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pnlbwh / pnlpipe

A Python-based framework for processing anatomical (T1, T2) and diffusion weighted images
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fs2dwi: unu error #49

Closed pawelwrobel2 closed 4 years ago

pawelwrobel2 commented 4 years ago

Dear pnlpipe-developers,

after setting up the pnlpipe (including pnlNipype and pnlutil) I have converted the dwis in nifti format to nrrd with ConvertBetweenFileFormats, which went smoothly and without any errors. Currently I am using fs2dwi to register the freesurfer_output to the dwis. However, during the process unu commands seem to have a problem with the execution

fs2dwi_output.txt

I sourced the entire software that comes with the pipe. Do you know how I could approach this issue? I will appreciate your help a lot!

Kind regards, Pawel

tashrifbillah commented 4 years ago

Hi @pawelwrobel2 , fs2dwi.sh is no longer supported. In fact, none of the .sh scripts from pnlutil are supported. We strongly discourage using them. This is the script for nrrd and this is for nifti. Can you try them instead?

pawelwrobel2 commented 4 years ago

Thank You Tashrif, I'll try these

pawelwrobel2 commented 4 years ago

Hello Tashrif, unfortunately after using both scripts (for nrrd and nifti files) I receive the message that "no comand was given". Prior to that, when testing with the --help flag I received the correct help-output and once testing it with false input files the script realises that the input is incorrect.

tashrifbillah commented 4 years ago

I see. After whatever you have written, try putting direct. Search this page for nifti_fs2dwi and see some examples.