Installation help for dsi-studio in a CentOS Linux 7 environment

[Debarun De]

Hello,

    I have a colleague that is trying to download the 2021_06 version of dsi-studio from the source code on github. My colleague downloaded the source .tar.gz file from github for the 2021_06 version, yet it did not seem to include an src directory. What are the precise download links and installation instructions to compile dsi-Studio (the 2021_06 source code version) for CentOS Linux 7?

Thanks.

[Frank Yeh]

There is no such directory in the source code.

Is there any problem compiling DSI Studio using the current source code?

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[Debarun De]

My Colleague is trying to install this into a Linux 7 cluster using this guide: http://dsi-studio.labsolver.org/dsi-studio-download/compile-dsi-studio-on-windows-mac-linux#TOC-Compile-DSI-Studio-on-Linux-Fedora. The guide references an src directory, which my colleague says is not in the current source code build  (the 2021_06 version). How would we compile the 2021_06 version? Is there another directory or guide?

Thanks.

[Michel Audette]

Dear Frank and DSI Studio experts, 

my collaborator Rohad Dod and I are trying to reconstruct a sciatic nerve from DTI and T1 data, and for some reason we are having trouble saving regions in axial slices in a robust manner. I managed to identify one region with the freehand drawing, at slice 142, and when I tried to do the same at slice 137, it would not convert the new region to a white contour that signifies that it is saved by the system. Can anyone tell me what I need to do to make sure that the putative colored contour gets saved properly? 

Secondly, I would like to draw a few of these freehand regions, and exercise some level of control on the fibers that go through these regions. In other words, I'd like to use two regions like poles of a clothesline that constrain the nerve fibers that travel through any given region pair, and then do the same with a series of region pairs (or constrain the fibers groupwise, not just pairwise). Are there parameters in the fiber reconstruction that allow me to exclude fibers that do not go through the regions at both ends? 

Thanks for your kind support. Best wishes,

Michel 

Michel Audette, Ph.D.
Associate Professor, Department of Computational Modeling and Simulation Engineering,
Graduate Program Director, Biomedical Engineering Institute,
Old Dominion University,
Norfolk, VA.

[Frank Yeh]

Sorry about the problem.

It seems to me that you are drawing on T1W images?

If yes, what I would suggest is the following:

1. open the t1w nifti file in [Step T3 Fiber Tracking] default file extension is fib.gz, but you can switch to nii.gz

2. draw regions and save them as NIFTI files(s)

3. To use the regions, open the FIB file in [Step T3 Fiber Tracking], insert the T1W using [Slices][Inset T1W/T2W...] and then load the regions from (2) using [Regions][Open]

Hope this works for you.

I would also suggest updating DSI Studio to the 2021 versions if you are using an older version.

Best regards,

Frank

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[Debarun De]

Hello,

 Are there precise instructions for compiling source code to a CentOS 7 Linux machine? If so, could you provide precise instructions for compiling the source code on a CentOS 7 Linux machine?

Thanks,

  Debarun De

[Frank Yeh]

Hi Debarun,

    Here's a sample of commands to install Qt and compile DSI Studio, but there may be a glitch that you may need to fix.

yum -y update && yum clean all

#Install custom packages
yum install -y epel-release

yum groups mark convert
yum groupinstall -y 'Development Tools'

yum install -y clang clang-devel llvm-devel cmake3 cmake python-testtools python-pip wget
yum install -y qt-creator protobuf-compiler graphviz libxml2-devel libxslt-devel
yes | pip install checksumdir

yum remove -y subversion*
yum clean all
yum install -y subversion

yum install gcc-c++

#install qt

wget -q http://download.qt.io/archive/qt/5.12/5.12.1/qt-opensource-linux-x64-5.12.1.run
chmod +x qt-opensource-linux-x64-5.12.1.run

./qt-opensource-linux-x64-5.12.1.run --platform minimal --script qt-installer-noninteractive.qs --verbose

/opt/Qt/Tools/QtCreator/bin/qbs setup-toolchains --detect
/opt/Qt/Tools/QtCreator/bin/qbs setup-qt '/opt/Qt/5.12.1/gcc_64/bin/qmake' QtProfile
/opt/Qt/Tools/QtCreator/bin/qbs config profiles.QtProfile.baseProfile clang

PATH="/opt/Qt/5.12.1/gcc_64/bin:${PATH}"
LD_LIBRARY_PATH="/opt/Qt/5.12.1/gcc_64/lib:${LD_LIBRARY_PATH}"


source /opt/qt512/bin/qt512-env.sh \
  && mkdir /opt/dsi-studio \
  && cd /opt/dsi-studio \
  && git clone https://github.com/frankyeh/DSI-Studio.git \
  && mv DSI-Studio src \
  && git clone https://github.com/frankyeh/TIPL.git \
  && mv TIPL src/tipl \
  && mkdir -p /opt/dsi-studio/build \
  && cd /opt/dsi-studio/build \
  && qmake ../src/dsi_studio.pro \
  && make -k -j1 \
  && cd /opt/dsi-studio \
  && curl -sSLO 'https://www.dropbox.com/s/pib533irglhnwy7/dsi_studio_64.zip' \
  && unzip dsi_studio_64.zip \
  && rm dsi_studio_64.zip \
  && cd dsi_studio_64 \
  && rm *.dll \
  && rm *.exe \
  && rm -rf iconengines \
  && rm -rf imageformats \
  && rm -rf platforms \
  && rm -rf styles \
  && mv ../build/dsi_studio . \
  && rm -rf /opt/dsi-studio/src /opt/dsi-studio/build

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[Debarun De]

Hello,

A few quick questions, one that revolves around this line:

 

source /opt/qt512/bin/qt512-env.sh

I had to modify this instruction to install to /appl/Qt-5.12.1 since that is on central storage that is mounted by our servers,

and so I don't see /opt/qt512 or any part of that line in /appl/Qt-5.12.1

Any advice?

Also I don't understand the point of the last bunch of steps...
why is the folder for the Windows version of dsi-studio used for a Linux environment?

Thank you for your help,

[Frank Yeh]

I had to modify this instruction to install to /appl/Qt-5.12.1 since that is on central storage that is mounted by our servers,

and so I don't see /opt/qt512 or any part of that line in /appl/Qt-5.12.1

You can change it to any directory name as you wish.

 

Also I don't understand the point of the last bunch of steps...
why is the folder for the Windows version of dsi-studio used for a Linux environment?

It needs the files from the atlas folder. The windows executives are not used.

Best regards,

Frank

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[Debarun De]

My colleague has managed to get the destination  installation of /appl/Qt-5.12.1,  but have not anywhere seen the equivalent of that qt512 dir or the qt512env.sh file, which is used to compile the files. Do you know of where we could find the qt512 dir or the qt512env.sh file?

Thanks,

[Debarun De]

Hello,

    Do you know where the qt512 dir or qt512env.sh file could be located from the source code download?

[Frank Yeh]

I am sorry that I have no idea.

If you upgrade to centos 8, then you can install qt5.12 runtime using

yum install -y qt5-qtbase-devel
yum install -y qt5-qtcharts

qmake-qt should be installed under /bin

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[Debarun De]

No worries, Thank you for your continued help!

[Ryan Salomon]

Hello! This is Ryan Salomon, Debraun's colleague. 

We have an existing Qt 5.12 install, which we load into the environment via modules.

Given this, are there modified instructions that could be provided, to integrate with that?

[Frank Yeh]

The compiling command will be very similar to those used in Ubuntu (qmake followed by make):

https://github.com/frankyeh/DSI-Studio/blob/master/build_packages/ubuntu_2004/Dockerfile

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