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Documentation.Install History
Hide minor edits - Show changes to output
Added lines 47-54:
As an example, the command to remove the error for @@VolumeInfo@@ looks like the following, assuming you are in the ${DTITK_ROOT}/bin directory:
->[@
sudo xattr -dr com.apple.quarantine VolumeInfo
@]
Note that, for security reasons, this will require you to enter the password of the system administrator.
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Thankfully, this can also be achieved through the command line interface (CLI) as described [[https://apple.stackexchange.com/questions/202169/how-can-i-open-an-app-from-an-unidentified-developer-without-using-the-gui/202172 |here], allowing the possibility of scripting the process for multiple binary executables.
to:
Thankfully, this can also be achieved through the command line interface (CLI) as described [[https://apple.stackexchange.com/questions/202169/how-can-i-open-an-app-from-an-unidentified-developer-without-using-the-gui/202172 |here]], allowing the possibility of scripting the process for multiple binary executables.
Changed lines 41-46 from:
For the more recent Mac OS versions, running any binary executable shipped with DTI-TK can trigger the error to:
For the more recent Mac OS versions, running any binary executable shipped with DTI-TK can trigger the error ''' ... can't be opened because it is from an unidentified developer'''.
One can override this through the graphical user interface (GUI) but it becomes tedious quickly to do this for all DTI-TK binary executables.
Thankfully, this can also be achieved through the command line interface (CLI) as described [[https://apple.stackexchange.com/questions/202169/how-can-i-open-an-app-from-an-unidentified-developer-without-using-the-gui/202172 |here], allowing the possibility of scripting the process for multiple binary executables.
Changed lines 41-42 from:
For the more recent Mac OS versions, running any binary executable shipped with DTI-TK can trigger the error can’t be opened because it is from an unidentified developer.
to:
For the more recent Mac OS versions, running any binary executable shipped with DTI-TK can trigger the error
Changed lines 41-42 from:
For the more recent Mac OS versions, running any binary executable shipped with DTI-TK
to:
For the more recent Mac OS versions, running any binary executable shipped with DTI-TK can trigger the error can’t be opened because it is from an unidentified developer.
Changed lines 41-42 from:
For the more recent Mac OS versions, running any binary executable shipped with DTI-TK can trigger the error '''can’t be opened because it is from an unidentified developer'''
to:
For the more recent Mac OS versions, running any binary executable shipped with DTI-TK
Changed lines 41-42 from:
For the more recent Mac OS versions, running any binary executable shipped with DTI-TK
to:
For the more recent Mac OS versions, running any binary executable shipped with DTI-TK can trigger the error '''can’t be opened because it is from an unidentified developer'''
Added lines 41-42:
For the more recent Mac OS versions, running any binary executable shipped with DTI-TK
Deleted lines 40-41:
For the more recent Mac OS versions, running any binary executable shipped with DTI-TK may trigger the error '''can’t be opened because it is from an unidentified developer'''.
Added lines 41-42:
For the more recent Mac OS versions, running any binary executable shipped with DTI-TK may trigger the error '''can’t be opened because it is from an unidentified developer'''.
Changed line 38 from:
3.Add the [[http://en.wikipedia.org/wiki/Path_%28computing%29 | path]]''' to the DTI-TK and define the DTITK_ROOT variable. (:showhide init=hide div=configure_path:)
to:
2.1 '''Mac OS specific instructions''' (:showhide init=hide div=configure_path:) Added lines 41-45:
>><<
3. '''Add the [[http://en.wikipedia.org/wiki/Path_%28computing%29 | path]]''' to the DTI-TK and define the DTITK_ROOT variable. (:showhide init=hide div=configure_path:)
>>id=configure_path padding=5px <<
Changed line 61 from:
->Include the above command to your .bashrc or .bash_profile files. The instruction for Mac is available [[http://macbasics101.com/2011/02/14/create-bash_profile-file-mac/ | here]] and for Linux [[http://www.hypexr.org/bash_tutorial.php | here]]. If you use [[http://en.wikipedia.org/wiki/Tcsh | tcsh]] instead of bash, change the command accordingly. Defining the environment variable DTITK_ROOT is now '''mandatory'''. to:
->Include the above command to your .bash_profile file (or equivalent on your unix system). The instruction for Mac is available [[http://macbasics101.com/2011/02/14/create-bash_profile-file-mac/ | here]] and for Linux [[http://www.hypexr.org/bash_tutorial.php | here]]. If you use [[http://en.wikipedia.org/wiki/Tcsh | tcsh]] instead of bash, change the command accordingly. Defining the environment variable DTITK_ROOT is now '''mandatory'''. Changed lines 105-106 from:
If your computing infrastructure includes/implements SGE-based cluster-computing support, you can optionally enable DTI-TK to utilize this feature. The environment variable that needs to be defined in your .bashrc file is DTITK_USE_QSUB. Setting the variable to 1 will enable the SGE support. To disable this feature, simply setting the variable to 0.
to:
If your computing infrastructure includes/implements SGE-based cluster-computing support, you can optionally enable DTI-TK to utilize this feature. The environment variable that needs to be defined in your .bash_profile file is DTITK_USE_QSUB. Setting the variable to 1 will enable the SGE support. To disable this feature, simply setting the variable to 0.
