Edit the script and remplace all the "WD" by your working directory:
Here, an example of script:
############################################
# Common
############################################
# fixed information on script -> mandatory
LIFEx.MTV.script = MTV
LIFEx.MTV.script.version = 1.0
# result file -> mandatory
LIFEx.MTV.output.file=WD/MTV_results.csv
########################################################################
# patients / ROI #
########################################################################
LIFEx.MTV.Session0.Img0=WD/PT1/IMG
LIFEx.MTV.Session0.Roi0=WD/PT1/ROI/R1.uint16.nii.gz
LIFEx.MTV.Session0.Roi1=WD/PT1/ROI/R2.uint16.nii.gz
LIFEx.MTV.Session0.Roi2=WD/PT1/ROI/R4.uint16.nii.gz
LIFEx.MTV.Session1.Img0=WD/PT2
LIFEx.MTV.Session1.Roi0=WD/PT2/ROI/R1.uint8.nii.gz
LIFEx.MTV.Session1.Roi1=WD/PT2/ROI/R2.uint8.nii.gz
LIFEx.MTV.Session1.Roi2=WD/PT2/ROI/R4.uint8.nii.gz
Here, an example of result:
INFO_PatientName INFO_PatientID INFO_PatientWeight(Kg) INFO_ProcessDateOfTexture INFO_SeriesDate INFO_Series TLG(SUV*mL) sTLG(SUV*mL/Kg) MTV(mL) sMTV(mL/Kg) Dmax(cm) sDmax(cm) DmaxVox(cm)
PT1 S00000 66.0 Wed Apr 13 17:38:08 CEST 2022 2015-10-02 Head to Thighs 3D MAC_PT 5544 84 961 14.56 54.8 55.1 63.3±0.1
PT1 S00001 66.0 Wed Apr 13 17:38:13 CEST 2022 2015-10-02 Head to Thighs 3D MAC_PT 5544 84 961 14.56 54.8 55.1 63.3±0.1
PT1 S00002 66.0 Wed Apr 13 17:38:08 CEST 2022 2015-10-02 Head to Thighs 3D MAC_PT 5544 84 961 14.56 54.8 55.1 63.3±0.1
PT2 S00000 66.0 Wed Apr 13 17:38:13 CEST 2022 2015-10-02 Head to Thighs 3D MAC_PT 5544 84 961 14.56 54.8 55.1 63.3±0.1
PT2 S00002 66.0 Wed Apr 13 17:38:08 CEST 2022 2015-10-02 Head to Thighs 3D MAC_PT 5544 84 961 14.56 54.8 55.1 63.3±0.1
PT2 S00003 66.0 Wed Apr 13 17:38:13 CEST 2022 2015-10-02 Head to Thighs 3D MAC_PT 5544 84 961 14.56 54.8 55.1 63.3±0.1
Edit the script and remplace all the "WD" by your working directory:
Here, an example of script:
############################################
# Common
############################################
# fixed information on script -> mandatory
LIFEx.script = MTV
LIFEx.script.version = 1.0
# result file -> mandatory
LIFEx.output.file=WD/MTV_results.csv
########################################################################
# patients / ROI #
########################################################################
LIFEx.Session0.Img0=WD/PT1/IMG
LIFEx.Session0.Roi0=WD/PT1/ROI/R1.uint16.nii.gz
LIFEx.Session0.Roi1=WD/PT1/ROI/R2.uint16.nii.gz
LIFEx.Session0.Roi2=WD/PT1/ROI/R4.uint16.nii.gz
LIFEx.Session1.Img0=WD/PT2
LIFEx.Session1.Roi0=WD/PT2/ROI/R1.uint8.nii.gz
LIFEx.Session1.Roi1=WD/PT2/ROI/R2.uint8.nii.gz
LIFEx.Session1.Roi2=WD/PT2/ROI/R4.uint8.nii.gz
Here, an example of result:
