diff --git a/content/haxby_data.md b/content/haxby_data.md index 96d0673..4086e4b 100644 --- a/content/haxby_data.md +++ b/content/haxby_data.md @@ -220,13 +220,13 @@ and of course, this also works for `interactive` plots. plotting.view_img(func_image_mean, cmap='magma', symmetric_cmap=False) ``` -The last type of `neuroimaging` file we need to check are the (`binary`) `masks`, so let's do it for one example `mask`: the `ventral temporal cortex`. This mask has been generated as part of the Haxby et al. (2001) study {cite:p}`Haxby2001-vt`, and highlights a part of the brain specialized in the processing of visual information, and which contains areas sensitive to different types of image categories {cite:p}`grill-spector_functional_2014` . As with the types before, we can `load`, +The last type of `neuroimaging` file we need to check are the (`binary`) `masks`, so let's do it for one example `mask`: the `ventral temporal cortex`. This mask has been generated as part of the Haxby et al. (2001) study {cite:p}`Haxby2001-vt`, and highlights a part of the brain specialized in the processing of visual information, and which contains areas sensitive to different types of image categories {cite:p}`grill-spector_functional_2014` . As with the types before, we can `load`, ```{code-cell} ipython3 vt_mask = load_img(haxby_dataset.mask_vt) ``` -`inspect` +`inspect` ```{code-cell} ipython3 print(vt_mask.header) @@ -240,7 +240,7 @@ vt_mask.get_data() vt_mask.dataobj.shape ``` -and `visualize` it (Here, we are going to plot it as an overlay on the `anatomical image`). +and `visualize` it (Here, we are going to plot it as an overlay on the `anatomical image`). ```{code-cell} ipython3 plotting.plot_roi(vt_mask, bg_img=anat_image, @@ -311,7 +311,8 @@ If you have any questions, please don't hesitate to ask us. Thank you very much ```{bibliography} :filter: docname in docnames ``` -``` + ++++ +++ @@ -319,8 +320,6 @@ If you have any questions, please don't hesitate to ask us. Thank you very much As you saw above, our `tutorial dataset` actually also contains the `stimuli` utilized in the experiment. This pretty unique (because of e.g. copyright problems) but really cool. As we could use the `stimuli` for certain analyses, e.g. [encoding]() and/or comparing their processing in `biological` and `artificial neural networks`. However, this is unfortunately outside the scope of this session. Thus, we are just going to plot a few of them so you get an impression. -+++ - We can examine one functional volume using nilearn's plotting tools. Because fmri data are 4D we use [nilearn.image.mean_img](https://nilearn.github.io/modules/generated/nilearn.image.mean_img.html#nilearn.image.mean_img) to extract the average brain volume. ```{code-cell} ipython3