Changed lines 115-116 from:
The supported animals include "MONKEY" and "RAT". You can add additional supported easily by editing the file ''dtitk_common.sh'' under the ''scripts'' directory.
to:
The supported animals include "MONKEY" and "RAT". You can add additional animal support easily by editing the file ''dtitk_common.sh'' under the ''scripts'' directory.
Changed lines 98-99 from:
to:
The '''optional''' steps are as follows:
Changed lines 98-100 from:
5. Optional '''Sun Grid Engine''' (SGE) support for cluster-computing (:showhide init=hide div=sge:)
to:
'''Optional'''
5. '''Sun Grid Engine''' (SGE) support for cluster-computing (:showhide init=hide div=sge:) Added lines 109-121:
6. Support for '''animal brains''' (:showhide init=hide div=species:)
>>id=species padding=5px<<
Animals, such as monkeys, have brain size very different from human. DTI-TK accounts for this difference using ''DTITK_SPECIES'' environment variable. This variable is default to "HUMAN". You need to set this variable if you want to apply DTI-TK to an animal study.
The supported animals include "MONKEY" and "RAT". You can add additional supported easily by editing the file ''dtitk_common.sh'' under the ''scripts'' directory.
Here is an example of setting the DTI-TK for a monkey study.
->[@
export DTITK_SPECIES="MONKEY"
@]
>><<
Changed lines 4-5 from:
Follow ALL the steps below to ensure DTI-TK working properly. If you have [[SourceCode.SourceCode | compiled DTI-TK from source]], skip the steps 1 and 2.
to:
Follow '''ALL''' the steps below (unless noted as optional) to ensure DTI-TK working properly.
If you have [[SourceCode.SourceCode | compiled DTI-TK from source]], skip the steps 1 and 2.
Changed line 98 from:
5. '''Sun Grid Engine''' (SGE) support for cluster-computing (:showhide init=hide div=sge:) to:
5. Optional '''Sun Grid Engine''' (SGE) support for cluster-computing (:showhide init=hide div=sge:)
Changed line 62 from:
4. '''Verify the installation''' with the command (:showhide init=hide div=verfiy:) to:
4. '''Verify the installation''' (:showhide init=hide div=verify:)
Changed lines 8-10 from:
2. '''Move the downloaded file''' to your location of choice, then uncompress and extract the contents of the package. (Skip to step 3, if you know how to do this). to:
2. '''Move the downloaded file''' to your location of choice, then uncompress and extract the contents of the package. (Skip to step 3, if you know how to do this). (:showhide init=hide div=extraction:)
>>id=extraction padding=5px <<
Changed lines 34-36 from:
3. '''Add the [[http://en.wikipedia.org/wiki/Path_%28computing%29 | path]]''' to the DTI-TK and define the DTITK_ROOT variable.
to:
>><<
3. '''Add the [[http://en.wikipedia.org/wiki/Path_%28computing%29 | path]]''' to the DTI-TK and define the DTITK_ROOT variable. (:showhide init=hide div=configure_path:)
>>id=configure_path padding=5px <<
Changed lines 60-62 from:
4. '''Verify the installation''' with the command
to:
>><<
4. '''Verify the installation''' with the command (:showhide init=hide div=verfiy:)
>>id=verify padding=5px <<
Changed lines 94-96 from:
5. '''Sun Grid Engine''' (SGE) support for cluster-computing
to:
>><<
5. '''Sun Grid Engine''' (SGE) support for cluster-computing (:showhide init=hide div=sge:)
>>id=sge padding=5px <<
Changed lines 103-104 from:
to:
Changed lines 33-36 from:
3. '''Add the [[http://en.wikipedia.org/wiki/Path_(computing) | path]]''' to the DTI-TK and define the DTITK_ROOT variable.
The following is written for the [[http://en.wikipedia.org/wiki/Bash_(Unix_shell) | bash shell]]. If you are using a different shell environment, adapt the commands accordingly.
to:
3. '''Add the [[http://en.wikipedia.org/wiki/Path_%28computing%29 | path]]''' to the DTI-TK and define the DTITK_ROOT variable.
The following is written for the [[http://en.wikipedia.org/wiki/Bash_%28Unix_shell%29 | bash shell]]. If you are using a different shell environment, adapt the commands accordingly.
