|
22 | 22 | "cell_type": "markdown", |
23 | 23 | "metadata": {}, |
24 | 24 | "source": [ |
25 | | - "# Imports\n", |
| 25 | + "## Imports\n", |
26 | 26 | "\n", |
27 | 27 | "First, we need to import all modules we later want to use." |
28 | 28 | ] |
|
49 | 49 | "cell_type": "markdown", |
50 | 50 | "metadata": {}, |
51 | 51 | "source": [ |
52 | | - "# Experiment parameters\n", |
| 52 | + "## Experiment parameters\n", |
53 | 53 | "\n", |
54 | 54 | "It's always a good idea to specify all parameters that might change between experiments at the beginning of your script." |
55 | 55 | ] |
|
83 | 83 | "cell_type": "markdown", |
84 | 84 | "metadata": {}, |
85 | 85 | "source": [ |
86 | | - "# Specify Nodes\n", |
| 86 | + "## Specify Nodes\n", |
87 | 87 | "\n", |
88 | 88 | "Initiate all the different interfaces (represented as nodes) that you want to use in your workflow." |
89 | 89 | ] |
|
123 | 123 | "cell_type": "markdown", |
124 | 124 | "metadata": {}, |
125 | 125 | "source": [ |
126 | | - "# Specify GLM contrasts\n", |
| 126 | + "## Specify GLM contrasts\n", |
127 | 127 | "\n", |
128 | 128 | "To do any GLM analysis, we need to also define the contrasts that we want to investigate. If we recap, we had three different conditions in the **fingerfootlips** task in this dataset:\n", |
129 | 129 | "\n", |
|
164 | 164 | "cell_type": "markdown", |
165 | 165 | "metadata": {}, |
166 | 166 | "source": [ |
167 | | - "# Specify GLM Model\n", |
| 167 | + "## Specify GLM Model\n", |
168 | 168 | "\n", |
169 | 169 | "The next step is now to get information such as stimuli onset, duration and other regressors into the GLM model. For this we need to create a helper function, in our case called ``subjectinfo``.\n", |
170 | 170 | "\n", |
|
482 | 482 | "cell_type": "markdown", |
483 | 483 | "metadata": {}, |
484 | 484 | "source": [ |
485 | | - "# Specify input & output stream\n", |
| 485 | + "## Specify input & output stream\n", |
486 | 486 | "\n", |
487 | 487 | "Specify where the input data can be found & where and how to save the output data." |
488 | 488 | ] |
|
535 | 535 | "cell_type": "markdown", |
536 | 536 | "metadata": {}, |
537 | 537 | "source": [ |
538 | | - "# Specify Workflow\n", |
| 538 | + "## Specify Workflow\n", |
539 | 539 | "\n", |
540 | 540 | "Create a workflow and connect the interface nodes and the I/O stream to each other." |
541 | 541 | ] |
|
586 | 586 | "cell_type": "markdown", |
587 | 587 | "metadata": {}, |
588 | 588 | "source": [ |
589 | | - "# Visualize the workflow\n", |
| 589 | + "## Visualize the workflow\n", |
590 | 590 | "\n", |
591 | 591 | "It always helps to visualize your workflow." |
592 | 592 | ] |
|
629 | 629 | "cell_type": "markdown", |
630 | 630 | "metadata": {}, |
631 | 631 | "source": [ |
632 | | - "# Run the Workflow\n", |
| 632 | + "## Run the Workflow\n", |
633 | 633 | "\n", |
634 | 634 | "Now that everything is ready, we can run the 1st-level analysis workflow. Change ``n_procs`` to the number of jobs/cores you want to use." |
635 | 635 | ] |
|
649 | 649 | "cell_type": "markdown", |
650 | 650 | "metadata": {}, |
651 | 651 | "source": [ |
652 | | - "# Inspect output\n", |
| 652 | + "## Inspect output\n", |
653 | 653 | "\n", |
654 | 654 | "Let's check the structure of the output folder, to see if we have everything we wanted to save. You should have nine contrast images (``con_*.nii`` for T-contrasts and ``ess_*.nii`` for T-contrasts) and nine statistic images (``spmT_*.nii`` and ``spmF_*.nii``) for every subject and smoothing kernel." |
655 | 655 | ] |
|
721 | 721 | "cell_type": "markdown", |
722 | 722 | "metadata": {}, |
723 | 723 | "source": [ |
724 | | - "# Visualize results\n", |
| 724 | + "## Visualize results\n", |
725 | 725 | "\n", |
726 | 726 | "Let's look at the contrasts of one subject that we've just computed. First, let's see what the difference of smoothing is for the contrast **`average`**" |
727 | 727 | ] |
|
907 | 907 | "cell_type": "markdown", |
908 | 908 | "metadata": {}, |
909 | 909 | "source": [ |
910 | | - "# Special case\n", |
| 910 | + "## Special case\n", |
911 | 911 | "\n", |
912 | 912 | "There is something special with the **Finger** contrast in all subjects. So let's take a look at all of them." |
913 | 913 | ] |
|
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