Closed richardbeare closed 2 years ago
Hi,
From those errors my best guess is that your error is related to this issue: https://github.com/DCAN-Labs/dcan_bold_processing/issues/5
The main issue is that the pipeline needs the run index suffix in filenames to have exactly two digits, (e.g. "task-rest01" or BIDS-style "task-rest_run-01", but not "task-enback101")
It should be addressed by https://github.com/DCAN-Labs/abcd-hcp-pipeline/pull/39, and there should be a new release of the pipeline with those changes within a few weeks.
If you're running via Docker/Singularity and want to try it sooner, I also have a build of that PR here: https://hub.docker.com/repository/docker/madisoth/abcd-hcp-pipeline (tag 10222021a)
That build uses the same version of DCAN-HCP (i.e. the pipeline code forked from HCP) as all previous release versions of abcd-hcp-pipeline, so there should be no differences in the image processing itself.
However, with the new build, output file and directory names won't be 100% consistent with output from older abcd-hcp-pipeline versions. So the safest option is to move/delete any old output and then rerun the pipeline from the start.
The other, time-saving option is to rerun from the FMRIVolume stage (--stage FMRIVolume
), which should work if you delete just the files generated between FMRIVolume and ExecutiveSummary stages:
That should leave just T1w, T2w, and MNINonLinear (minus the Results subdir) under files/ which should avoid problems from leftover files from any previous pipeline run.
Let me know if that helps!
Hi, I've been doing further testing and continue to run into problems. I tweaked the bids configuration so that files are named:
sub-rpb21jdr00005_ses-01_task-enbacka_bold.json
sub-rpb21jdr00005_ses-01_task-enbacka_bold.nii.gz
sub-rpb21jdr00005_ses-01_task-enbackb_bold.json
sub-rpb21jdr00005_ses-01_task-enbackb_bold.nii.gz
sub-rpb21jdr00005_ses-01_task-rest_bold.json
sub-rpb21jdr00005_ses-01_task-rest_bold.nii.gz
so no numbers in the end of the task name.
Tail of the .out is:
Assembling series images to build panel...
task-rest01 image expected and not found in summary directory
./img/DVARS_and_FD_task-rest01.png
Making series panel for task-rest01
./img/DVARS_and_FD_task-enbacka01.png
Writing series panel but series type is unknown; program exiting...
./img/postreg_DVARS_and_FD_task-enbacka01.png
Writing series panel but series type is unknown; program exiting...
./img/rpb21jdr00005_task-enbacka01_in_t1.gif
Writing series panel but series type is unknown; program exiting...
./img/rpb21jdr00005_t1_in_task-enbacka01.gif
Writing series panel but series type is unknown; program exiting...
./img/task-enbacka01_sbref.png
Writing series panel but series type is unknown; program exiting...
Making series panel for Unknown
I haven't checked yet whether enback
is hard coded somewhere. I haven't tested with the new versions mentioned above. This was a clean run after rerunning bids conversion to create new names.
Also note - I don't have any data derived from the eprime files available yet. Is that required?
Hey Richard!
When you named the tasks "enbacka" and "enbackb" the BIDS app recognized those as different tasks as opposed to the same task but different sessions.
As @madisoth mentioned above, I think filename needs exactly two digits in order to run properly. So I think you should rename them to this:
sub-rpb21jdr00005_ses-01_task-enback_run-01_bold.json
sub-rpb21jdr00005_ses-01_task-enback_run-01_bold.nii.gz
sub-rpb21jdr00005_ses-01_task-enback_run-02_bold.json
sub-rpb21jdr00005_ses-01_task-enback_run-02_bold.nii.gz
sub-rpb21jdr00005_ses-01_task-rest_run-01_bold.json
sub-rpb21jdr00005_ses-01_task-rest_run-01_bold.nii.gz
Also, to answer your question, the ABCD-BIDS pipeline does not use the event files for anything, so you should be fine without them :)
Hope this helps!
Thanks - a couple of updates.
First - running as above with this container https://hub.docker.com/repository/docker/madisoth/abcd-hcp-pipeline (tag 10222021a) does work.
Second, the resting state seems to pass in the form above? And it has no digits, with the pipeline introducing its own. Is there a reason why the non resting state bold needs to be constructed of separate runs? What if there are different tasks? Am I thinking about this the right way? At this stage I don't have a problem with them being recognised as different tasks.
@ericfeczko @madisoth do you have any answers for @richardbeare's question above?
Second, the resting state seems to pass in the form above? And it has no digits, with the pipeline introducing its own. Is there a reason why the non resting state bold needs to be constructed of separate runs? What if there are different tasks? Am I thinking about this the right way? At this stage I don't have a problem with them being recognised as different tasks.
In the 10222021a build and v0.1.0 release, the pipeline should no longer add those digits (please correct if I'm mistaken).
I believe in the past, it was done at least in part to accommodate the dcan_bold_processing "two-digit ending" assumption mentioned above ([https://github.com/DCAN-Labs/dcan_bold_processing/issues/5]()), and how it names the per-task concatenated timeseries output by stripping the run numbering from the input.
That said, with the current version any of the below should work for your BIDS input:
multiple tasks, 1 run each "task-enback1", "task-enback2" "task-enback1_run-01", "task-enback2_run-01" "task-enbackA", "task-enbackB" "task-enbackA_run-01", "task-enbackB_run-01"
1 task with multiple runs "task-enback_run-01", "task-enback_run-02"
@richardbeare I am goin to close this item as I think it is resolved, but please do feel free to reopen it if our responses aren't sufficient. Thank you!
Hi, I have the following error:
logs/ExecutiveSummary/ExecutiveSummary.err
Tail of the .out: