Skip to content

Commit

Permalink
enh: add information about the outputs of the different sequences to …
Browse files Browse the repository at this point in the history
…better explain the procedure
  • Loading branch information
helenelajous committed May 25, 2023
1 parent f15155a commit c7db90a
Showing 1 changed file with 7 additions and 6 deletions.
13 changes: 7 additions & 6 deletions docs/data-collection/scanning.md
Original file line number Diff line number Diff line change
Expand Up @@ -20,12 +20,12 @@

![launch_sequence.jpg](../assets/images/launch_sequence.jpg)

- [ ] Once the scout is finished, you can drag the localizer into the scan viewing window by draging the three superposed squares next to the sequence name to check its quality. A localizer of bad quality will present noise in the background. If the localizer is not ok, unplug and replug the head coil and reacquire the AAhead_scout sequence.
- [ ] Once the scout is finished, you can drag the corresponding images (four superposed squares next to the sequence name that correspond to the images actually acquired in a sagittal view, and the interpolated images in the strict coronal, sagittal and transverse planes) to the MR image viewer to check their quality. A localizer of bad quality will present noise in the background. If the localizer is not ok, unplug and replug the head coil and reacquire the AAhead_scout sequence.

![drag_t1w.jpg](../assets/images/drag_t1w.jpg)

- [ ] Launch the T1w by pressing `Go`.
- [ ] While you run the T1w, there are a few important points to address:
- [ ] Launch the T1-weighted MPRAGE sequence by pressing `Go`.
- [ ] While you run the MPRAGE sequence, there are a few important points to address:


!!!warning "Important"
Expand All @@ -34,15 +34,16 @@
- [ ] Open the DWI sequence and under the section [WHAT?], uncheck all the derivatives except `Diffusion weighted image`.

!!!note "Essentials for running an MRI session"
Once the T1w is finished, you can drag the T1w into the scan viewing window. This will allow to tweek the field-of-view (FOV) for the DWI and BOLD sequences.
Once the T1-weighted sequence is finished, you can drag the corresponding high-resolution images to the MR image viewer. This will allow to position the field-of-view (FOV) for the DWI and BOLD sequences more accurately than the initial scout.

- [ ] Open the next sequence by double clicking on it.
- [ ] Make sure that the FOV (yellow square) includes the whole brain by tilting or translating the FOV. If the full brain, including the cerebellum, do not fit in the FOV, favorise making sure that the cortex is fully enclosed in the yellow square. For reproduciblity, it is better if the FOV across sequences have a similar center and a similar tilt. However, if it is not possible, the priority remains to include the whole brain in the FOV.
- [ ] If two sequences have the same resolution and the same number of slices, you can copy paste the FOV
- [ ] Right click on the sequence for which the FOV was set
- [ ] Open the sequence for which you want to adjust the FOV/geometry
- [ ] Right click on the sequence for which the FOV has already been carefully positioned
- [ ] Select `Copy Parameters`
- [ ] `Center [WHAT WAS THE NAME]`
- [ ] Once the FOV is well placed, launch the sequence by pressing `Go`.
- [ ] Once the FOV is well positioned, launch the sequence by pressing `Go`.

![adjustFOV.jpg](../assets/images/adjustFOV.jpg)

Expand Down

0 comments on commit c7db90a

Please sign in to comment.