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Create version 1.9.1, Plus a few small fixes #1504

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Create version 1.9.1, Plus a few small fixes #1504

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b02d2c3
1.9.1 changes to fix space-in-paths issue
Getkablue Sep 12, 2022
519303a
Update linux-makeself to avoid weirdness
Getkablue Sep 12, 2022
c8054fb
Update docs
Getkablue Sep 12, 2022
167b06b
Update docs
Getkablue Sep 12, 2022
0986e70
fixes to argument passing
Getkablue Sep 12, 2022
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54 changes: 54 additions & 0 deletions 3_HowToGuides.txt
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Expand Up @@ -616,6 +616,33 @@ This application provides the detection of EGFRvIII mutation status of <i>de nov
-# Co-registered Multimodal MRI: T1, T1-Gd, T2, T2-FLAIR, DTI-AX, DTI-FA, DTI-RAD, DTI-TR, DSC-PH, DSC-PSR, DSC-rCBV.
-# Segmentation labels of the tumor sub-regions: Non-enhancing tumor core (Label=1), Enhancing tumor core (Label=4), as well as the Edema (Label=2)
-# Segmentation labels in a common atlas space: Non-enhancing tumor core (Label=1), Enhancing tumor core (Label=4), Edema (Label=2), as well as the Ventricle (Label=7)

Standard Atlas reference:

Value | Region
--------|-------------
1 | Right frontal lobe
2 | Right temporal lobe
3 | Left temporal lobe
4 | Left thalamus
5 | Right parietal lobe
6 | Left insula
7 | Right basal ganglia
8 | Right occipital lobe
9 | Left basal ganglia
10 | corpus callosum
11 | Left frontal lobe
12 | Left parietal lobe
13 | Left occipital lobe
14 | brain stem
15 | Right thalamus
16 | Right fornix
17 | Left cingulate region
18 | Left fornix
19 | Right insula
20 | cerebellum
21 | Right cingulate region

-# Clinical data: A csv file having patient's demographics (Note that the CSV file should be in ASCII format). Should have age (in first column) and EGFRvIII status (in second column, binarized values like 0 and 1) for training a new model, and age only for mutation detection of new patients.
-# The data for each patient should be organized in the following directory structure. When running in the command-line, filenames must include words in <b>BOLD</b> to be identified as respective required files.
- Subject_ID
Expand Down Expand Up @@ -681,6 +708,33 @@ This application facilitates the users to generate population atlases for patien
<b>REQUIREMENTS:</b>
-# Segmentation labels of the tumor sub-regions: Non-enhancing tumor core (Label=1), Enhancing tumor core (Label=4)
-# Standard atlas: A standard atlas to map all the patients in a unified space. Atlas should have region numbers in the ascending order, such as 1,2,3,...,n.

Standard Atlas reference:

Value | Region
--------|-------------
1 | Right frontal lobe
2 | Right temporal lobe
3 | Left temporal lobe
4 | Left thalamus
5 | Right parietal lobe
6 | Left insula
7 | Right basal ganglia
8 | Right occipital lobe
9 | Left basal ganglia
10 | corpus callosum
11 | Left frontal lobe
12 | Left parietal lobe
13 | Left occipital lobe
14 | brain stem
15 | Right thalamus
16 | Right fornix
17 | Left cingulate region
18 | Left fornix
19 | Right insula
20 | cerebellum
21 | Right cingulate region

-# Batch File: A csv file having patients' IDs, group (atlas) number, and path to the actual segmented image. Atlas numbers should be in the ascending order, such as 1,2,3,...,n. Segmentation images should be in the same space as the standard atlas (Note that the CSV file should be in ASCII format, and the CSV file should have the following column headers in any sequence: PATIENT_IDS,IMAGES, ATLAS_LABELS).