INFO_PatientName INFO_PatientID INFO_PatientWeight(Kg) INFO_ProcessDateOfTexture INFO_SeriesDate INFO_Series TLG(SUV*mL) sTLG(SUV*mL/Kg) MTV(mL) sMTV(mL/Kg) Dmax(cm) sDmax(cm) DmaxVox(cm)
PT1 S00000 66.0 Wed Apr 13 17:38:08 CEST 2022 2015-10-02 Head to Thighs 3D MAC_PT 5544 84 961 14.56 54.8 55.1 63.3±0.1
PT1 S00001 66.0 Wed Apr 13 17:38:13 CEST 2022 2015-10-02 Head to Thighs 3D MAC_PT 5544 84 961 14.56 54.8 55.1 63.3±0.1
PT1 S00002 66.0 Wed Apr 13 17:38:08 CEST 2022 2015-10-02 Head to Thighs 3D MAC_PT 5544 84 961 14.56 54.8 55.1 63.3±0.1
PT2 S00000 66.0 Wed Apr 13 17:38:13 CEST 2022 2015-10-02 Head to Thighs 3D MAC_PT 5544 84 961 14.56 54.8 55.1 63.3±0.1
PT2 S00002 66.0 Wed Apr 13 17:38:08 CEST 2022 2015-10-02 Head to Thighs 3D MAC_PT 5544 84 961 14.56 54.8 55.1 63.3±0.1
PT2 S00003 66.0 Wed Apr 13 17:38:13 CEST 2022 2015-10-02 Head to Thighs 3D MAC_PT 5544 84 961 14.56 54.8 55.1 63.3±0.1
Available data files:
- DataFile1_CT_Anonym.zip
- DataFile1_PT_Anonym.zip
- DataFile1_PT_Anonym_RoiVolume_healthy.nii.zip
- DataFile1_PT_Anonym_RoiVolume_tumor.nii.zip
- DataFile1_PT_Anonym_LIFEx_Texture_Script.txt
- DataFile2_MR_Anonym.zip
- DataFile2_PT_Anonym.zip
- DataFile3_US_Anonym.nii
- DataFile4_US_Anonym.dcm
More sample scripts are available here:
- PT.NII_0_Check_script.txt
- PT.NII_0_Texture_C1_MeanFilter_script.txt
- PT.NII_0_Texture_C1_WaveletFilter_script.txt
- PT.NII_0_Texture_C1_LaplacianFilter_script.txt
- PT.NII_0_Texture_C1_GaussianFilter_script.txt
- PT.NII_0_Texture_C1_scriptAll.txt
- PT.NII_0_Texture_C1_LawsFilter_script.txt
- PT.NII_0_Texture_C1_script.txt
As specified in the license, when using LIFEx to produce results included in a paper, poster or presentation, please cite:
C Nioche, F Orlhac, S Boughdad, S Reuzé, J Goya-Outi, C Robert, C Pellot-Barakat, M Soussan, F Frouin, and I Buvat. LIFEx: a freeware for radiomic feature calculation in multimodality imaging to accelerate advances in the characterization of tumor heterogeneity. Cancer Research 2018; 78(16):4786-4789 (link).
as well as www.lifexsoft.org
Since its availability early 2016, many scientists, medical doctors, engineers and students have chosen LIFEx for their work. Here are a few comments about their experience:
Dr. Lee
Korea
It is a pleasure for me to be on the contributor list.
I used a matlab-based software for texture analysis, which is cumbersome and redundant.
For me, LIFEx is really user-friendly and quite intuitive.
I hope that I can help improve the software in the future
Phd student, wenchao gu
Maebashi, Japan
The other thing i want to tell you is, i have been looking for 1 year to find the best software for doing texture analyzing.(including Mazda, Matlab....ect).
LIFEx is the best software i have ever used.
I am working in China, Shanghai Cancer Center.
Now i'm studying Gunma university in Japan as a Phd student.
