From 945aca718faa5aee5599eeaedbf0c16541c04545 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Wed, 4 May 2022 11:03:28 +0200 Subject: [PATCH 1/9] [DATALAD] Added subdataset --- .gitmodules | 5 +++++ ds002799 | 1 + 2 files changed, 6 insertions(+) create mode 160000 ds002799 diff --git a/.gitmodules b/.gitmodules index 05e903a..e810272 100644 --- a/.gitmodules +++ b/.gitmodules @@ -41,3 +41,8 @@ url = https://gin.g-node.org/markiewicz/ds000003-fmriprep datalad-id = b099d04a-a2d7-4082-9660-05a9019ed8fe datalad-url = https://gin.g-node.org/markiewicz/ds000003-fmriprep +[submodule "ds002799"] + path = ds002799 + url = https://github.com/OpenNeuroDatasets/ds002799.git + datalad-id = d5b52178-970c-11ea-a09a-1e09d750626b + datalad-url = https://github.com/OpenNeuroDatasets/ds002799.git diff --git a/ds002799 b/ds002799 new file mode 160000 index 0000000..2e4b903 --- /dev/null +++ b/ds002799 @@ -0,0 +1 @@ +Subproject commit 2e4b90395ea5f91dd309cb21fe4d446e14ea6bae From ed1d36454a6bcd3e1e6097483f209996a5fa6577 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Wed, 4 May 2022 11:03:57 +0200 Subject: [PATCH 2/9] move dataset --- .gitignore | 2 ++ .gitmodules | 4 ++++ ds2799/ds002799 | 1 + 3 files changed, 7 insertions(+) create mode 160000 ds2799/ds002799 diff --git a/.gitignore b/.gitignore index 87620ac..d34110a 100644 --- a/.gitignore +++ b/.gitignore @@ -1 +1,3 @@ .ipynb_checkpoints/ + +.vscode \ No newline at end of file diff --git a/.gitmodules b/.gitmodules index e810272..59c7ddb 100644 --- a/.gitmodules +++ b/.gitmodules @@ -46,3 +46,7 @@ url = https://github.com/OpenNeuroDatasets/ds002799.git datalad-id = d5b52178-970c-11ea-a09a-1e09d750626b datalad-url = https://github.com/OpenNeuroDatasets/ds002799.git +[submodule "ds2799/ds002799"] + path = ds2799/ds002799 + url = https://github.com/OpenNeuroDatasets/ds002799.git + datalad-id = d5b52178-970c-11ea-a09a-1e09d750626b diff --git a/ds2799/ds002799 b/ds2799/ds002799 new file mode 160000 index 0000000..2e4b903 --- /dev/null +++ b/ds2799/ds002799 @@ -0,0 +1 @@ +Subproject commit 2e4b90395ea5f91dd309cb21fe4d446e14ea6bae From 785a576daf7e9704605e8f30cd8993b371e9d229 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Wed, 4 May 2022 11:40:54 +0200 Subject: [PATCH 3/9] add models for denoising --- ds2799/model-ds2799-desc-compcop_smdl.json | 29 ++++++++++++++++++ ds2799/model-ds2799-desc-scrubbing_smdl.json | 32 ++++++++++++++++++++ ds2799/model-ds2799-desc-simple_smdl.json | 30 ++++++++++++++++++ 3 files changed, 91 insertions(+) create mode 100644 ds2799/model-ds2799-desc-compcop_smdl.json create mode 100644 ds2799/model-ds2799-desc-scrubbing_smdl.json create mode 100644 ds2799/model-ds2799-desc-simple_smdl.json diff --git a/ds2799/model-ds2799-desc-compcop_smdl.json b/ds2799/model-ds2799-desc-compcop_smdl.json new file mode 100644 index 0000000..23a75fa --- /dev/null +++ b/ds2799/model-ds2799-desc-compcop_smdl.json @@ -0,0 +1,29 @@ +{ + "Name": "ds2799_compcor", + "Description": "scrubbing compcor, see https://nilearn.github.io/stable/modules/generated/nilearn.interfaces.fmriprep.load_confounds_strategy.html", + "BIDSModelVersion": "1.0.0", + "Input": { + "task": "rest", + "space": "MNI152NLin2009cAsym" + }, + "Nodes": [ + { + "Level": "run", + "Name": "run", + "GroupBy": [ + "run" + ], + "Model": { + "X": [ + "rot*", + "trans*", + "a_comp_cor_??" + ], + "Options": { + "HighPassFilterCutoffHz" : 1, + "LowPassFilterCutoffHz" : 1 + } + } + } + ] +} \ No newline at end of file diff --git a/ds2799/model-ds2799-desc-scrubbing_smdl.json b/ds2799/model-ds2799-desc-scrubbing_smdl.json new file mode 100644 index 0000000..10ecf12 --- /dev/null +++ b/ds2799/model-ds2799-desc-scrubbing_smdl.json @@ -0,0 +1,32 @@ +{ + "Name": "ds2799_scrubbing", + "Description": "scrubbing denoising, see https://nilearn.github.io/stable/modules/generated/nilearn.interfaces.fmriprep.load_confounds_strategy.html", + "BIDSModelVersion": "1.0.0", + "Input": { + "task": "rest", + "space": "MNI152NLin2009cAsym" + }, + "Nodes": [ + { + "Level": "run", + "Name": "run", + "GroupBy": [ + "run" + ], + "Model": { + "X": [ + "rot*", + "trans*", + "motion_outlier*", + "non_steady*", + "white_matter*", + "csf*" + ], + "Options": { + "HighPassFilterCutoffHz" : 1, + "LowPassFilterCutoffHz" : 1 + } + } + } + ] +} \ No newline at end of file diff --git a/ds2799/model-ds2799-desc-simple_smdl.json b/ds2799/model-ds2799-desc-simple_smdl.json new file mode 100644 index 0000000..48ec7fc --- /dev/null +++ b/ds2799/model-ds2799-desc-simple_smdl.json @@ -0,0 +1,30 @@ +{ + "Name": "ds2799_simple", + "Description": "simple denoising, see https://nilearn.github.io/stable/modules/generated/nilearn.interfaces.fmriprep.load_confounds_strategy.html", + "BIDSModelVersion": "1.0.0", + "Input": { + "task": "rest", + "space": "MNI152NLin2009cAsym" + }, + "Nodes": [ + { + "Level": "run", + "Name": "run", + "GroupBy": [ + "run" + ], + "Model": { + "X": [ + "rot*", + "trans*", + "white_matter", + "csf" + ], + "Options": { + "HighPassFilterCutoffHz" : 1, + "LowPassFilterCutoffHz" : 1 + } + } + } + ] +} \ No newline at end of file From 18ae1b2899e8517bbb68548d0c840d5b61006c53 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Fri, 6 May 2022 10:26:01 +0200 Subject: [PATCH 4/9] fix with validator and update fitler cutoffs --- ds2799/model-ds2799-desc-compcop_smdl.json | 11 ++++++----- ds2799/model-ds2799-desc-scrubbing_smdl.json | 11 ++++++----- ds2799/model-ds2799-desc-simple_smdl.json | 11 ++++++----- 3 files changed, 18 insertions(+), 15 deletions(-) diff --git a/ds2799/model-ds2799-desc-compcop_smdl.json b/ds2799/model-ds2799-desc-compcop_smdl.json index 23a75fa..66a927e 100644 --- a/ds2799/model-ds2799-desc-compcop_smdl.json +++ b/ds2799/model-ds2799-desc-compcop_smdl.json @@ -3,12 +3,12 @@ "Description": "scrubbing compcor, see