Changed line 44 from:
to:
Changed lines 87-88 from:
->If this is not what you get, this means that the binary does not work on your system. This can be the case if you are using the pre-compiled binary packages. Due to limited resources, we can only target a small number of platforms with precompiled binaries. If your system is not among them, you can either switch to a supported platform or will need to [[SourceCode.SourceCode | compile from the source code]].
to:
->If this is not what you get, this means that the binary does not work on your system. This can be the case if you are using the pre-compiled binary packages. Due to limited resources, we can only target a small number of platforms with pre-compiled binaries. If your system is not among them, you can either switch to a supported platform or will need to [[SourceCode.SourceCode | compile from the source code]].
Changed lines 65-66 from:
Use the example as above (for downloaded binary packages), if the installation is done correctly, the command should return the following
to:
->Use the example as above (for downloaded binary packages), if the installation is done correctly, the command should return the following
Changed lines 71-72 from:
This shows that we have placed the DTI-TK under the directory "/Users/huiz/unix/".
to:
->This shows that we have placed the DTI-TK under the directory "/Users/huiz/unix/".
Changed lines 79-80 from:
If the binary works correctly, you should see
to:
->If the binary works correctly, you should see
Changed lines 85-88 from:
(This is typical of most DTI-TK commands. If you do not supply any arguments to the command, it will print out its usage instructions. In this example, the instruction means that you need to provide a single argument.)
If this is not what you get, this means that the binary does not work on your system. This can be the case if you are using the pre-compiled binary packages. Due to limited resources, we can only target a small number of platforms with precompiled binaries. If your system is not among them, you can either switch to a supported platform or will need to [[SourceCode.SourceCode | compile from the source code]].
to:
->(This is typical of most DTI-TK commands. If you do not supply any arguments to the command, it will print out its usage instructions. In this example, the instruction means that you need to provide a single argument.)
->If this is not what you get, this means that the binary does not work on your system. This can be the case if you are using the pre-compiled binary packages. Due to limited resources, we can only target a small number of platforms with precompiled binaries. If your system is not among them, you can either switch to a supported platform or will need to [[SourceCode.SourceCode | compile from the source code]].
Added lines 59-60:
* First check the path is set correctly
Changed lines 65-67 from:
Use the same example as above, if the installation is done correctly, the command should return the following to:
Use the example as above (for downloaded binary packages), if the installation is done correctly, the command should return the following
->[@ Changed lines 69-70 from:
to:
Changed lines 73-76 from:
5. '''Sun Grid Engine''' (SGE) support for cluster-computing
If your computing infrastructure includes/implements SGE-based cluster-computing support, you can optionally enable DTI-TK to utilize this feature. The environment variable that needs to be defined in your .bashrc file is DTITK_USE_QSUB. Setting the variable to 1 will enable the SGE support. To disable this feature, simply setting the variable to 0.
to:
* Next check if the binary works as expected
Added lines 76-93:
VolumeInfo
@]
If the binary works correctly, you should see
->[@
Usage: VolumeInfo filename
@]
(This is typical of most DTI-TK commands. If you do not supply any arguments to the command, it will print out its usage instructions. In this example, the instruction means that you need to provide a single argument.)
If this is not what you get, this means that the binary does not work on your system. This can be the case if you are using the pre-compiled binary packages. Due to limited resources, we can only target a small number of platforms with precompiled binaries. If your system is not among them, you can either switch to a supported platform or will need to [[SourceCode.SourceCode | compile from the source code]].
5. '''Sun Grid Engine''' (SGE) support for cluster-computing
If your computing infrastructure includes/implements SGE-based cluster-computing support, you can optionally enable DTI-TK to utilize this feature. The environment variable that needs to be defined in your .bashrc file is DTITK_USE_QSUB. Setting the variable to 1 will enable the SGE support. To disable this feature, simply setting the variable to 0.
->[@
Changed lines 55-56 from:
->Include the above command to your .bashrc or .bash_profile files. If you use [[http://en.wikipedia.org/wiki/Tcsh | tcsh]] instead of bash, change the command accordingly. Defining the environment variable DTITK_ROOT is now '''mandatory'''.
to:
->Include the above command to your .bashrc or .bash_profile files. The instruction for Mac is available [[http://macbasics101.com/2011/02/14/create-bash_profile-file-mac/ | here]] and for Linux [[http://www.hypexr.org/bash_tutorial.php | here]]. If you use [[http://en.wikipedia.org/wiki/Tcsh | tcsh]] instead of bash, change the command accordingly. Defining the environment variable DTITK_ROOT is now '''mandatory'''.
Changed lines 4-5 from:
Follow ALL the steps below to ensure DTI-TK working properly. If you have compiled DTI-TK from source, skip the steps 1 and 2.
to:
Follow ALL the steps below to ensure DTI-TK working properly. If you have [[SourceCode.SourceCode | compiled DTI-TK from source]], skip the steps 1 and 2.
