From d94be6de803603c0b363d4beb14af8d213004463 Mon Sep 17 00:00:00 2001 From: Martin Craig Date: Mon, 17 May 2021 12:23:24 +0100 Subject: [PATCH] Minor updates to data set names for qBOLD tutorial --- doc/qbold/tutorial.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/doc/qbold/tutorial.rst b/doc/qbold/tutorial.rst index c2c603a0..5dc1c11d 100644 --- a/doc/qbold/tutorial.rst +++ b/doc/qbold/tutorial.rst @@ -128,7 +128,7 @@ 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 @@ -136,8 +136,8 @@ Click ``Run`` and an ROI should be generated covering the brain and displayed as .. 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 @@ -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