amakropoulos / structural-pipeline-measures Goto Github PK

Hi all,

Will the docker image compile the measurements if only T2 images were used? Is there some work around to get it to run in this case. Thanks!

Best,
Alex

Hello, I have successfully run the dhcp-structural-pipeline with the docker image.
However, when I tried to run the structural-pipeline-measures with the docker image using 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"
the error occurred

**feifei@feifei-virtual-machine:/var/lib/docker$ sudo docker run --rm -t -v $PWD/data:/data -u $(id -u):$(id -g) biomedia/dhcp-structural-pipeline-measures:latest /data/participants.tsv --reporting
Reporting for the dHCP pipeline

Derivatives directory: /data/derivatives
participants.tsv: /data/participants.tsv
datadir: /data
scriptdir: /usr/src/structural-pipeline-measures/scripts
reportsdir: /data/reports
logdir: /data/logs
reporting: 1

/usr/src/structural-pipeline-measures/pipeline.sh /data/participants.tsv --reporting

CC00060XX03 bad gender 12501
computing volume/surface measurements of subjects...
gathering volume/surface measurements of subjects...
completed volume/surface measurements

computing QC measurements for subjects...

gathering QC measurements of subjects...
creating QC reports...
structural_dhcp_mriqc -o /data/reports -w /data/reports/workdir --dhcp-measures /data/reports/dhcp-measurements.json --qc-measures /data/reports/qc-measurements.json --nthreads 1 failed**

The "qc.err" file:
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 37, in ms_anat_dhcp
with open(settings['qc_measures'], 'r') as jsondata:
FileNotFoundError: [Errno 2] No such file or directory: '/data/reports/qc-measurements.json'
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'

How to deal with this problem?

Thanks in advance

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

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

When running the QC code over a dataset which has only T2 images, Nipype seems to fail.

The failing workflow is here.
https://github.com/amakropoulos/structural-pipeline-measures/blob/master/packages/structural_dhcp_mriqc/structural_dhcp_mriqc/utils/mriqc_run.py#L146

We were able to workaround by try-excepting RuntimeError, and Nipype runs through at least on the T2.

Thanks,
Ash

The script doesn't find the surfaces despite their existence (image attached).

CC00050XX01-7201-measures.log

I'd tried to change the compute-measurements.sh because it was searching for a file with a different name:

if [ ! -f $subj/$subj-curvature-regions ];then if [ ! -f $surfdir/${subj}_left_white.surf.gii ];then echo "The left WM surface for subject $subj doesn't exist"; exit;fi if [ ! -f $surfdir/${subj}_right_white.surf.gii ];then echo "The right WM surface for subject $subj doesn't exist"; exit;fi

to:

if [ ! -f $subj/$subj-curvature-regions ];then if [ ! -f $surfdir/${subj}_hemi-left_wm.surf.gii ];then echo "The left WM surface for subject $subj doesn't exist"; exit;fi if [ ! -f $surfdir/${subj}_hemi-right_wm.surf.gii ];then echo "The right WM surface for subject $subj doesn't exist"; exit;fi

but did not work as well. Does anyone have any suggestions on how to overcome this?

Thank you!

hi, i have installed the BioMedIA/dhcp-structural-pipeline using the docker method, and running it through powershell. Is someone able to give me an idiots guide to actually running this through the powershell command line...

when entered into the command line, nothing happens:
. [dHCP_structural_pipeline_path]/parameters/path.sh

Thanks!

Hi,
I'm not sure if this might be a specific error due to our use of a Singularity container.

/usr/lib/python3.5/re.py:203: FutureWarning: split() requires a non-empty pattern match.
  return _compile(pattern, flags).split(string, maxsplit)
<string>:17: (WARNING/2) Block quote ends without a blank line; unexpected unindent.
Traceback (most recent call last):
  File "/usr/local/bin/structural_dhcp_mriqc", line 10, in <module>
    sys.exit(main())
  File "/flush2/van483/software/structural-pipeline-measures-master/packages/structural_dhcp_mriqc/structural_dhcp_mriqc/utils/mriqc_run.py", line 152, in main
    workflow_report(dtype, settings)
  File "/flush2/van483/software/structural-pipeline-measures-master/packages/structural_dhcp_mriqc/structural_dhcp_mriqc/reports/generators.py", line 113, in workflow_report
    summary_cover(dframe, qctype, dframe2, out_file=out_sum)
  File "/flush2/van483/software/structural-pipeline-measures-master/packages/structural_dhcp_mriqc/structural_dhcp_mriqc/reports/generators.py", line 332, in summary_cover
    text=template.compile(context), output=out_file, compressed=True)
  File "/usr/local/lib/python3.5/dist-packages/structural_dhcp_rst2pdf/createpdf.py", line 642, in createPdf
    subtitle=self.doc_subtitle
  File "/usr/local/lib/python3.5/dist-packages/structural_dhcp_rst2pdf/createpdf.py", line 139, in renderTemplate
    return templateEngine.render(tname, context)
  File "/usr/local/lib/python3.5/dist-packages/tenjin.py", line 1960, in render
    template = self.get_template(template_name, context, globals)
  File "/usr/local/lib/python3.5/dist-packages/tenjin.py", line 1890, in get_template
    cache.set(cachepath, template)
  File "/usr/local/lib/python3.5/dist-packages/tenjin.py", line 1271, in set
    return self._store(cachepath, dct)
  File "/usr/local/lib/python3.5/dist-packages/tenjin.py", line 1325, in _store
    _write_binary_file(cachepath, data)
  File "/usr/local/lib/python3.5/dist-packages/tenjin.py", line 56, in _write_binary_file
    f = open(tmpfile, 'w+b')     # on windows, 'w+b' is preffered than 'wb'
PermissionError: [Errno 13] Permission denied: '/usr/local/lib/python3.5/dist-packages/structural_dhcp_rst2pdf/templates/cover.tmpl.cache.19878839980185548'

Is this unexpected? Any comments are greatly appreciated.

Thanks,
Ash

Hello,
I am running this pipeline to extract the morphological measurements from the dHCP database. I set the derivatives as the rel3_dhcp_anat_pipeline folder (directly downloaded from the server) and selected a few subjects (file appended). However, I am getting the following error (.log file as example appended):

Image Exception : #63 :: No image files match: sub-CC00050XX01_ses-7201/temp/tissue_labels terminate called after throwing an instance of 'std::runtime_error' what(): No image files match: sub-CC00050XX01_ses-7201/temp/tissue_labels /mnt/4T/dHCP/structural-pipeline-measures-master/scripts/compute-QC-measurements.sh, linha 22: 32243 Abortado "$@"

How do I overcome this? shouldn't this rel3 directory have all the necessary files from the structural pipeline?

Thank you!

dataset.csv
CC00050XX01-7201-measures.log
.