From 9bd722f3feb19b1cb759cbb904ec8daf7434ebdc Mon Sep 17 00:00:00 2001
From: Jon Tamir <jtamir@eecs.berkeley.edu>
Date: Mon, 15 Oct 2018 14:35:45 -0700
Subject: [PATCH] use squeeze instead of reshape

---
 demos/pics-phantom/demo.md | 8 ++------
 demos/pics-phantom/demo.sh | 4 +---
 2 files changed, 3 insertions(+), 9 deletions(-)

diff --git a/demos/pics-phantom/demo.md b/demos/pics-phantom/demo.md
index 9974d31..a717e56 100755
--- a/demos/pics-phantom/demo.md
+++ b/demos/pics-phantom/demo.md
@@ -38,11 +38,6 @@ dim=256 # ky/kz dims
 bart phantom -x $dim -k -s $nmaps ksp_orig
 ```
 
-To match to the MRI-specific tools, we tranpose the spatial dimensions
-```
-bart reshape 7 1 $dim $dim ksp_orig ksp_orig
-```
-
 Add noise
 ```bash
 noisevar=100
@@ -57,12 +52,13 @@ rmcfl cimg_noise
 ```
 
 Create a variable density Poisson disc sampling pattern and sample k-space. The acceleration factor is given by `yaccel` and `zaccel`.
-A fully sampled calibration region of size `caldim` is added.
+A fully sampled calibration region of size `caldim` is added. To match the 2D k-space dimensions, we will remove singleton dimensions.
 ```bash
 yaccel=1.5
 zaccel=1.5
 caldim=32
 bart poisson -Y $dim -Z $dim -y $yaccel -z $zaccel -C $caldim -v -e mask
+bart squeeze mask mask
 bart fmac ksp_noise mask ksp_und
 ```
 
diff --git a/demos/pics-phantom/demo.sh b/demos/pics-phantom/demo.sh
index 7a74ba4..c5247cc 100755
--- a/demos/pics-phantom/demo.sh
+++ b/demos/pics-phantom/demo.sh
@@ -40,9 +40,6 @@ nmaps=8
 bart phantom -x $dim -k -s $nmaps ksp_orig
 
 
-# To match to the MRI-specific tools, we reshape the spatial dimensions
-bart reshape 7 1 $dim $dim ksp_orig ksp_orig
-
 # Add noise
 noisevar=100
 bart noise -n $noisevar ksp_orig ksp_noise
@@ -58,6 +55,7 @@ yaccel=1.5
 zaccel=1.5
 caldim=32
 bart poisson -Y $dim -Z $dim -y $yaccel -z $zaccel -C $caldim -v -e mask
+bart squeeze mask mask
 bart fmac ksp_noise mask ksp_und
 
 # View the mask