Measurements Pipeline Problems

t2784 · January 25, 2021, 12:59pm

Hi the measurements pipeline (from amakropoulos) is showing this error when I run it using subject I have downloaded from the dhCP data release. I have saved the folders within the derivatives dir within the dhcp-structural-pipeline dir. I note that there is no ‘native’ dir within the dhcp data release folder tree… is this an issue (given that a native folder is generated by the segmentation pipeline)?

any thoughts? Thank you

gathering volume/surface measurements of subjects…
cat: /home/tay/Downloads/structural-pipeline-measures-master/reports/workdir/sub-CC00073XX08_ses-27800/sub-CC00073XX08_ses-27800-thickness: No such file or directory
cat: /home/tay/Downloads/structural-pipeline-measures-master/reports/workdir/sub-CC00073XX08_ses-27800/sub-CC00073XX08_ses-27800-thickness-regions: No such file or directory
cat: /home/tay/Downloads/structural-pipeline-measures-master/reports/workdir/sub-CC00073XX08_ses-27800/sub-CC00073XX08_ses-27800-sulc: No such file or directory
cat: /home/tay/Downloads/structural-pipeline-measures-master/reports/workdir/sub-CC00073XX08_ses-27800/sub-CC00073XX08_ses-27800-sulc-regions: No such file or directory
cat: /home/tay/Downloads/structural-pipeline-measures-master/reports/workdir/sub-CC00073XX08_ses-27800/sub-CC00073XX08_ses-27800-curvature: No such file or directory
cat: /home/tay/Downloads/structural-pipeline-measures-master/reports/workdir/sub-CC00073XX08_ses-27800/sub-CC00073XX08_ses-27800-curvature-regions: No such file or directory
cat: /home/tay/Downloads/structural-pipeline-measures-master/reports/workdir/sub-CC00073XX08_ses-27800/sub-CC00073XX08_ses-27800-GI: No such file or directory
cat: /home/tay/Downloads/structural-pipeline-measures-master/reports/workdir/sub-CC00073XX08_ses-27800/sub-CC00073XX08_ses-27800-GI-regions: No such file or directory
cat: /home/tay/Downloads/structural-pipeline-measures-master/reports/workdir/sub-CC00073XX08_ses-27800/sub-CC00073XX08_ses-27800-surface-area: No such file or directory
cat: /home/tay/Downloads/structural-pipeline-measures-master/reports/workdir/sub-CC00073XX08_ses-27800/sub-CC00073XX08_ses-27800-surface-area-regions: No such file or directory
cat: /home/tay/Downloads/structural-pipeline-measures-master/reports/workdir/sub-CC00073XX08_ses-27800/sub-CC00073XX08_ses-27800-rel-surface-area-regions: No such file or directory

jcupitt · January 25, 2021, 3:35pm

Hello @t2784, thanks for the report, I’ll try to have a look at this tomorrow.

t2784 · January 25, 2021, 7:57pm

Hi thanks
Happy to provide more info that might help solve this. Kind regards!

jcupitt · January 26, 2021, 5:02pm

Hi again, the measurements pipeline runs on the output of the structural pipeline, not on the data release.

The data release contains some files from the struct pipeline run, though not all, and gives them different, BIDS-compliant names. It’s rather unfortunate

You’ll have to run the struct pipeline yourself, then run measure on the output directory from that.

t2784 · January 28, 2021, 9:43am

Thank you for your helpful answer, I hope you wont mind a follow up question related to this pipeline.
I have segmented a couple of brains (apparently successfully), and now run the measures pipeline, but the output looks odd. I have copied the csv output, and there are many parameters that are empty, some values are negative, and the volume values dont seem to correspond to those generated by ITK snap. I have attached some corresponding files, and at this link:

Thank you very much for your help with this.

jcupitt · January 28, 2021, 11:43am

I remember finding the measures pipeline hard to build. Perhaps there is some issue with the versions of the various packages?

We have the binary we use as an image on dockerhub. You could try running that – there are some notes in the README:

t2784 · January 29, 2021, 9:41am

Hi John, thank you for your help with this. I feel like I am failing at the final hurdle now!
I ran the segmentation pipeline overnight using docker, and that has worked nicely. However the (docker) measures pipeline is still having an error.
Couple of points:

the readme now wants a ‘gender’ in the participants.tsv, which is a new requirement. I have tried every combination of sequence with subject id etc… if this is something stupid I am doing please let me know
The anat_group_measurements.csv is not created… is that because of point 1? or something else.

artemis · September 15, 2022, 8:36am

Hi @t2784,

were you able to fix the issue with the ‘bad gender’ error?

Thank you!

Best,
Artemis