adds more clarity on data path preparation in relevant sections of itksnap and setup

Author: mxochicale

episodes/itksnap.Rmd

@@ -31,48 +31,56 @@ We are using CT Ventilation as a Functional Imaging Modality for Lung Cancer Rad
 The CT-vs-PET-Ventilation-Imaging collection is distributed under the Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/). 
 The `CT-vs-PET-Ventilation-Imaging` dataset contains 20 lung cancer patients underwent exhale/inhale breath hold CT (BHCT), free-breathing four-dimensional CT (4DCT) and Galligas PET ventilation scans in a single session on a combined 4DPET/CT scanner.    
 
-We recommend using the BHCT scans for participants `CT-PET-VI-02` and `CT-PET-VI-03` showing very little motion between inhale and exhale (for PET scan and accompanying CT scan), and BHCT scans for participants `CT-PET-VI-05` and `CT-PET-VI-07` (the inhale and exhale CT scans), where 05 has a different number of slices between the inhale and exhale:
+We recommend using the BHCT scans for participants `CT-PET-VI-02` and `CT-PET-VI-03` showing very little motion between inhale and exhale (for PET scan and accompanying CT scan), and BHCT scans for participants `CT-PET-VI-05` and `CT-PET-VI-07` (the inhale and exhale CT scans), where 05 has a different number of slices between the inhale and exhale.
+
+Data paths contain:
+* `inhale_BH_CT` and `exhale_BH_CT` contain CT scans acquired during an inhalation breath hold and exhalation breath hold respectively.
+* `PET` contains a PET scan that measures the local lung function, 
+* `CT_for_PET` contains a CT scan acquired at the same time as the PET scan for attenuation correction of the PET scan and to provide anatomical reference for the PET data.
+
 
 * CT-PET-VI-02
 ```bash
-CT-PET-VI-02$ tree -d
-.
-└── 05-28-1996-RTRTRespLowBreathRateRNS Adult-05441
-    ├── 3.000000-CT Lung  3.0  B31f-61322
-    ├── 4.000000-Galligas Lung-03537
+├── CT-PET-VI-02
+│   ├── CT_for_PET
+│   ├── exhale_BH_CT
+│   ├── inhale_BH_CT
+│   └── PET
 ```
 
 * CT-PET-VI-03
 ```bash
 /CT-PET-VI-03$ tree -d
-.
-├── 06-25-1996-RTRTRespLowBreathRateRNS Adult-43080
-│   ├── 3.000000-CT Lung  3.0  B31f-08354
-│   └── 4.000000-Galligas Lung-15379
+├── CT-PET-VI-03
+│   ├── CT_for_PET
+│   └── PET
 ```
 
 * CT-PET-VI-05
 
 ```bash
 CT-PET-VI-05$ tree -d
 .
-└── 12-10-1996-RTRTRespLowBreathRateRNS Adult-37585
-    ├── 5.000000-Thorax Insp  2.0  B70f-45546
-    ├── 7.000000-Thorax Exp  2.0  B70f-31579
+├── CT-PET-VI-05
+│   ├── CT_for_PET
+│   ├── exhale_BH_CT
+│   ├── inhale_BH_CT
+│   └── PET
 ```
 
 * CT-PET-VI-07
 ```bash
 /CT-PET-VI-07$ tree -d
 .
-└── 02-14-1997-RTRTRespLowBreathRateRNS Adult-80512
-    ├── 5.000000-Thorax Insp  2.0  B70f-20440
-    ├── 7.000000-Thorax Exp  2.0  B70f-03567
+└── CT-PET-VI-07
+    ├── exhale_BH_CT
+    ├── inhale_BH_CT
+    └── PET
 ```
 
-Refer to `Summary and Setup` section for further details on CT-vs-PET-Ventilation-Imaging dataset.
+Refer to [`Summary and Setup`](https://healthbioscienceideas.github.io/Medical-Image-Registration-Short-Course/#data-sets) section for further details on CT-vs-PET-Ventilation-Imaging dataset.
 
-For examples in this episode, we are going to use DICOM data "CT-PET-VI-02/3.000000-CT Lung 3.0 B31f-61322" but others can be used!
+For examples in this episode, we are going to use DICOM data `CT-PET-VI-02/CT_forPET` but others can be used.
 