Changed lines 55-56 from:
->Include the above command to your .bashrc or .bash_profile files. [[<<]] If you use tcsh instead of bash, change the command accordingly. Defining the environment variable DTITK_ROOT is now mandatory.
to:
->Include the above command to your .bashrc or .bash_profile files. If you use [[http://en.wikipedia.org/wiki/Tcsh | tcsh]] instead of bash, change the command accordingly. Defining the environment variable DTITK_ROOT is now '''mandatory'''.
Changed lines 33-34 from:
3. '''Add the [[http://en.wikipedia.org/wiki/Path_(computing) | path]]''' to the DTI-TK and define the DTITK_ROOT variable. If you use the bash shell, use the following command
to:
3. '''Add the [[http://en.wikipedia.org/wiki/Path_(computing) | path]]''' to the DTI-TK and define the DTITK_ROOT variable.
The following is written for the [[http://en.wikipedia.org/wiki/Bash_(Unix_shell) | bash shell]]. If you are using a different shell environment, adapt the commands accordingly.
* To make temporary changes for the purpose of testing
Changed lines 44-45 from:
Replace ${DIR} with the full pathname of the directory where you've unpacked the binary package. e.g., if the full pathname to the directory is "/Users/huiz/unix", then the command to use will be
to:
'''IMPORTANT''':
** If you download the binary package, replace ${DIR} with the full pathname of the directory where you've unpacked the binary package. e.g., if the full pathname to the directory is "/Users/huiz/unix", then the command to use will be
Changed lines 51-52 from:
To add the path to the DTI-TK permanently, you can include the above command to your .bashrc or .bash_profile files. [[<<]] If you use tcsh instead of bash, change the command accordingly. Defining the environment variable DTITK_ROOT is now mandatory.
to:
** If you compile DTI-TK from source, replace ${DIR} with the full pathname of your installation directory.
* To add the path to the DTI-TK permanently
->Include the above command to your .bashrc or .bash_profile files. [[<<]] If you use tcsh instead of bash, change the command accordingly. Defining the environment variable DTITK_ROOT is now mandatory.
Changed lines 74-82 from:
@]
6. If you have '''compiled the code''' from the source code, it is always good to '''check the paths''' that are defined in the files contained in ${DTITK_ROOT}/scripts. Ideally you would check them all. In most of the scripts, you will find a line that says:
->[@
# source dtitk_common.sh
. ${DTITK_ROOT}/scripts/dtitk_common.sh
@]
Make sure that dtitk_common.sh is at this location on your machine, or change the path in each script if necessary.
You might also want to check the first line of the very file called ''dtitk_common.sh'', to make sure the path to DTITK is well defined. to:
Changed lines 33-34 from:
3. '''Add the path''' to the DTI-TK and define the DTITK_ROOT variable. If you use the bash shell, use the following command
to:
3. '''Add the [[http://en.wikipedia.org/wiki/Path_(computing) | path]]''' to the DTI-TK and define the DTITK_ROOT variable. If you use the bash shell, use the following command
Changed line 73 from:
You might also want to check the first line of the very file called ''dtitk_common.sh'', to make sure the path to DTITK is well defined. to:
You might also want to check the first line of the very file called ''dtitk_common.sh'', to make sure the path to DTITK is well defined.
Changed lines 4-5 from:
Follow ALL the steps below to ensure DTI-TK working properly.
to:
Follow ALL the steps below to ensure DTI-TK working properly. If you have compiled DTI-TK from source, skip the steps 1 and 2.
Changed line 67 from:
6. If you have compiled the code from the source code, it is always good to '''check several paths''' that are defined in the files contained in ${DTITK_ROOT}/scripts. Ideally you would check them all. In most of the scripts, you will find a line that says: to:
6. If you have '''compiled the code''' from the source code, it is always good to '''check the paths''' that are defined in the files contained in ${DTITK_ROOT}/scripts. Ideally you would check them all. In most of the scripts, you will find a line that says: Changed line 73 from:
You might also want to check the first line of the very file called ''dtitk_common.sh'', to make sure that the path is correctly defined. to:
You might also want to check the first line of the very file called ''dtitk_common.sh'', to make sure the path to DTITK is well defined.
Added lines 66-73:
6. If you have compiled the code from the source code, it is always good to '''check several paths''' that are defined in the files contained in ${DTITK_ROOT}/scripts. Ideally you would check them all. In most of the scripts, you will find a line that says:
->[@
# source dtitk_common.sh
. ${DTITK_ROOT}/scripts/dtitk_common.sh
@]
Make sure that dtitk_common.sh is at this location on your machine, or change the path in each script if necessary.
You might also want to check the first line of the very file called ''dtitk_common.sh'', to make sure that the path is correctly defined.
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