open-discussion
open-discussion > RE: DWIConvert
Mar 22, 2018 08:03 PM | Micah Johnson - UCLA Department of Psychology
RE: DWIConvert
Thank you both very much. Yes fortunately I'm running on Linux
(well, it's bash on windows). The unu command for unzipped output
worked, and now I'm running the zipped version (see code below,
it's taking much longer, still running)
Can I confirm with you that the code I'm runningn for DWIConvert is still accurate, given the new Slicer 4.8? (see below)
## Running DWIConvert to go from nii to nrrd
$SlicerNew --launch DWIConvert --inputVolume ${origDWI}.nii.gz --conversionMode FSLToNrrd --inputBValues ${bval}.txt --inputBVectors ${bvec}.txt --outputVolume ${nrrdraw}.nrrd
## Using the unu command
$SlicerOld --launch unu convert -t short -clamp -i ${DTIPREPDIR}/${SUBJ}_dwi_QCed.nrrd | $SlicerOld --launch unu save -e gzip -f nrrd -o ${DTIPREPDIR}/${SUBJ}_dwi_QCed_unu.nrrd
## Running the DWIConvert take unu output and go from nrrd to nii
$SlicerNew --launch DWIConvert --inputVolume ${nrrdraw}_QCed_unu.nrrd --conversionMode NrrdToFSL --outputBValues ${bval}_QCed.txt --outputBVectors ${bvec}_QCed.txt --outputVolume ${nrrdraw}_QCed.nii.gz
Another strange thing is that now I cannot run this code from my original .sh script (it only works on the command line), from the script produces the error below:
--launch: command not found
Have you seen this before?
Is it possible it's because I deleted the NA-MIC settings folder? (as instructed on the website, copied below)
[On Linux, remove the directory where the application is located. To clean up settings, remove "~/.config/NA-MIC/"]
Can I confirm with you that the code I'm runningn for DWIConvert is still accurate, given the new Slicer 4.8? (see below)
## Running DWIConvert to go from nii to nrrd
$SlicerNew --launch DWIConvert --inputVolume ${origDWI}.nii.gz --conversionMode FSLToNrrd --inputBValues ${bval}.txt --inputBVectors ${bvec}.txt --outputVolume ${nrrdraw}.nrrd
## Using the unu command
$SlicerOld --launch unu convert -t short -clamp -i ${DTIPREPDIR}/${SUBJ}_dwi_QCed.nrrd | $SlicerOld --launch unu save -e gzip -f nrrd -o ${DTIPREPDIR}/${SUBJ}_dwi_QCed_unu.nrrd
## Running the DWIConvert take unu output and go from nrrd to nii
$SlicerNew --launch DWIConvert --inputVolume ${nrrdraw}_QCed_unu.nrrd --conversionMode NrrdToFSL --outputBValues ${bval}_QCed.txt --outputBVectors ${bvec}_QCed.txt --outputVolume ${nrrdraw}_QCed.nii.gz
Another strange thing is that now I cannot run this code from my original .sh script (it only works on the command line), from the script produces the error below:
--launch: command not found
Have you seen this before?
Is it possible it's because I deleted the NA-MIC settings folder? (as instructed on the website, copied below)
[On Linux, remove the directory where the application is located. To clean up settings, remove "~/.config/NA-MIC/"]
Threaded View
Title | Author | Date |
---|---|---|
Jacek M | Apr 8, 2016 | |
Micah Johnson | Mar 22, 2018 | |
Daniel Berge | Mar 22, 2018 | |
Micah Johnson | Mar 22, 2018 | |
Daniel Berge | Mar 22, 2018 | |
Martin Styner | Mar 22, 2018 | |
Micah Johnson | Mar 22, 2018 | |
Micah Johnson | Mar 22, 2018 | |
Daniel Berge | Mar 22, 2018 | |
Micah Johnson | Mar 22, 2018 | |
Daniel Berge | Mar 22, 2018 | |
Micah Johnson | Mar 22, 2018 | |
Micah Johnson | Mar 22, 2018 | |
Ryan H | Jan 23, 2018 | |
Martin Styner | Jan 26, 2018 | |
Ryan H | Jan 26, 2018 | |
Martin Styner | Jan 26, 2018 | |
Ryan H | Jan 26, 2018 | |
Martin Styner | Jan 26, 2018 | |
Ryan H | Jan 26, 2018 | |
Martin Styner | Jan 29, 2018 | |
Ryan H | Jan 29, 2018 | |
Martin Styner | Jan 30, 2018 | |
Ryan H | Jan 30, 2018 | |
Martin Styner | Jan 31, 2018 | |
Ryan H | Feb 2, 2018 | |
Martin Styner | Feb 19, 2018 | |
Ryan H | Feb 19, 2018 | |
Martin Styner | Feb 21, 2018 | |
Ryan H | Jan 31, 2018 | |
Maike Kleemeyer | Jan 10, 2018 | |
Martin Styner | Jan 10, 2018 | |
Maike Kleemeyer | Jan 11, 2018 | |
Martin Styner | Jan 11, 2018 | |
Maike Kleemeyer | Jan 15, 2018 | |
Martin Styner | Jan 17, 2018 | |
Maike Kleemeyer | Jan 18, 2018 | |
Martin Styner | Jan 18, 2018 | |
Marie Drottar | Jun 7, 2016 | |
Jacek M | Apr 27, 2016 | |
Martin Styner | Apr 27, 2016 | |
Jacek M | Apr 15, 2016 | |
Martin Styner | Apr 15, 2016 | |
Micah Johnson | Mar 27, 2018 | |
Daniel Berge | Apr 2, 2018 | |
Micah Johnson | Apr 2, 2018 | |
Juan Prieto | Apr 8, 2016 | |
Jacek M | Apr 13, 2016 | |
Martin Styner | Apr 13, 2016 | |
Jacek M | Apr 13, 2016 | |
Martin Styner | Apr 8, 2016 | |