From a0db689a714968b74724bbdecffb47ee8a638b9d Mon Sep 17 00:00:00 2001 From: sarthakpati Date: Fri, 2 Oct 2020 13:08:45 -0400 Subject: [PATCH] updated instructions for brats pipeline --- 3_HowToGuides.txt | 30 ++++++++++++++++++++++++++++++ docs/preprocessing_brats.html | 33 ++++++++++++++++++++++++++++++++- 2 files changed, 62 insertions(+), 1 deletion(-) diff --git a/3_HowToGuides.txt b/3_HowToGuides.txt index d81d32663..74fa12c90 100644 --- 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 REQUIREMENTS: -# 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. USAGE: @@ -260,6 +261,35 @@ ${CaPTk_InstallDir}/bin/BraTSPipeline.exe -t1 C:/test/t1.nii.gz -t1c C:/test/t1c NOTE: This applications takes ~30 minutes to finish on an 8-core Intel i7 with 16GB of RAM. +Explanation of output files: + +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 index 5634880ea..dcc5a875d 100644 --- a/docs/preprocessing_brats.html +++ b/docs/preprocessing_brats.html @@ -63,7 +63,10 @@

This pipeline is also available from the web on the CBICA Image Processing Portal. Please see the experiment on the portal for details.

REQUIREMENTS:

    -
  1. 4 structural MRI images (T1, T1CE, T2, FLAIR), preferably in NIfTI format
    2. +
  2. 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.
      • +
    +

USAGE:

This CLI-only application takes 4 structural brain MRIs as input and performs the following steps [1-3]:

@@ -81,6 +84,34 @@

Example command: 

${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

NOTE: This applications takes ~30 minutes to finish on an 8-core Intel i7 with 16GB of RAM.

+

Explanation of output files:

+

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: