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KUL-Radneuron / KUL_VBG

A workflow to allow Freesurfer recon-all to run on brain image with gliomas
Mozilla Public License 2.0
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Script doesn't find the data files #3

Closed vilsaira closed 3 years ago

vilsaira commented 3 years ago

Hi,

Here is the running command I tried: ~/KUL_VBG/KUL_VBG.sh -p pat001 -a sub-pat001.nii.gz -l sub-01_ses-001_roCFM.nii.gz -z T1 -o uVBG -t -F -n 6 -B 1

I ran the script in the directory where I had the data. I also tried to give the full path and it gave the same error below:

Inputs are -p pat001 -lesion sub-01_ses-001_roCFM.nii.gz -lesion_space T1 /root/KUL_VBG/KUL_VBG.sh: line 283: : No such file or directory T1 images provided as sub-pat001.nii.gz /root/KUL_VBG/KUL_VBG.sh: line 398: : No such file or directory Preproc dir is <fullpath>/VBG_out/proc_VBG/sub-pat001 and output dir is uVBG/output_VBG/sub-pat001 You are using KUL_VBG.sh version 0.48_08022021

You have specified HD-BET for brain extraction, please make sure it is called correctly from within KUL_VBG In case of BET problems see lines 1124 - 1200

update function path to reflect funciton name line 514

Ideas how to fix this? I should have all the prerequisites installed and I also tried with -B 2 but it gave again the same error expect for the HD-BET part.

Lesion mask and T1 volumes are identical so that shouldn't be the problem.

vilsaira commented 3 years ago

Got forward, the script required replacing ${prep_log} with "${prep_log}" in few locations and adding the script location to the path.

Rad-dude commented 3 years ago

Hi vilsaira,

I was indeed going to suggest adding it to path first.

this is line 283: echo "Inputs are -p ${subj} -lesion ${L_mask} -lesion_space ${L_mask_space}" >> ${prep_log} and this is line 398: echo " We found T1 WIs ${T1_orig}" >> ${prep_log}

Indeed as you suggest this was due to incorrect referral to ${prep_log}.

I'm now fixing this and will push the fixed version.

Thanks for your feedback.

Rad-dude commented 3 years ago

I've just pushed the fixed version if you would like to clone and try it out. We can keep this issue open till then also.

Best, AR

vilsaira commented 3 years ago

Thanks, pulled the new version and it seems to work out of the box (with ANTs bet). I didn't get the HD-BET working, unfortunately.

Rad-dude commented 3 years ago

Glad to hear it's working, for help with HD-BET maybe check out their github repo for installation instructions (https://github.com/MIC-DKFZ/HD-BET), HD-BET has a number of dependencies that are listed also on their page.

You can install it via a conda virtual environment for example if it's conflicting with any other packages in your default python environment.

I will close this issue for now since the main issue is resolved.