updated instructions for brats pipeline

CBICA · Oct 2, 2020 · a0db689 · a0db689
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diff --git a/3_HowToGuides.txt b/3_HowToGuides.txt
@@ -239,6 +239,7 @@ This pipeline is also available from the web on the [CBICA Image Processing Port
 
 <b>REQUIREMENTS:</b>
 	-# 4 structural MRI images (T1, T1CE, T2, FLAIR), preferably in NIfTI format
+		- For DICOM images, please pass the first image in each of the series as input, not the folder.
 
 <b>USAGE:</b>
 
@@ -260,6 +261,35 @@ ${CaPTk_InstallDir}/bin/BraTSPipeline.exe -t1 C:/test/t1.nii.gz -t1c C:/test/t1c
 
 <b>NOTE</b>: This applications takes ~30 minutes to finish on an 8-core Intel i7 with 16GB of RAM.
 
+<b>Explanation of output files:</b>
+
+Final co-registered images:
+
+-	T1_to_SRI.nii.gz : Co-registered T1 image
+-	T1CE_to_SRI.nii.gz: Co-registered T1CE image
+-	T2_to_SRI.nii.gz: Co-registered T2 image
+-	FL_to_SRI.nii.gz: Co-registered FLAIR image
+
+(Optional) Deep Learning based masks:
+
+-	brainMask_SRI.nii.gz
+-	brainTumorMask_SRI.nii.gz
+
+(Optional) Co-registered images, with brain mask applied:
+
+-	T1_to_SRI_brain.nii.gz
+-	T1CE_to_SRI_brain.nii.gz
+-	T2_to_SRI_brain.nii.gz
+-	FL_to_SRI_brain.nii.gz
+
+(Optional) Intermediate files (similar for T1CE, T2, FLAIR):
+
+-	T1_raw.nii.gz : NifTi file converted from input DICOM, or copy of input NifTI file
+-	T1_rai.nii.gz : Image re-oriented to LPS/RAI
+-	T1_rai_n4.nii.gz : Image with N4 bias correction applied to T1_rai.nii.gz
+-	T1_to_T1CE.mat : transformation matrix of Rigid registration, T1 to T1CE
+-	T1CE_to_SRI.mat : transformation matrix of Rigid registration, T1CE to SRI
+
 --------
 
 Reference:

diff --git a/docs/preprocessing_brats.html b/docs/preprocessing_brats.html
@@ -63,7 +63,10 @@
 <div class="contents">
 <div class="textblock"><p>This pipeline is also available from the web on the <a href="https://ipp.cbica.upenn.edu/">CBICA Image Processing Portal</a>. Please see the experiment on the portal for details.</p>
 <p><b>REQUIREMENTS:</b></p><ol type="1">
-<li>4 structural MRI images (T1, T1CE, T2, FLAIR), preferably in NIfTI format</li>
+<li>4 structural MRI images (T1, T1CE, T2, FLAIR), preferably in NIfTI format<ul>
+<li>For DICOM images, please pass the first image in each of the series as input, not the folder.</li>
+</ul>
+</li>
 </ol>
 <p><b>USAGE:</b></p>
 <p>This CLI-only application takes 4 structural brain MRIs as input and performs the following steps [1-3]:</p>
@@ -81,6 +84,34 @@
 </ol>
 <p>Example command: </p><pre class="fragment">${CaPTk_InstallDir}/bin/BraTSPipeline.exe -t1 C:/test/t1.nii.gz -t1c C:/test/t1ce.nii.gz -t2 C:/test/t2.nii.gz -fl C:/test/flair.nii.gz -o C:/test/outputDir 
 </pre><p><b>NOTE</b>: This applications takes ~30 minutes to finish on an 8-core Intel i7 with 16GB of RAM.</p>
+<p><b>Explanation of output files:</b></p>
+<p>Final co-registered images:</p>
+<ul>
+<li>T1_to_SRI.nii.gz : Co-registered T1 image</li>
+<li>T1CE_to_SRI.nii.gz: Co-registered T1CE image</li>
+<li>T2_to_SRI.nii.gz: Co-registered T2 image</li>
+<li>FL_to_SRI.nii.gz: Co-registered FLAIR image</li>
+</ul>
+<p>(Optional) Deep Learning based masks:</p>
+<ul>
+<li>brainMask_SRI.nii.gz</li>
+<li>brainTumorMask_SRI.nii.gz</li>
+</ul>
+<p>(Optional) Co-registered images, with brain mask applied:</p>
+<ul>
+<li>T1_to_SRI_brain.nii.gz</li>
+<li>T1CE_to_SRI_brain.nii.gz</li>
+<li>T2_to_SRI_brain.nii.gz</li>
+<li>FL_to_SRI_brain.nii.gz</li>
+</ul>
+<p>(Optional) Intermediate files (similar for T1CE, T2, FLAIR):</p>
+<ul>
+<li>T1_raw.nii.gz : NifTi file converted from input DICOM, or copy of input NifTI file</li>
+<li>T1_rai.nii.gz : Image re-oriented to LPS/RAI</li>
+<li>T1_rai_n4.nii.gz : Image with N4 bias correction applied to T1_rai.nii.gz</li>
+<li>T1_to_T1CE.mat : transformation matrix of Rigid registration, T1 to T1CE</li>
+<li>T1CE_to_SRI.mat : transformation matrix of Rigid registration, T1CE to SRI</li>
+</ul>
 <hr  />
 <p>Reference:</p>
 <ol type="1">