Skip to content

Commit 8c97ad7

Browse files
committed
update haxby section
1 parent 9dc237c commit 8c97ad7

1 file changed

Lines changed: 5 additions & 6 deletions

File tree

content/haxby_data.md

Lines changed: 5 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -220,13 +220,13 @@ and of course, this also works for `interactive` plots.
220220
plotting.view_img(func_image_mean, cmap='magma', symmetric_cmap=False)
221221
```
222222

223-
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`,
223+
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`,
224224

225225
```{code-cell} ipython3
226226
vt_mask = load_img(haxby_dataset.mask_vt)
227227
```
228228

229-
`inspect`
229+
`inspect`
230230

231231
```{code-cell} ipython3
232232
print(vt_mask.header)
@@ -240,7 +240,7 @@ vt_mask.get_data()
240240
vt_mask.dataobj.shape
241241
```
242242

243-
and `visualize` it (Here, we are going to plot it as an overlay on the `anatomical image`).
243+
and `visualize` it (Here, we are going to plot it as an overlay on the `anatomical image`).
244244

245245
```{code-cell} ipython3
246246
plotting.plot_roi(vt_mask, bg_img=anat_image,
@@ -311,16 +311,15 @@ If you have any questions, please don't hesitate to ask us. Thank you very much
311311
```{bibliography}
312312
:filter: docname in docnames
313313
```
314-
```
314+
315+
+++
315316

316317
+++
317318

318319
## Bonus: checking the stimuli
319320

320321
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.
321322

322-
+++
323-
324323
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.
325324

326325
```{code-cell} ipython3

0 commit comments

Comments
 (0)