<b>USAGE:</b>
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2 changes: 1 addition & 1 deletion CMakeLists.txt
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Expand Up @@ -13,7 +13,7 @@ SET( ${PROJECT_NAME}_Variant "Full" ) # the particular variant of CaPTk (Full/Ne

SET( PROJECT_VERSION_MAJOR 1 )
SET( PROJECT_VERSION_MINOR 9 )
SET( PROJECT_VERSION_PATCH 0 )
SET( PROJECT_VERSION_PATCH 1 )
SET( PROJECT_VERSION_TWEAK )

# check for the string "nonRelease" in the PROJECT_VERSION_PATCH variable
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6 changes: 3 additions & 3 deletions data/deepMedic/saved_models/brainTumorSegmentation/VERSION.yaml
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@@ -1,3 +1,3 @@
Version: 1.9.0
Minimum: 1.9.0
Maximum: 1.9.0
Version: 1.9.1
Minimum: 1.9.1
Maximum: 1.9.1
6 changes: 3 additions & 3 deletions data/deepMedic/saved_models/skullStripping/VERSION.yaml
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Version: 1.9.0
Minimum: 1.9.0
Maximum: 1.9.0
Version: 1.9.1
Minimum: 1.9.1
Maximum: 1.9.1
2 changes: 1 addition & 1 deletion docs/1_credits.html
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<br>
<img src="functionalityRepresentation.png"></center>
<br>
Cancer Imaging Phenomics Toolkit (CaPTk) v.1.9.0 &emsp;|&emsp;<b>Contact:</b> [email protected]
Cancer Imaging Phenomics Toolkit (CaPTk) v.1.9.1 &emsp;|&emsp;<b>Contact:</b> [email protected]
<br>
<b>Disclaimer:</b> CaPTk has been designed for non-commercial research purposes only and has not been reviewed or approved by the Food and Drug Administration (FDA). It is not intended or recommended for clinical application.
<br>
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2 changes: 1 addition & 1 deletion docs/BraTS_Metrics.html
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<tr style="height: 56px;">
<td id="projectalign" style="padding-left: 0.5em;">
<div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
&#160;<span id="projectnumber">1.9.0</span>
&#160;<span id="projectnumber">1.9.1</span>
</div>
</td>
</tr>
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2 changes: 1 addition & 1 deletion docs/BreastCancer_LIBRA.html
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<tr style="height: 56px;">
<td id="projectalign" style="padding-left: 0.5em;">
<div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
&#160;<span id="projectnumber">1.9.0</span>
&#160;<span id="projectnumber">1.9.1</span>
</div>
</td>
</tr>
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2 changes: 1 addition & 1 deletion docs/BreastCancer_breastSegmentation.html
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<tr style="height: 56px;">
<td id="projectalign" style="padding-left: 0.5em;">
<div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
&#160;<span id="projectnumber">1.9.0</span>
&#160;<span id="projectnumber">1.9.1</span>
</div>
</td>
</tr>
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2 changes: 1 addition & 1 deletion docs/BreastCancer_texture.html
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<tr style="height: 56px;">
<td id="projectalign" style="padding-left: 0.5em;">
<div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
&#160;<span id="projectnumber">1.9.0</span>
&#160;<span id="projectnumber">1.9.1</span>
</div>
</td>
</tr>
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2 changes: 1 addition & 1 deletion docs/Diffusion_Derivatives.html
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<tr style="height: 56px;">
<td id="projectalign" style="padding-left: 0.5em;">
<div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
&#160;<span id="projectnumber">1.9.0</span>
&#160;<span id="projectnumber">1.9.1</span>
</div>
</td>
</tr>
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2 changes: 1 addition & 1 deletion docs/Download.html
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<tr style="height: 56px;">
<td id="projectalign" style="padding-left: 0.5em;">
<div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
&#160;<span id="projectnumber">1.9.0</span>
&#160;<span id="projectnumber">1.9.1</span>
</div>
</td>
</tr>
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2 changes: 1 addition & 1 deletion docs/FAQ.html
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<tr style="height: 56px;">
<td id="projectalign" style="padding-left: 0.5em;">
<div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
&#160;<span id="projectnumber">1.9.0</span>
&#160;<span id="projectnumber">1.9.1</span>
