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Просмотр исходного кода

[DATALAD RUNCMD] run with afni and isometric smoothing

=== Do not change lines below ===
{
 "chain": [],
 "cmd": "fitlins ds003/ds003_fmriprep/sourcedata ds003/afni_smooth/out dataset -d ds003/ds003_fmriprep/ -m /data/MBDU/nielsond/dccc2019/try_gnode/fitlins_tests/ds003/models/model-001_smdl.json -w /lscratch/6790822/afni_smooth  --participant-label 01 02 03 --space MNI152NLin2009cAsym --estimator afni  --n-cpus 8 --mem-gb 8 -vv -s 10.0:l1:iso",
 "dsid": "87b71dea-dec5-4034-9c38-ff4bd27cf5dc",
 "exit": 0,
 "extra_inputs": [],
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^
shotgunosine 3 лет назад
Родитель
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100 измененных файлов с 13713 добавлено и 0 удалено
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+{"Name": "Fitlins output", "BIDSVersion": "1.1.0", "PipelineDescription": {"Name": "FitLins", "Version": "0.8.0+74.g9440822.dirty", "CodeURL": "https://github.com/poldracklab/fitlins", "Estimator": "afni", "Smoothing": "10.0:l1:iso"}, "CodeURL": "https://github.com/poldracklab/fitlins", "HowToAcknowledge": "https://github.com/poldracklab/fitlins", "License": "This dataset is made available under the Public Domain Dedication and License \nv1.0, whose full text can be found at \nhttp://www.opendatacommons.org/licenses/pddl/1.0/. \nWe hope that all users will follow the ODC Attribution/Share-Alike \nCommunity Norms (http://www.opendatacommons.org/norms/odc-by-sa/); \nin particular, while not legally required, we hope that all users \nof the data will acknowledge the OpenfMRI project and NSF Grant \nOCI-1131441 (R. Poldrack, PI) in any publications."}

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+}
 
+summary.heading-1 {
 
+    font-size: 12pt;
 
+    font-weight: bold;
 
+}
 
+summary.heading-2 {
 
+    font-size: 11pt;
 
+    font-weight: bold;
 
+}
 
+</style>
 
+</head>
 
+<body>
 
+    <div id="summary">
 
+        <h1 class="sub-report-title">Summary</h1>
 
+        <ul class="elem-desc">
 
+            <li>Dataset: Rhyme judgment</li>
 
+            <li>Model: ds003_model001</li>
 
+            <li>Participants (3): 01, 02, 03
 
+        </ul>
 
+    </div>
 
+    <div id="model">
 
+        <h1 class="sub-report-title">Model</h1>
 
+        <details>
 
+        <summary>Model specification</summary>
 
+        <pre>{
 
+  "description": "",
 
+  "input": {
 
+    "task": "rhymejudgment"
 
+  },
 
+  "name": "ds003_model001",
 
+  "steps": [
 
+    {
 
+      "contrasts": [
 
+        {
 
+          "condition_list": [
 
+            "trial_type.word",
 
+            "trial_type.pseudoword"
 
+          ],
 
+          "name": "word_gt_pseudo",
 
+          "type": "t",
 
+          "weights": [
 
+            1,
 
+            -1
 
+          ]
 
+        },
 
+        {
 
+          "condition_list": [
 
+            "trial_type.word",
 
+            "trial_type.pseudoword"
 
+          ],
 
+          "name": "task_vs_baseline",
 
+          "type": "t",
 
+          "weights": [
 
+            0.5,
 
+            0.5
 
+          ]
 
+        }
 
+      ],
 
+      "dummy_contrasts": {
 
+        "conditions": [
 
+          "trial_type.word",
 
+          "trial_type.pseudoword"
 
+        ],
 
+        "type": "t"
 
+      },
 
+      "level": "run",
 
+      "model": {
 
+        "x": [
 
+          "trial_type.word",
 
+          "trial_type.pseudoword",
 
+          "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"
 
+        ]
 
+      },
 
+      "transformations": [
 
+        {
 
+          "input": [
 
+            "trial_type"
 
+          ],
 
+          "name": "Factor"
 
+        },
 
+        {
 
+          "input": [
 
+            "trial_type.word",
 
+            "trial_type.pseudoword"
 
+          ],
 
+          "model": "spm",
 
+          "name": "Convolve"
 