https://nilearn.github.io/stable/modules/generated/nilearn.interfaces.fmriprep.load_confounds_strategy.html", "BIDSModelVersion": "1.0.0", "Input": { - "task": "rest", - "space": "MNI152NLin2009cAsym" + "task": ["rest"], + "space": ["MNI152NLin2009cAsym"] }, "Nodes": [ { - "Level": "run", + "Level": "Run", "Name": "run", "GroupBy": [ "run" @@ -19,9 +19,10 @@ "trans*", "a_comp_cor_??" ], + "Type": "glm", "Options": { - "HighPassFilterCutoffHz" : 1, - "LowPassFilterCutoffHz" : 1 + "HighPassFilterCutoffHz" : 0.01, + "LowPassFilterCutoffHz" : 0.15 } } } diff --git a/ds2799/model-ds2799-desc-scrubbing_smdl.json b/ds2799/model-ds2799-desc-scrubbing_smdl.json index 10ecf12..87da804 100644 --- a/ds2799/model-ds2799-desc-scrubbing_smdl.json +++ b/ds2799/model-ds2799-desc-scrubbing_smdl.json @@ -3,12 +3,12 @@ "Description": "scrubbing denoising, see https://nilearn.github.io/stable/modules/generated/nilearn.interfaces.fmriprep.load_confounds_strategy.html", "BIDSModelVersion": "1.0.0", "Input": { - "task": "rest", - "space": "MNI152NLin2009cAsym" + "task": ["rest"], + "space": ["MNI152NLin2009cAsym"] }, "Nodes": [ { - "Level": "run", + "Level": "Run", "Name": "run", "GroupBy": [ "run" @@ -22,9 +22,10 @@ "white_matter*", "csf*" ], + "Type": "glm", "Options": { - "HighPassFilterCutoffHz" : 1, - "LowPassFilterCutoffHz" : 1 + "HighPassFilterCutoffHz" : 0.01, + "LowPassFilterCutoffHz" : 0.15 } } } diff --git a/ds2799/model-ds2799-desc-simple_smdl.json b/ds2799/model-ds2799-desc-simple_smdl.json index 48ec7fc..db6d25b 100644 --- a/ds2799/model-ds2799-desc-simple_smdl.json +++ b/ds2799/model-ds2799-desc-simple_smdl.json @@ -3,12 +3,12 @@ "Description": "simple denoising, see https://nilearn.github.io/stable/modules/generated/nilearn.interfaces.fmriprep.load_confounds_strategy.html", "BIDSModelVersion": "1.0.0", "Input": { - "task": "rest", - "space": "MNI152NLin2009cAsym" + "task": ["rest"], + "space": ["MNI152NLin2009cAsym"] }, "Nodes": [ { - "Level": "run", + "Level": "Run", "Name": "run", "GroupBy": [ "run" @@ -20,9 +20,10 @@ "white_matter", "csf" ], + "Type": "glm", "Options": { - "HighPassFilterCutoffHz" : 1, - "LowPassFilterCutoffHz" : 1 + "HighPassFilterCutoffHz" : 0.01, + "LowPassFilterCutoffHz" : 0.15 } } } From fb89bd5b9ac004b490df06a924b657e88e857ef4 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Fri, 6 May 2022 10:27:49 +0200 Subject: [PATCH 5/9] update groub by --- ds2799/model-ds2799-desc-compcop_smdl.json | 4 +--- ds2799/model-ds2799-desc-scrubbing_smdl.json | 4 +--- ds2799/model-ds2799-desc-simple_smdl.json | 4 +--- 3 files changed, 3 insertions(+), 9 deletions(-) diff --git a/ds2799/model-ds2799-desc-compcop_smdl.json b/ds2799/model-ds2799-desc-compcop_smdl.json index 66a927e..4bb4649 100644 --- a/ds2799/model-ds2799-desc-compcop_smdl.json +++ b/ds2799/model-ds2799-desc-compcop_smdl.json @@ -10,9 +10,7 @@ { "Level": "Run", "Name": "run", - "GroupBy": [ - "run" - ], + "GroupBy": ["run", "session", "subject"], "Model": { "X": [ "rot*", diff --git a/ds2799/model-ds2799-desc-scrubbing_smdl.json