Yasser Abdelhafez, MBBCh, MSc, MD
South Egypt Cancer Institute
Postdoctoral Scholar Department of Radiology
University of California Davis Medical Center
Dear LifeX developers,
First, thank you for the great effort you put together in this remarkable software LifeX.
I am interested in texture analysis of PET images and find your software to be the best user-friendly tool for physician.
...
Thank you for your input. I tried it and it works perfectly.
By the way, congratulations to all of you for the recent great paper in Cancer Research.
I appreciate your efforts.
Thank you,
Dr. Constantinos Zamboglou
University Medical Center Freiburg, Radiation Oncology
Germany
Since one month I am using your software and I am quite happy. It is a great opportunity to have such a nice tool as a freeware platform. Thank you very much.
Natalia Dubljevic
Delta, Canada
I tried this, and it works! Thank you so much-- excellent customer support :)
Masao Watanabe
The Department of Diagnostic Radiology, Kobe City Medical Center, General Hospital
I am so sorry that I had so many questions to solve and that my questions took you a lot of time to reply. Your replies were so helpful and meaningful to me. I really appreciate your kind support.
Thank you so much.
Roberto Lantieri
Università degli studi di Padova
close2D works fine and it speed up 4x my work! thank you very much for your exceptional support! Is there a way to support your software with a donation?
Non exhaustive list of systems that have been validated as LIFEx-compatible so far:
DICOM Philips Medical Systems :
- GEMINI (TF TOF 16 , GXL 16)
- Intera 1.5T
- Guardian Body(C)
- Brilliance 16P
Read more: List of systems already validated as LIFEx-compatible
- Main:
- License: here is the LIFEx license you have to agree with before being granted access to the LIFEx software.
- Step-by-step protocols: (>= 7.1.15)
- Texture protocol: here is a demonstration of the protocol. You will also learn how to set the parameters inside the protocol menu. You will learn how to modify the settings and where to find your results.
- MTV protocol: here you will have a detailed explanation on the segmentation methods used inside the protocol and how they are combine. You will also learn how to obtain and save the protocol results. The MTV protocol is also introduced with demonstrations.
Tutorial videos on LIFEx features:
- Series: (>= 7.1.15)
- How to load series of images
- How to get your series metadata, save and convert your series
- How to resample your image series
- Filtering a series: Mean, LoG, Wavelets & Laws
- How to clear a table from a CT series and how to clear VOI from a series
- Basic features for series & how to measure angle and distance
- How to add and remove time points from a time series
- How to do basic operation on a time series (from a series to a parametric image)
- How to level your windows
- How to modify your series relative orientation and position
- Operations on 2 series: merging and basic calculations
- ROI manipulation: (>= 7.1.7)
- How to load, create and save ROI
- Basic edition of ROI
- Advanced features to reformat ROI
- How to change ROI morphology
- Basic measures on ROI and VOI
- How to measure angle and distance in LIFEx
- How to draw 3D ROI
- How to draw 2D ROI
- Basic image segmentation method in LIFEx
- How to find peak volume
- LIFEx advanced segmentation methods
- Handling of several ROI at once: (>= 7.1.7)
Quick demonstrations on LIFEx tools and basic commands :
- Series:
- Loading CTDICOM-RS: here, you will see how to load a CT scan and associated regions saved as RT Struct (v5.10)
- Loading MR DICOM-RS: here, you will see how to load an MR scan and associated regions saved as RT Struct (v5.10)
- Series Loading PET MR: here, you will see how to load a combined PET-MR scan (v5.10)
- Loading DICOM-REG: here, you will see how to use DICOM-REG file for registering two datasets (v5.10)
Software documentation includes written text or presentations that describe the software. They either explain its functionalities or how to use it. Movies (mp4) also show you how to perform a number of tasks with LIFEx. If you'd like more movies to illustrate specific features, let us know !
The version numbers displayed on this page refer to the versions of the application from which the given information applies. If you are unsure, also use the latest version available.