+        }
 
+      ]
 
+    },
 
+    {
 
+      "dummy_contrasts": {
 
+        "type": "FEMA"
 
+      },
 
+      "level": "subject"
 
+    },
 
+    {
 
+      "contrasts": [
 
+        {
 
+          "condition_list": [
 
+            "trial_type.word",
 
+            "trial_type.pseudoword"
 
+          ],
 
+          "name": "any_words",
 
+          "type": "F",
 
+          "weights": [
 
+            [
 
+              1,
 
+              0
 
+            ],
 
+            [
 
+              0,
 
+              1
 
+            ]
 
+          ]
 
+        }
 
+      ],
 
+      "dummy_contrasts": {
 
+        "conditions": [
 
+          "word_gt_pseudo",
 
+          "task_vs_baseline"
 
+        ],
 
+        "type": "t"
 
+      },
 
+      "level": "dataset"
 
+    }
 
+  ]
 
+}</pre>
 
+        </details>
 
+
 
+        <!-- { % for step in steps % } -->
 
+        
+        <h2>Run level</h2>
 
+
 
+        <!-- { % if loop.first %} -->
 
+        <h3>Design matrices</h3>
 
+        <p>A design matrix was generated for each run. All but the
 
+        first are collapsed, but each should be inspected for correctness.
 
+        
+        <details open>
 
+        <summary class="heading-1">Subject: 01, Task: rhymejudgment</summary>
 
+        <div class="warning">
 
+    The following confounds had NaN values for the first volume: framewise_displacement.
 
+    The mean of non-zero values for the remaining entries was imputed.
 
+    If another strategy is desired, it must be explicitly specified in
 
+    the model.
 
+</div>
 
+
 
+        <img src="sub-01/figures/sub-01_task-rhymejudgment_design.svg" />
 
+        <h4>Correlation matrix</h4>
 
+        
+        <p>The correlation matrix of a design matrix shows the correlation between
 
+        each pair of regressors. Very high or low correlations among variables of
 
+        interest (top left) or between variables of interest and nuisance regressors
 
+        (top right) can indicate deficiency in the design. High correlations among
 
+        nuisance regressors will generally have little effect on the model.
 
+        </p>
 
+        
+        <img src="sub-01/figures/sub-01_task-rhymejudgment_corr.svg" />
 
+        </details>
 
+        
+        <details>
 
+        <summary><em>...</em></summary>
 
+        
+        
+        <details>
 
+        <summary class="heading-1">Subject: 02, Task: rhymejudgment</summary>
 
+        <div class="warning">
 
+    The following confounds had NaN values for the first volume: framewise_displacement.
 
+    The mean of non-zero values for the remaining entries was imputed.
 
+    If another strategy is desired, it must be explicitly specified in
 
+    the model.
 
+</div>
 
+
 
+        <img src="sub-02/figures/sub-02_task-rhymejudgment_design.svg" />
 
+        <h4>Correlation matrix</h4>
 
+        
+        <img src="sub-02/figures/sub-02_task-rhymejudgment_corr.svg" />
 
+        </details>
 
+        
+        
+        <details>
 
+        <summary class="heading-1">Subject: 03, Task: rhymejudgment</summary>
 
+        <div class="warning">
 
+    The following confounds had NaN values for the first volume: framewise_displacement.
 
+    The mean of non-zero values for the remaining entries was imputed.
 
+    If another strategy is desired, it must be explicitly specified in
 
+    the model.
 
+</div>
 
+
 
+        <img src="sub-03/figures/sub-03_task-rhymejudgment_design.svg" />
 
+        <h4>Correlation matrix</h4>
 
+        
+        <img src="sub-03/figures/sub-03_task-rhymejudgment_corr.svg" />
 