 ![Figure. CT-PET-VI-02 dataset](fig/CT-PET-VI-02.png)
 

learners/setup.md

@@ -22,13 +22,23 @@ Download the [data zip file](https://example.com/FIXME) and unzip it to your Des
 
 ### CT-vs-PET-Ventilation-Imaging 
 CT Ventilation as a Functional Imaging Modality for Lung Cancer Radiotherapy from [TCIA](https://www.cancerimagingarchive.net/collection/ct-vs-pet-ventilation-imaging/).
-We recomend to focus on exhale/inhale breath hold CT (BHCT) Dicoms which belog to: 
+We recomend to focus on exhale/inhale breath hold CT (BHCT) Dicoms. 
+Bare in mind that:
 * The BHCT scans for CT-PET-VI-02 & CT-PET-VI-03 show very little motion between inhale and exhale
 * The BHCT scans for CT-PET-VI-05 have a different number of slices between the inhale and exhale
 
-
-Data paths look like these:
+#### Extracting and renaming data paths
+Original data directory paths for this work were renamed for easy interpretability as follows:
+```callout
+`5.000000-Thorax Insp 2.0 B*` ranamed as `inhale_BH_CT`
+`7.000000-Thorax Exp 2.0 B*` renamed as `exhale_BH_CT`
+`3.000000-CT Lung 3.0 B*` ranamed as `CT_for_PET`
+`4.000000-Galligas Lung-0*` renamed as `PET`
 ```
+
+See how the original data paths and renamed look like
+```bash
+#Original directory paths
 /CT-PET-VI-02$ tree -d 
 .
 ├── 1000.000000-PET SUV Factors-26496 [1 item, with size 42.1 kB]
@@ -37,7 +47,18 @@ Data paths look like these:
 ├── 5.000000-Thorax Insp  2.0  B70f-29873 [167 items, totalling 88.1 MB]
 ├── 7.000000-Thorax Exp  2.0  B70f-73355 [167 items, totalling 88.1 MB]
 └── 8.000000-RespLow  2.0  B30s  80  Ex - 100  In-44317 [810 items, totalling 426.9 MB]
+#Renamed directory paths
+.
+├── CT-PET-VI-02
+│   ├── CT_for_PET
+│   ├── exhale_BH_CT
+│   ├── inhale_BH_CT
+│   └── PET
+
 
+
+
+#Original directory paths
 /CT-PET-VI-03$ tree -d
 .
 ├── 06-25-1996-RTRTRespLowBreathRateRNS Adult-43080
@@ -48,7 +69,16 @@ Data paths look like these:
     ├── 5.000000-Thorax Insp  2.0  B70f-42000
     ├── 7.000000-Thorax Exp  2.0  B70f-45310
     └── 8.000000-RespLow  2.0  B30s  80  Ex - 100  In-54790
+#Renamed directory paths for `06-25-1996-RTRTRespLowBreathRateRNS Adult-43080`
+├── CT-PET-VI-03
+│   ├── CT_for_PET
+│   └── PET
+
+
 
+
+
+#Original directory paths
 /CT-PET-VI-05$ tree -d
 └── 12-10-1996-RTRTRespLowBreathRateRNS Adult-37585
     ├── 1000.000000-PET SUV Factors-63910
@@ -57,6 +87,31 @@ Data paths look like these:
     ├── 5.000000-Thorax Insp  2.0  B70f-45546
     ├── 7.000000-Thorax Exp  2.0  B70f-31579
     └── 8.000000-RespLow  2.0  B30s  80  Ex - 100  In-16454
+#Renamed directory paths
+├── CT-PET-VI-05
+│   ├── CT_for_PET
+│   ├── exhale_BH_CT
+│   ├── inhale_BH_CT
+│   └── PET
+
+
+
+
+
+#Original directory paths
+/CT-PET-VI-07$ tree -d
+.
+└── 02-14-1997-RTRTRespLowBreathRateRNS Adult-80512
+    ├── 1000.000000-PET SUV Factors-99730
+    ├── 4.000000-Galligas Lung-82849
+    ├── 5.000000-Thorax Insp  2.0  B70f-20440
+    ├── 7.000000-Thorax Exp  2.0  B70f-03567
+    └── 8.000000-RespLow  2.0  B30s  80  Ex - 100  In-01782
+#Renamed directory paths
+└── CT-PET-VI-07
+    ├── exhale_BH_CT
+    ├── inhale_BH_CT
+    └── PET
 ```