Skip to content

Commit

Permalink
Minor updates to data set names for qBOLD tutorial
Browse files Browse the repository at this point in the history
  • Loading branch information
mcraig-ibme committed May 17, 2021
1 parent 0599981 commit d94be6d
Showing 1 changed file with 4 additions and 4 deletions.
8 changes: 4 additions & 4 deletions doc/qbold/tutorial.rst
Original file line number Diff line number Diff line change
Expand Up @@ -128,16 +128,16 @@ Before brain extraction we will need to take the mean of the 4D data as Bet can
If you know Python and Numpy you will recognize this code - we can use any simple Numpy expression in the widget.

Now, from the ``Widgets`` menu select ``FSL->BET`` and then as input data choose the mean data we have just generated.
Check the ``Output brain mask`` option so we get a binary ROI mask for the brain.
Check the ``Output brain mask`` option so we get a binary ROI mask for the brain and change the intensity threshold value to 0.4.

.. image:: /screenshots/qbold/bet.png

Click ``Run`` and an ROI should be generated covering the brain and displayed as follows:

.. image:: /screenshots/qbold/brain.png

When viewing the output of modelling, it may be clearer if the ROI is displayed as an outline rather than a shaded
region. To do this, click on the icon to the right of the ROI selector (below the image view):
When viewing the output of modelling, it may be clearer if the ROI is displayed as an outline, as shown in this screenshot,
rather than a shaded region. To do this, click on the icon to the right of the ROI selector (below the image view):

.. image:: /screenshots/cest_tutorial_roi_contour.png

Expand Down Expand Up @@ -210,7 +210,7 @@ Data and sequence section
~~~~~~~~~~~~~~~~~~~~~~~~~

To begin with, make sure the ``sub-01_sqbold_gase_reg_smoothed`` data set is selected as the qBOLD data,
and the ``sub-01_sqbold_gase_bet_mask`` brain mask is selected as the ROI.
and the ``sub-01_sqbold_gase_mean_brain_mask`` brain mask is selected as the ROI.

Next we will specify the spin echo displacement times, or Taus - they represent the different
:math:`R_2^\prime` weightings acquired in the data set. You can enter them manually, or if they are stored in a
Expand Down

0 comments on commit d94be6d

Please sign in to comment.