+        </details>
 
+        
+        
+        </details>
 
+        <!-- { % endif %} -->
 
+
 
+        <h3>Contrasts</h3>
 
+        <p>A contrast matrix was generated for each run. Except
 
+        in very rare cases, these should be identical, so these should be
 
+        inspected to ensure no unexpected differences are present.</p>
 
+        
+        <details open>
 
+        <summary class="heading-1">Subject: 01, Task: rhymejudgment</summary>
 
+        <img src="sub-01/figures/sub-01_task-rhymejudgment_contrasts.svg" />
 
+        </details>
 
+        
+        <details>
 
+        <summary><em>...</em></summary>
 
+        
+        
+        <details>
 
+        <summary class="heading-1">Subject: 02, Task: rhymejudgment</summary>
 
+        <img src="sub-02/figures/sub-02_task-rhymejudgment_contrasts.svg" />
 
+        </details>
 
+        
+        
+        <details>
 
+        <summary class="heading-1">Subject: 03, Task: rhymejudgment</summary>
 
+        <img src="sub-03/figures/sub-03_task-rhymejudgment_contrasts.svg" />
 
+        </details>
 
+        
+        
+        </details>
 
+
 
+        <!-- { % endfor %} -->
 
+    </div>
 
+    <div id="contrasts">
 
+        <h1 class="sub-report-title">Contrasts</h1>
 
+
 
+        
+        <h2>Run level</h2>
 
+        
+        <h3>Subject: 01, Task: rhymejudgment</h3>
 
+        
+        <h4>word &gt; pseudo</h4>
 
+        
+        <img src="sub-01/figures/sub-01_task-rhymejudgment_space-MNI152NLin2009cAsym_contrast-wordGtPseudo_stat-FEMA_ortho.png" />
 
+        
+        
+        <h4>task vs. baseline</h4>
 
+        
+        <img src="sub-01/figures/sub-01_task-rhymejudgment_space-MNI152NLin2009cAsym_contrast-taskVsBaseline_stat-FEMA_ortho.png" />
 
+        
+        
+        <h4>trial_type.word</h4>
 
+        
+        <p> Missing contrast skipped (used: <code>--drop-missing</code>) </p>
 
+        
+        
+        <h4>trial_type.pseudoword</h4>
 
+        
+        <p> Missing contrast skipped (used: <code>--drop-missing</code>) </p>
 
+        
+        
+        
+        <h3>Subject: 02, Task: rhymejudgment</h3>
 
+        
+        <h4>word &gt; pseudo</h4>
 
+        
+        <img src="sub-02/figures/sub-02_task-rhymejudgment_space-MNI152NLin2009cAsym_contrast-wordGtPseudo_stat-FEMA_ortho.png" />
 
+        
+        
+        <h4>task vs. baseline</h4>
 
+        
+        <img src="sub-02/figures/sub-02_task-rhymejudgment_space-MNI152NLin2009cAsym_contrast-taskVsBaseline_stat-FEMA_ortho.png" />
 
+        
+        
+        <h4>trial_type.word</h4>
 
+        
+        <p> Missing contrast skipped (used: <code>--drop-missing</code>) </p>
 
+        
+        
+        <h4>trial_type.pseudoword</h4>
 
+        
+        <p> Missing contrast skipped (used: <code>--drop-missing</code>) </p>
 
+        
+        
+        
+        <h3>Subject: 03, Task: rhymejudgment</h3>
 
+        
+        <h4>word &gt; pseudo</h4>
 
+        
+        <img src="sub-03/figures/sub-03_task-rhymejudgment_space-MNI152NLin2009cAsym_contrast-wordGtPseudo_stat-FEMA_ortho.png" />
 
+        
+        
+        <h4>task vs. baseline</h4>
 
+        
+        <img src="sub-03/figures/sub-03_task-rhymejudgment_space-MNI152NLin2009cAsym_contrast-taskVsBaseline_stat-FEMA_ortho.png" />
 
+        
+        
+        <h4>trial_type.word</h4>
 
+        
+        <p> Missing contrast skipped (used: <code>--drop-missing</code>) </p>
 
+        
+        
+        <h4>trial_type.pseudoword</h4>
 
+        
+        <p> Missing contrast skipped (used: <code>--drop-missing</code>) </p>
 
+        
+        
+        
+        
+        <h2>Subject level</h2>
 
+        
+        <h3>Subject: 01, Task: rhymejudgment</h3>
 
+        
+        <h4>task vs. baseline</h4>
 
+        
+        <img src="sub-01/figures/sub-01_task-rhymejudgment_space-MNI152NLin2009cAsym_contrast-taskVsBaseline_stat-FEMA_ortho.png" />
 
+        
+        
+        <h4>trial_type.pseudoword</h4>
 
+        
+        <p> Missing contrast skipped (used: <code>--drop-missing</code>) </p>
 