</div>
</td>
</tr>
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2 changes: 1 addition & 1 deletion docs/Getting_Started.html
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<tr style="height: 56px;">
<td id="projectalign" style="padding-left: 0.5em;">
<div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
&#160;<span id="projectnumber">1.9.0</span>
&#160;<span id="projectnumber">1.9.1</span>
</div>
</td>
</tr>
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51 changes: 50 additions & 1 deletion docs/Glioblastoma_Atlas.html
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<tr style="height: 56px;">
<td id="projectalign" style="padding-left: 0.5em;">
<div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
&#160;<span id="projectnumber">1.9.0</span>
&#160;<span id="projectnumber">1.9.1</span>
</div>
</td>
</tr>
Expand Down Expand Up @@ -65,6 +65,55 @@
<p><b>REQUIREMENTS:</b></p><ol type="1">
<li>Segmentation labels of the tumor sub-regions: Non-enhancing tumor core (Label=1), Enhancing tumor core (Label=4)</li>
<li>Standard atlas: A standard atlas to map all the patients in a unified space. Atlas should have region numbers in the ascending order, such as 1,2,3,...,n.</li>
</ol>
<p>Standard Atlas reference:</p>
<table class="markdownTable">
<tr class="markdownTableHead">
<th class="markdownTableHeadNone">Value </th><th class="markdownTableHeadNone">Region </th></tr>
<tr class="markdownTableRowOdd">
<td class="markdownTableBodyNone">1 </td><td class="markdownTableBodyNone">Right frontal lobe </td></tr>
<tr class="markdownTableRowEven">
<td class="markdownTableBodyNone">2 </td><td class="markdownTableBodyNone">Right temporal lobe </td></tr>
<tr class="markdownTableRowOdd">
<td class="markdownTableBodyNone">3 </td><td class="markdownTableBodyNone">Left temporal lobe </td></tr>
<tr class="markdownTableRowEven">
<td class="markdownTableBodyNone">4 </td><td class="markdownTableBodyNone">Left thalamus </td></tr>
<tr class="markdownTableRowOdd">
<td class="markdownTableBodyNone">5 </td><td class="markdownTableBodyNone">Right parietal lobe </td></tr>
<tr class="markdownTableRowEven">
<td class="markdownTableBodyNone">6 </td><td class="markdownTableBodyNone">Left insula </td></tr>
<tr class="markdownTableRowOdd">
<td class="markdownTableBodyNone">7 </td><td class="markdownTableBodyNone">Right basal ganglia </td></tr>
<tr class="markdownTableRowEven">
<td class="markdownTableBodyNone">8 </td><td class="markdownTableBodyNone">Right occipital lobe </td></tr>
<tr class="markdownTableRowOdd">
<td class="markdownTableBodyNone">9 </td><td class="markdownTableBodyNone">Left basal ganglia </td></tr>
<tr class="markdownTableRowEven">
<td class="markdownTableBodyNone">10 </td><td class="markdownTableBodyNone">corpus callosum </td></tr>
<tr class="markdownTableRowOdd">
<td class="markdownTableBodyNone">11 </td><td class="markdownTableBodyNone">Left frontal lobe </td></tr>
<tr class="markdownTableRowEven">
<td class="markdownTableBodyNone">12 </td><td class="markdownTableBodyNone">Left parietal lobe </td></tr>
<tr class="markdownTableRowOdd">
<td class="markdownTableBodyNone">13 </td><td class="markdownTableBodyNone">Left occipital lobe </td></tr>
<tr class="markdownTableRowEven">
<td class="markdownTableBodyNone">14 </td><td class="markdownTableBodyNone">brain stem </td></tr>
<tr class="markdownTableRowOdd">
<td class="markdownTableBodyNone">15 </td><td class="markdownTableBodyNone">Right thalamus </td></tr>
<tr class="markdownTableRowEven">
<td class="markdownTableBodyNone">16 </td><td class="markdownTableBodyNone">Right fornix </td></tr>
<tr class="markdownTableRowOdd">
<td class="markdownTableBodyNone">17 </td><td class="markdownTableBodyNone">Left cingulate region </td></tr>
<tr class="markdownTableRowEven">
<td class="markdownTableBodyNone">18 </td><td class="markdownTableBodyNone">Left fornix </td></tr>
<tr class="markdownTableRowOdd">
<td class="markdownTableBodyNone">19 </td><td class="markdownTableBodyNone">Right insula </td></tr>
<tr class="markdownTableRowEven">
<td class="markdownTableBodyNone">20 </td><td class="markdownTableBodyNone">cerebellum </td></tr>
<tr class="markdownTableRowOdd">
<td class="markdownTableBodyNone">21 </td><td class="markdownTableBodyNone">Right cingulate region </td></tr>
</table>
<ol type="1">
<li>Batch File: A csv file having patients' IDs, group (atlas) number, and path to the actual segmented image. Atlas numbers should be in the ascending order, such as 1,2,3,...,n. Segmentation images should be in the same space as the standard atlas (Note that the CSV file should be in ASCII format, and the CSV file should have the following column headers in any sequence: PATIENT_IDS,IMAGES, ATLAS_LABELS).</li>
</ol>
<p><b>USAGE:</b></p><ol type="1">
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2 changes: 1 addition & 1 deletion docs/Glioblastoma_Confetti.html
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<tr style="height: 56px;">
<td id="projectalign" style="padding-left: 0.5em;">
<div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
&#160;<span id="projectnumber">1.9.0</span>
&#160;<span id="projectnumber">1.9.1</span>
</div>
</td>
</tr>
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2 changes: 1 addition & 1 deletion docs/Glioblastoma_Directionality.html
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<tr style="height: 56px;">
<td id="projectalign" style="padding-left: 0.5em;">
<div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
&#160;<span id="projectnumber">1.9.0</span>
&#160;<span id="projectnumber">1.9.1</span>
</div>
</td>
</tr>
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51 changes: 50 additions & 1 deletion docs/Glioblastoma_EGFRvIII.html
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<tr style="height: 56px;">
<td id="projectalign" style="padding-left: 0.5em;">
<div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
&#160;<span id="projectnumber">1.9.0</span>
&#160;<span id="projectnumber">1.9.1</span>
</div>
</td>
</tr>
Expand Down Expand Up @@ -66,6 +66,55 @@
<li>Co-registered Multimodal MRI: T1, T1-Gd, T2, T2-FLAIR, DTI-AX, DTI-FA, DTI-RAD, DTI-TR, DSC-PH, DSC-PSR, DSC-rCBV.</li>
<li>Segmentation labels of the tumor sub-regions: Non-enhancing tumor core (Label=1), Enhancing tumor core (Label=4), as well as the Edema (Label=2)</li>
<li>Segmentation labels in a common atlas space: Non-enhancing tumor core (Label=1), Enhancing tumor core (Label=4), Edema (Label=2), as well as the Ventricle (Label=7)</li>
</ol>
<p>Standard Atlas reference:</p>
<table class="markdownTable">
<tr class="markdownTableHead">
<th class="markdownTableHeadNone">Value </th><th class="markdownTableHeadNone">Region </th></tr>
<tr class="markdownTableRowOdd">
<td class="markdownTableBodyNone">1 </td><td class="markdownTableBodyNone">Right frontal lobe </td></tr>
<tr class="markdownTableRowEven">
<td class="markdownTableBodyNone">2 </td><td class="markdownTableBodyNone">Right temporal lobe </td></tr>
<tr class="markdownTableRowOdd">
<td class="markdownTableBodyNone">3 </td><td class="markdownTableBodyNone">Left temporal lobe </td></tr>
<tr class="markdownTableRowEven">
<td class="markdownTableBodyNone">4 </td><td class="markdownTableBodyNone">Left thalamus </td></tr>
<tr class="markdownTableRowOdd">
<td class="markdownTableBodyNone">5 </td><td class="markdownTableBodyNone">Right parietal lobe </td></tr>
<tr class="markdownTableRowEven">
<td class="markdownTableBodyNone">6 </td><td class="markdownTableBodyNone">Left insula </td></tr>
<tr class="markdownTableRowOdd">
<td class="markdownTableBodyNone">7 </td><td class="markdownTableBodyNone">Right basal ganglia </td></tr>
<tr class="markdownTableRowEven">
<td class="markdownTableBodyNone">8 </td><td class="markdownTableBodyNone">Right occipital lobe </td></tr>
<tr class="markdownTableRowOdd">
<td class="markdownTableBodyNone">9 </td><td class="markdownTableBodyNone">Left basal ganglia </td></tr>
<tr class="markdownTableRowEven">
<td class="markdownTableBodyNone">10 </td><td class="markdownTableBodyNone">corpus callosum </td></tr>
<tr class="markdownTableRowOdd">
<td class="markdownTableBodyNone">11 </td><td class="markdownTableBodyNone">Left frontal lobe </td></tr>
<tr class="markdownTableRowEven">
<td class="markdownTableBodyNone">12 </td><td class="markdownTableBodyNone">Left parietal lobe </td></tr>
<tr class="markdownTableRowOdd">
<td class="markdownTableBodyNone">13 </td><td class="markdownTableBodyNone">Left occipital lobe </td></tr>
<tr class="markdownTableRowEven">
<td class="markdownTableBodyNone">14 </td><td class="markdownTableBodyNone">brain stem </td></tr>
<tr class="markdownTableRowOdd">
<td class="markdownTableBodyNone">15 </td><td class="markdownTableBodyNone">Right thalamus </td></tr>
<tr class="markdownTableRowEven">
<td class="markdownTableBodyNone">16 </td><td class="markdownTableBodyNone">Right fornix </td></tr>
<tr class="markdownTableRowOdd">
<td class="markdownTableBodyNone">17 </td><td class="markdownTableBodyNone">Left cingulate region </td></tr>