b/ds2799/model-ds2799-desc-scrubbing_smdl.json index 87da804..4c6cf30 100644 --- a/ds2799/model-ds2799-desc-scrubbing_smdl.json +++ b/ds2799/model-ds2799-desc-scrubbing_smdl.json @@ -10,9 +10,7 @@ { "Level": "Run", "Name": "run", - "GroupBy": [ - "run" - ], + "GroupBy": ["run", "session", "subject"], "Model": { "X": [ "rot*", diff --git a/ds2799/model-ds2799-desc-simple_smdl.json b/ds2799/model-ds2799-desc-simple_smdl.json index db6d25b..fe9d4e2 100644 --- a/ds2799/model-ds2799-desc-simple_smdl.json +++ b/ds2799/model-ds2799-desc-simple_smdl.json @@ -10,9 +10,7 @@ { "Level": "Run", "Name": "run", - "GroupBy": [ - "run" - ], + "GroupBy": ["run", "session", "subject"], "Model": { "X": [ "rot*", From d644d37181515ebe1e33dd26c378247019519d42 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sat, 7 May 2022 09:59:38 +0200 Subject: [PATCH 6/9] add constant and comments as Description --- ds2799/model-ds2799-desc-compcop_smdl.json | 23 +++++++++++++----- ds2799/model-ds2799-desc-scrubbing_smdl.json | 25 ++++++++++++++------ ds2799/model-ds2799-desc-simple_smdl.json | 23 +++++++++++++----- 3 files changed, 52 insertions(+), 19 deletions(-) diff --git a/ds2799/model-ds2799-desc-compcop_smdl.json b/ds2799/model-ds2799-desc-compcop_smdl.json index 4bb4649..31758c9 100644 --- a/ds2799/model-ds2799-desc-compcop_smdl.json +++ b/ds2799/model-ds2799-desc-compcop_smdl.json @@ -3,24 +3,35 @@ "Description": "scrubbing compcor, see https://nilearn.github.io/stable/modules/generated/nilearn.interfaces.fmriprep.load_confounds_strategy.html", "BIDSModelVersion": "1.0.0", "Input": { - "task": ["rest"], - "space": ["MNI152NLin2009cAsym"] + "task": [ + "rest" + ], + "space": [ + "MNI152NLin2009cAsym" + ] }, "Nodes": [ { "Level": "Run", "Name": "run", - "GroupBy": ["run", "session", "subject"], + "GroupBy": [ + "run", + "session", + "subject" + ], "Model": { + "Description": "removes effect of 1) realigment parameters, their squares, their derivatives and the derivatives squared and 2) the a_comp_cor noise regressors computer by fmriprep to explain 50% of the noise variance in a noise region.", "X": [ "rot*", "trans*", - "a_comp_cor_??" + "a_comp_cor_??", + 1 ], "Type": "glm", "Options": { - "HighPassFilterCutoffHz" : 0.01, - "LowPassFilterCutoffHz" : 0.15 + "Description": "define a bandpass filter", + "HighPassFilterCutoffHz": 0.01, + "LowPassFilterCutoffHz": 0.15 } } } diff --git a/ds2799/model-ds2799-desc-scrubbing_smdl.json b/ds2799/model-ds2799-desc-scrubbing_smdl.json index 4c6cf30..d2f9dea 100644 --- a/ds2799/model-ds2799-desc-scrubbing_smdl.json +++ b/ds2799/model-ds2799-desc-scrubbing_smdl.json @@ -3,27 +3,38 @@ "Description": "scrubbing denoising, see https://nilearn.github.io/stable/modules/generated/nilearn.interfaces.fmriprep.load_confounds_strategy.html", "BIDSModelVersion": "1.0.0", "Input": { - "task": ["rest"], - "space": ["MNI152NLin2009cAsym"] + "task": [ + "rest" + ], + "space": [ + "MNI152NLin2009cAsym" + ] }, "Nodes": [ { "Level": "Run", "Name": "run", - "GroupBy": ["run", "session", "subject"], + "GroupBy": [ + "run", + "session", + "subject" + ], "Model": { + "Description": "1) removes effect of realigment parameters, their squares, their derivatives and the derivatives squared, 2) removes effect of the mean signal measured in CSF, white matter as well as their derivatives and squares and 3) do scrubbing by removing time points flagged as outliers by fmriprep", "X": [ "rot*", "trans*", + "white_matter*", + "csf*", "motion_outlier*", "non_steady*", - "white_matter*", - "csf*" + 1 ], "Type": "glm", "Options": { - "HighPassFilterCutoffHz" : 0.01, - "LowPassFilterCutoffHz" : 0.15 + "Description": "define a bandpass filter", + "HighPassFilterCutoffHz": 0.01, + "LowPassFilterCutoffHz": 0.15 } } } diff --git a/ds2799/model-ds2799-desc-simple_smdl.json b/ds2799/model-ds2799-desc-simple_smdl.json index fe9d4e2..a65e7f7 100644 --- a/ds2799/model-ds2799-desc-simple_smdl.json +++ b/ds2799/model-ds2799-desc-simple_smdl.json @@ -3,25 +3,36 @@ "Description": "simple denoising, see https://nilearn.github.io/stable/modules/generated/nilearn.interfaces.fmriprep.load_confounds_strategy.html", "BIDSModelVersion": "1.0.0", "Input": { - "task": ["rest"], - "space": ["MNI152NLin2009cAsym"] + "task": [ + "rest" + ], + "space": [ + "MNI152NLin2009cAsym" + ] }, "Nodes": [ { "Level": "Run", "Name": "run", - "GroupBy": ["run", "session", "subject"], + "GroupBy": [ + "run", + "session", + "subject" + ], "Model": { + "Description": "removes effect of 1) realigment parameters, their squares, their derivatives and the derivatives squared and 2) the mean signal measured in CSF, white matter", "X": [ "rot*", "trans*", "white_matter", - "csf" + "csf", + 1 ], "Type": "glm", "Options": { - "HighPassFilterCutoffHz" : 0.01, - "LowPassFilterCutoffHz" : 0.15 + "Description": "define a bandpass filter", + "HighPassFilterCutoffHz": 0.01, + "LowPassFilterCutoffHz": 0.15 } } } From 56335b9931ea39b054f1439bc2a7e2d89a0028ec Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sat, 7 May 2022 17:02:05 +0200 Subject: [PATCH 7/9] remove duplicate dataset --- .gitmodules | 5 ----- ds002799 | 1 - 2 files changed, 6 deletions(-) delete mode 160000 ds002799 diff --git a/.gitmodules b/.gitmodules index 59c7ddb..353697c 100644 --- a/.gitmodules +++ b/.gitmodules @@ -41,11 +41,6 @@ url = https://gin.g-node.org/markiewicz/ds000003-fmriprep datalad-id = b099d04a-a2d7-4082-9660-05a9019ed8fe datalad-url = https://gin.g-node.org/markiewicz/ds000003-fmriprep -[submodule "ds002799"] - path = ds002799 - url = https://github.com/OpenNeuroDatasets/ds002799.git - datalad-id = d5b52178-970c-11ea-a09a-1e09d750626b - datalad-url = https://github.com/OpenNeuroDatasets/ds002799.git [submodule "ds2799/ds002799"] path = ds2799/ds002799 url = https://github.com/OpenNeuroDatasets/ds002799.git diff --git a/ds002799 b/ds002799 deleted file mode 160000 index 2e4b903..0000000 --- a/ds002799 +++ /dev/null @@ -1 +0,0 @@ -Subproject commit 2e4b90395ea5f91dd309cb21fe4d446e14ea6bae From 2cedb6b963079d5cc1b002fe2392d027b3bcd3be Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sat, 7 May 2022 17:10:20 +0200 Subject: [PATCH 8/9] Update ds2799/model-ds2799-desc-compcop_smdl.json Co-authored-by: Chris Markiewicz --- ds2799/model-ds2799-desc-compcop_smdl.json | 3 --- 1 file changed, 3 deletions(-) diff --git a/ds2799/model-ds2799-desc-compcop_smdl.json b/ds2799/model-ds2799-desc-compcop_smdl.json index 31758c9..a88110c 100644 --- a/ds2799/model-ds2799-desc-compcop_smdl.json +++ b/ds2799/model-ds2799-desc-compcop_smdl.json @@ -5,9 +5,6 @@ "Input": { "task": [ "rest" - ], - "space": [ - "MNI152NLin2009cAsym" ] }, "Nodes": [ From 56de80a468defbe7234ceddaca3855c1fc07dfdb Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sat, 7 May 2022 17:11:57 +0200 Subject: [PATCH 9/9] remove space and add line at end of file --- ...compcop_smdl.json => model-ds2799_desc-compcop_smdl.json} | 2 +- ...bbing_smdl.json => model-ds2799_desc-scrubbing_smdl.json} | 5 +---- ...c-simple_smdl.json => model-ds2799_desc-simple_smdl.json} | 5 +---- 3 files changed, 3 insertions(+), 9 deletions(-) rename ds2799/{model-ds2799-desc-compcop_smdl.json => model-ds2799_desc-compcop_smdl.json} (99%) rename ds2799/{model-ds2799-desc-scrubbing_smdl.json => model-ds2799_desc-scrubbing_smdl.json} (95%) rename ds2799/{model-ds2799-desc-simple_smdl.json => model-ds2799_desc-simple_smdl.json} (94%) diff --git a/ds2799/model-ds2799-desc-compcop_smdl.json b/ds2799/model-ds2799_desc-compcop_smdl.json similarity index 99% rename from ds2799/model-ds2799-desc-compcop_smdl.json rename to ds2799/model-ds2799_desc-compcop_smdl.json index a88110c..13bcdae 100644 --- a/ds2799/model-ds2799-desc-compcop_smdl.json +++ b/ds2799/model-ds2799_desc-compcop_smdl.json @@ -33,4 +33,4 @@ } } ] -} \ No newline at end of file +} diff --git a/ds2799/model-ds2799-desc-scrubbing_smdl.json b/ds2799/model-ds2799_desc-scrubbing_smdl.json similarity index 95% rename from ds2799/model-ds2799-desc-scrubbing_smdl.json rename to ds2799/model-ds2799_desc-scrubbing_smdl.json index d2f9dea..5d767b5 100644 --- a/ds2799/model-ds2799-desc-scrubbing_smdl.json +++ b/ds2799/model-ds2799_desc-scrubbing_smdl.json @@ -5,9 +5,6 @@ "Input": { "task": [ "rest" - ], - "space": [ - "MNI152NLin2009cAsym" ] }, "Nodes": [ @@ -39,4 +36,4 @@ } } ] -} \ No newline at end of file +} diff --git a/ds2799/model-ds2799-desc-simple_smdl.json b/ds2799/model-ds2799_desc-simple_smdl.json similarity index 94% rename from ds2799/model-ds2799-desc-simple_smdl.json rename to ds2799/model-ds2799_desc-simple_smdl.json index a65e7f7..553f537 100644 --- a/ds2799/model-ds2799-desc-simple_smdl.json +++ b/ds2799/model-ds2799_desc-simple_smdl.json @@ -5,9 +5,6 @@ "Input": { "task": [ "rest" - ], - "space": [ - "MNI152NLin2009cAsym" ] }, "Nodes": [ @@ -37,4 +34,4 @@ } } ] -} \ No newline at end of file +}