+        
+        
+        <h4>trial_type.word</h4>
 
+        
+        <p> Missing contrast skipped (used: <code>--drop-missing</code>) </p>
 
+        
+        
+        <h4>word &gt; pseudo</h4>
 
+        
+        <img src="sub-01/figures/sub-01_task-rhymejudgment_space-MNI152NLin2009cAsym_contrast-wordGtPseudo_stat-FEMA_ortho.png" />
 
+        
+        
+        
+        <h3>Subject: 02, Task: rhymejudgment</h3>
 
+        
+        <h4>task vs. baseline</h4>
 
+        
+        <img src="sub-02/figures/sub-02_task-rhymejudgment_space-MNI152NLin2009cAsym_contrast-taskVsBaseline_stat-FEMA_ortho.png" />
 
+        
+        
+        <h4>trial_type.pseudoword</h4>
 
+        
+        <p> Missing contrast skipped (used: <code>--drop-missing</code>) </p>
 
+        
+        
+        <h4>trial_type.word</h4>
 
+        
+        <p> Missing contrast skipped (used: <code>--drop-missing</code>) </p>
 
+        
+        
+        <h4>word &gt; pseudo</h4>
 
+        
+        <img src="sub-02/figures/sub-02_task-rhymejudgment_space-MNI152NLin2009cAsym_contrast-wordGtPseudo_stat-FEMA_ortho.png" />
 
+        
+        
+        
+        <h3>Subject: 03, Task: rhymejudgment</h3>
 
+        
+        <h4>task vs. baseline</h4>
 
+        
+        <img src="sub-03/figures/sub-03_task-rhymejudgment_space-MNI152NLin2009cAsym_contrast-taskVsBaseline_stat-FEMA_ortho.png" />
 
+        
+        
+        <h4>trial_type.pseudoword</h4>
 
+        
+        <p> Missing contrast skipped (used: <code>--drop-missing</code>) </p>
 
+        
+        
+        <h4>trial_type.word</h4>
 
+        
+        <p> Missing contrast skipped (used: <code>--drop-missing</code>) </p>
 
+        
+        
+        <h4>word &gt; pseudo</h4>
 
+        
+        <img src="sub-03/figures/sub-03_task-rhymejudgment_space-MNI152NLin2009cAsym_contrast-wordGtPseudo_stat-FEMA_ortho.png" />
 
+        
+        
+        
+        
+        <h2>Dataset level</h2>
 
+        
+        <h3>Task: rhymejudgment</h3>
 
+        
+        <h4>any_words</h4>
 
+        
+        <img src="figures/task-rhymejudgment_space-MNI152NLin2009cAsym_contrast-anyWords_stat-F_ortho.png" />
 
+        
+        
+        <h4>word &gt; pseudo</h4>
 
+        
+        <img src="figures/task-rhymejudgment_space-MNI152NLin2009cAsym_contrast-wordGtPseudo_stat-t_ortho.png" />
 
+        
+        
+        <h4>task vs. baseline</h4>
 
+        
+        <img src="figures/task-rhymejudgment_space-MNI152NLin2009cAsym_contrast-taskVsBaseline_stat-t_ortho.png" />
 
+        
+        
+        
+        
+    </div>
 
+    <div id="about">
 
+        <h1 class="sub-report-title">About</h1>
 
+        <ul>
 
+            <li>Fitlins version: 0.8.0+74.g9440822.dirty</li>
 
+            <li>Fitlins command: <tt>/data/MBDU/midla/env/bin/fitlins ds003/ds003_fmriprep/sourcedata ds003/afni_smooth/out dataset -d ds003/ds003_fmriprep/ -m /data/MBDU/nielsond/dccc2019/try_gnode/fitlins_tests/ds003/models/model-001_smdl.json -w /lscratch/6790822/afni_smooth --participant-label 01 02 03 --space MNI152NLin2009cAsym --estimator afni --n-cpus 8 --mem-gb 8 -vv -s 10.0:l1:iso</tt></li>
 
+            <li>Date processed: 2021-01-28 12:20:19 -0500</li>
 
+        </ul>
 
+    </div>
 
+</body>
 
+</html>

+ 870 - 0
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Просмотреть файл 

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Просмотреть файл 

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Просмотреть файл 

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Просмотреть файл 

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Просмотреть файл 

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Просмотреть файл 

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Просмотреть файл 

@@ -0,0 +1,161 @@
 
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