open-discussion
open-discussion > RE: DTIPrep CLI setup
Nov 30, 2021 07:11 PM | Michelle Han
RE: DTIPrep CLI setup
Hi Martin,
Thanks so much for the very quick response! I appreciate it. It looks like when I was trying to use that particular binary it was triggering the GUI to pop up because I wasn't giving it any parameters (I was expecting it to give me the "help" text if given no parameters). I've just tried it with some arbitrary parameters and it looks like that's what I was missing!
Thanks again for the help,
Michelle
Originally posted by Martin Styner:
Thanks so much for the very quick response! I appreciate it. It looks like when I was trying to use that particular binary it was triggering the GUI to pop up because I wasn't giving it any parameters (I was expecting it to give me the "help" text if given no parameters). I've just tried it with some arbitrary parameters and it looks like that's what I was missing!
Thanks again for the help,
Michelle
Originally posted by Martin Styner:
MacOS X generates
App packages, not simple binaries. But, a binary executable is
still generated as part of the package, which is located
in DTIPrep.app/Contents/MacOS and is called DTIPrep. You
should be able to call that DTIPrep with the usual CLI,
i.e. DTIPrep.app/Contents/MacOS/DTIPrep -p myProtocol.xml -c
-f myOutputFolder -w myInputDWI.nrrd
Best
Martin
Originally posted by Michelle Han:
Best
Martin
Originally posted by Michelle Han:
Hi,
I've been trying to set up the CLI for DTIPrep on OSX to write some DWI processing pipelines using DTIPrep. I've cloned into the GitHub repository and have built it (had to use "make -i" for errors in downloading ExternalData but otherwise, no errors). I see other binaries in DTIPrep-build/DTIPrepTools-install/bin but the DTIPrep itself is an app. And the DTIPrep.app contents in the bin folder, executing DTIPrep brings up the GUI.
Have I missed a step in the installation or am I not looking in the right place? I've included the error I was running into during installation in case that might be relevant to how the package was ultimately installed.
Thanks so much!
Michelle
--------------
CMake Error at /work/DTIPrep-build/BRAINSTools/CMake/ExternalData.cmake:1012 (message):
Object MD5=94839def0264128ad7f42119a08bc66f not found at:
file:////work/DTIPrep-build/BRAINSTools/... ("Couldn't read a file:// file")
http://slicer.kitware.com/midas3/api/res... ("HTTP response code said error")
http://midas3.kitware.com/midas/api/rest... ("HTTP response code said error")
http://www.itk.org/files/ExternalData/MD... ("HTTP response code said error")
file:////work/DTIPrep-build/BRAINSTools/... ("Couldn't read a file:// file")
http://slicer.kitware.com/midas3/api/res... ("HTTP response code said error")
http://midas3.kitware.com/midas/api/rest... ("HTTP response code said error")
http://www.itk.org/files/ExternalData/MD... ("HTTP response code said error")
Call Stack (most recent call first):
/work/DTIPrep-build/BRAINSTools/CMake/ExternalData.cmake:1034 (_ExternalData_download_object)
I've been trying to set up the CLI for DTIPrep on OSX to write some DWI processing pipelines using DTIPrep. I've cloned into the GitHub repository and have built it (had to use "make -i" for errors in downloading ExternalData but otherwise, no errors). I see other binaries in DTIPrep-build/DTIPrepTools-install/bin but the DTIPrep itself is an app. And the DTIPrep.app contents in the bin folder, executing DTIPrep brings up the GUI.
Have I missed a step in the installation or am I not looking in the right place? I've included the error I was running into during installation in case that might be relevant to how the package was ultimately installed.
Thanks so much!
Michelle
--------------
CMake Error at /work/DTIPrep-build/BRAINSTools/CMake/ExternalData.cmake:1012 (message):
Object MD5=94839def0264128ad7f42119a08bc66f not found at:
file:////work/DTIPrep-build/BRAINSTools/... ("Couldn't read a file:// file")
http://slicer.kitware.com/midas3/api/res... ("HTTP response code said error")
http://midas3.kitware.com/midas/api/rest... ("HTTP response code said error")
http://www.itk.org/files/ExternalData/MD... ("HTTP response code said error")
file:////work/DTIPrep-build/BRAINSTools/... ("Couldn't read a file:// file")
http://slicer.kitware.com/midas3/api/res... ("HTTP response code said error")
http://midas3.kitware.com/midas/api/rest... ("HTTP response code said error")
http://www.itk.org/files/ExternalData/MD... ("HTTP response code said error")
Call Stack (most recent call first):
/work/DTIPrep-build/BRAINSTools/CMake/ExternalData.cmake:1034 (_ExternalData_download_object)
Threaded View
| Title | Author | Date |
|---|---|---|
| Michelle Han | Nov 30, 2021 | |
| Martin Styner | Nov 30, 2021 | |
| Michelle Han | Nov 30, 2021 | |