips" - ], - "variables": [ + "Model": { + "X": [ "trial_type.Finger", "trial_type.Foot", "trial_type.Lips", - "FramewiseDisplacement", - "X", - "Y", - "Z", - "RotX", - "RotY", - "RotZ", - "aCompCor00", - "aCompCor01", - "aCompCor02", - "aCompCor03", - "aCompCor04", - "aCompCor05" - ] + "framewise_displacement", + "trans_x", "trans_y", "trans_z", "rot_x", "rot_y", "rot_z", + "a_comp_cor_00", "a_comp_cor_01", "a_comp_cor_02", + "a_comp_cor_03", "a_comp_cor_04", "a_comp_cor_05" + ], + "Options": { + "high_pass_filter_cutoff_secs": 128 + }, }, - "contrasts": [ + "Contrasts": [ { - "name": "finger_vs_others", - "condition_list": [ + "Name": "finger_vs_others", + "ConditionList": [ "trial_type.Finger", "trial_type.Foot", "trial_type.Lips" ], - "weights": [ - 1, - -0.5, - -0.5 - ], - "type": "T" + "Weights": [1, -0.5, -0.5], + "Type": "t" }, - { - "name": "lips_vs_others", - "condition_list": [ - "trial_type.Finger", - "trial_type.Foot", - "trial_type.Lips" - ], - "weights": [ - -0.5, - -0.5, - 1 - ], - "type": "T" - } ] }, { - "level": "session", - "transformations": [ + "Level": "subject", + "Transformations": [ { - "name": "split", - "input": [ - "finger_vs_others" - ], - "by": "session" + "Name": "Split", + "Input": ["finger_vs_others"], + "By": "session" } ] - }, - { - "level": "subject", - "model": { - "variables": [ + "Model": { + "X": [ "finger_vs_others.test", "finger_vs_others.retest" ] }, - "contrasts": [ + "Contrasts": [ { - "name": "session_diff", - "condition_list": [ + "Name": "test_vs_retest", + "ConditionList": [ "finger_vs_others.test", "finger_vs_others.retest" ], - "weights": [ - 1, - -1 - ], - "type": "T" + "Weights": [1, -1] } ] }, { - "level": "dataset", - "model": { - "variables": [ - "session_diff" - ] - }, - "contrasts": [ - { - "name": "session_diff_finger_vs_others", - "condition_list": [ - "session_diff" - ], - "weights": [ - 1 - ], - "type": "T" - } - ] + "Level": "dataset", + "AutoContrasts": ["test_vs_retest"] } ] } From fae443a990f63dc181c4686751314835466ffa6a Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Thu, 1 Nov 2018 10:27:00 -0400 Subject: [PATCH 4/7] FIX: JSON syntax --- ds114/models/model-1_smdl.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ds114/models/model-1_smdl.json b/ds114/models/model-1_smdl.json index 05173420b..e7ce77d94 100644 --- a/ds114/models/model-1_smdl.json +++ b/ds114/models/model-1_smdl.json @@ -48,7 +48,7 @@ "Input": ["finger_vs_others"], "By": "session" } - ] + ], "Model": { "X": [ "finger_vs_others.test", From dcc0a06b1e3ee1c872a54ebdfc4d5fa49bf8adeb Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Thu, 1 Nov 2018 21:25:37 -0400 Subject: [PATCH 5/7] FIX: Re-convolve DS003 regressors --- ds003/models/model-001_smdl.json | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/ds003/models/model-001_smdl.json b/ds003/models/model-001_smdl.json index 50491c4eb..aa59f99da 100644 --- a/ds003/models/model-001_smdl.json +++ b/ds003/models/model-001_smdl.json @@ -11,6 +11,11 @@ { "Name": "Factor", "Input": ["trial_type"] + }, + { + "Name": "Convolve", + "Input": ["trial_type.word", "trial_type.pseudoword"], + "Model": "DoubleGamma" } ], "Model": { From 31f4c1322d596e803593ff48c5c5f9cecb25cb0f Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Thu, 1 Nov 2018 21:26:18 -0400 Subject: [PATCH 6/7] FIX: Re-convolve DS114 regressors --- ds114/models/model-1_smdl.json | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/ds114/models/model-1_smdl.json b/ds114/models/model-1_smdl.json index e7ce77d94..6ee702ade 100644 --- a/ds114/models/model-1_smdl.json +++ b/ds114/models/model-1_smdl.json @@ -11,6 +11,11 @@ { "Name": "Factor", "Input": ["trial_type"] + }, + { + "Name": "Convolve", + "Input": ["trial_type.Finger", "trial_type.Foot", "trial_type.Lips"], + "Model": "DoubleGamma" } ], "Model": { From 6cddab73174fcc77e4f95098fb365094be4143df Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Thu, 24 Jan 2019 15:37:15 -0500 Subject: [PATCH 7/7] FIX: Update ds003 model --- ds003/models/model-001_smdl.json | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/ds003/models/model-001_smdl.json b/ds003/models/model-001_smdl.json index aa59f99da..d42678145 100644 --- a/ds003/models/model-001_smdl.json +++ b/ds003/models/model-001_smdl.json @@ -10,12 +10,14 @@ "Transformations": [ { "Name": "Factor", - "Input": ["trial_type"] + "Input": [ + "trial_type" + ] }, { "Name": "Convolve", "Input": ["trial_type.word", "trial_type.pseudoword"], - "Model": "DoubleGamma" + "Model": "spm" } ], "Model": { @@ -26,14 +28,11 @@ "trans_x", "trans_y", "trans_z", "rot_x", "rot_y", "rot_z", "a_comp_cor_00", "a_comp_cor_01", "a_comp_cor_02", "a_comp_cor_03", "a_comp_cor_04", "a_comp_cor_05" - ], - "Options": { - "high_pass_filter_cutoff_secs": 128 - }, + ] }, "Contrasts": [ { - "Name": "wordness", + "Name": "word_gt_pseudo", "ConditionList": [ "trial_type.word", "trial_type.pseudoword" @@ -45,7 +44,7 @@ }, { "Level": "dataset", - "AutoContrasts": true + "AutoContrasts": ["word_gt_pseudo"] } ] }