structural-pipeline-measures fails

[yuniorcf]

Hello, I am trying to run the pipeline but I don't get it to work. Please see below what I get in the terminal:

(base) yunior@pc-Neonat:~/DHCP/structural-pipeline-measures$ ./pipeline.sh /home/yunior/DHCP/data/derivatives/ /home/yunior/DHCP/data/dataset_11.csv --reporting Reporting for the dHCP pipeline Derivatives directory: /home/yunior/DHCP/data/derivatives/ Dataset CSV: /home/yunior/DHCP/data/dataset_11.csv

./pipeline.sh /home/yunior/DHCP/data/derivatives/ /home/yunior/DHCP/data/dataset_11.csv --reporting

computing volume/surface measurements of subjects... subject-11 session-1

gathering volume/surface measurements of subjects... cat: /home/yunior/DHCP/structural-pipeline-measures/reports/workdir/sub-subject-11_ses-session-1/sub-subject-11_ses-session-1-thickness: No such file or directory cat: /home/yunior/DHCP/structural-pipeline-measures/reports/workdir/sub-subject-11_ses-session-1/sub-subject-11_ses-session-1-thickness-regions: No such file or directory cat: /home/yunior/DHCP/structural-pipeline-measures/reports/workdir/sub-subject-11_ses-session-1/sub-subject-11_ses-session-1-sulc: No such file or directory cat: /home/yunior/DHCP/structural-pipeline-measures/reports/workdir/sub-subject-11_ses-session-1/sub-subject-11_ses-session-1-sulc-regions: No such file or directory cat: /home/yunior/DHCP/structural-pipeline-measures/reports/workdir/sub-subject-11_ses-session-1/sub-subject-11_ses-session-1-curvature: No such file or directory cat: /home/yunior/DHCP/structural-pipeline-measures/reports/workdir/sub-subject-11_ses-session-1/sub-subject-11_ses-session-1-curvature-regions: No such file or directory cat: /home/yunior/DHCP/structural-pipeline-measures/reports/workdir/sub-subject-11_ses-session-1/sub-subject-11_ses-session-1-GI: No such file or directory cat: /home/yunior/DHCP/structural-pipeline-measures/reports/workdir/sub-subject-11_ses-session-1/sub-subject-11_ses-session-1-GI-regions: No such file or directory cat: /home/yunior/DHCP/structural-pipeline-measures/reports/workdir/sub-subject-11_ses-session-1/sub-subject-11_ses-session-1-surface-area: No such file or directory cat: /home/yunior/DHCP/structural-pipeline-measures/reports/workdir/sub-subject-11_ses-session-1/sub-subject-11_ses-session-1-surface-area-regions: No such file or directory cat: /home/yunior/DHCP/structural-pipeline-measures/reports/workdir/sub-subject-11_ses-session-1/sub-subject-11_ses-session-1-rel-surface-area-regions: No such file or directory completed volume/surface measurements

computing QC measurements for subjects... subject-11 session-1

gathering QC measurements of subjects... creating QC reports... copying reports... cp: cannot stat '/home/yunior/DHCP/structural-pipeline-measures/reports/anatomical_subject-11.pdf': No such file or directory

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When looking to the error file it seems to have a problem to run mirtk (see attached files).

Additionally, to make it clear, I am unable to run the original pipeline for segmentation using for example the following command line: ./dhcp-pipeline.sh subject11 session1 34 -T2 subject11-T2.nii.gz -T1 subject11-T1.nii.gz -t 8 it only work if i use instead: $ sudo docker run --rm -t -u $(id -u):$(id -g) -v $PWD/data:/data biomedia/dhcp-structural-pipeline:latest subject11 session1 34 -T1 data/T1w.nii.gz -T2 data/T2w.nii.gz -t 8

I wonder whether is there a way to run structural-pipeline-measures by using a simmilar command line intead of the one posted in this web page

Thanks in advance

subject-11-session-1-measures.log subject-11-session-1-measures.err.txt

[feifei6699]

Hello, have you solved this problem? I met the same problem: "The left WM surface for subject sub-CC00099AN18_ses-34200 doesn't exist".

[yuniorcf-80]

Hi, unfortunately I was not able to run the structural-pipeline-measures sucessfully in my own machine. However I could made it work by using the following command: sudo docker run --rm -t -v $PWD/data:/data -u $(id -u):$(id -g) biomedia/dhcp-structural-pipeline-measures:latest /data/participants.tsv --reporting

hope it also works for you

[feifei6699]

Thanks so much for your helpful info!

[feifei6699]

Hi, unfortunately I was not able to run the structural-pipeline-measures sucessfully in my own machine. However I could made it work by using the following command: sudo docker run --rm -t -v $PWD/data:/data -u $(id -u):$(id -g) biomedia/dhcp-structural-pipeline-measures:latest /data/participants.tsv --reporting

hope it also works for you

Hello, when I used the command: "sudo docker run --rm -t -v $PWD/data:/data -u $(id -u):$(id -g) biomedia/dhcp-structural-pipeline-measures:latest /data/participants.tsv --reporting", I had this problem:

Traceback (most recent call last): File "/usr/local/bin/structural_dhcp_mriqc", line 11, in sys.exit(main()) File "/usr/local/lib/python3.5/dist-packages/structural_dhcp_mriqc/utils/mriqc_run.py", line 144, in main run_id=opts.run_id, settings=settings) File "/usr/local/lib/python3.5/dist-packages/structural_dhcp_mriqc/workflows/core.py", line 49, in ms_anat_dhcp raise RuntimeError('No scans found in %s' % settings['dhcp_data']) KeyError: 'dhcp_data'

Do you know how to solve this problem? Thanks for your time!

[moraesfernanda]

I am with the same problem with mirtk running natively. Do you have any suggestions for a version of this command "sudo docker run --rm -t -v (id -u):$(id -g) biomedia/dhcp-structural-pipeline-measures:latest /data/participants.tsv --reporting" out of docker?

[moraesfernanda]

Hi, i mange to fiz the erro by installing mirtk using

wget -O mirtk https://bintray.com/schuhschuh/AppImages/download_file?file_path=MIRTK%2Bview-latest-x86_64-glibc2.15.AppImage
chmod a+x mirtk
sudo mv mirtk /usr/bin

from their website https://mirtk.github.io/getstarted.html.