<tr class="markdownTableRowEven">
<td class="markdownTableBodyNone">18 </td><td class="markdownTableBodyNone">Left fornix </td></tr>
<tr class="markdownTableRowOdd">
<td class="markdownTableBodyNone">19 </td><td class="markdownTableBodyNone">Right insula </td></tr>
<tr class="markdownTableRowEven">
<td class="markdownTableBodyNone">20 </td><td class="markdownTableBodyNone">cerebellum </td></tr>
<tr class="markdownTableRowOdd">
<td class="markdownTableBodyNone">21 </td><td class="markdownTableBodyNone">Right cingulate region </td></tr>
</table>
<ol type="1">
<li>Clinical data: A csv file having patient's demographics (Note that the CSV file should be in ASCII format). Should have age (in first column) and EGFRvIII status (in second column, binarized values like 0 and 1) for training a new model, and age only for mutation detection of new patients.</li>
<li>The data for each patient should be organized in the following directory structure. When running in the command-line, filenames must include words in <b>BOLD</b> to be identified as respective required files.<ul>
<li>Subject_ID<ol type="a">
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2 changes: 1 addition & 1 deletion docs/Glioblastoma_PHI.html
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<tr style="height: 56px;">
<td id="projectalign" style="padding-left: 0.5em;">
<div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
&#160;<span id="projectnumber">1.9.0</span>
&#160;<span id="projectnumber">1.9.1</span>
</div>
</td>
</tr>
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2 changes: 1 addition & 1 deletion docs/Glioblastoma_Pseudoprogression.html
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<tr style="height: 56px;">
<td id="projectalign" style="padding-left: 0.5em;">
<div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
&#160;<span id="projectnumber">1.9.0</span>
&#160;<span id="projectnumber">1.9.1</span>
</div>
</td>
</tr>
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2 changes: 1 addition & 1 deletion docs/Glioblastoma_Recurrence.html
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<tr style="height: 56px;">
<td id="projectalign" style="padding-left: 0.5em;">
<div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
&#160;<span id="projectnumber">1.9.0</span>
&#160;<span id="projectnumber">1.9.1</span>
</div>
</td>
</tr>
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2 changes: 1 addition & 1 deletion docs/Glioblastoma_Survival.html
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<tr style="height: 56px;">
<td id="projectalign" style="padding-left: 0.5em;">
<div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
&#160;<span id="projectnumber">1.9.0</span>
&#160;<span id="projectnumber">1.9.1</span>
</div>
</td>
</tr>
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2 changes: 1 addition & 1 deletion docs/Glioblastoma_WhiteStripe.html
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<tr style="height: 56px;">
<td id="projectalign" style="padding-left: 0.5em;">
<div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
&#160;<span id="projectnumber">1.9.0</span>
&#160;<span id="projectnumber">1.9.1</span>
</div>
</td>
</tr>
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2 changes: 1 addition & 1 deletion docs/How_To_Guides.html
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<tr style="height: 56px;">
<td id="projectalign" style="padding-left: 0.5em;">
<div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
&#160;<span id="projectnumber">1.9.0</span>
&#160;<span id="projectnumber">1.9.1</span>
</div>
</td>
</tr>
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2 changes: 1 addition & 1 deletion docs/ITCR_Connectivity.html
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<tr style="height: 56px;">
<td id="projectalign" style="padding-left: 0.5em;">
<div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
&#160;<span id="projectnumber">1.9.0</span>
&#160;<span id="projectnumber">1.9.1</span>
</div>
</td>
</tr>
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2 changes: 1 addition & 1 deletion docs/Installation.html
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<tr style="height: 56px;">
<td id="projectalign" style="padding-left: 0.5em;">
<div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
&#160;<span id="projectnumber">1.9.0</span>
&#160;<span id="projectnumber">1.9.1</span>
</div>
</td>
</tr>
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