C-PAC on Habanero v.1.0.1
2020 May 20 ‒ 2020 June 25
Run 
rest_test_CPACv1.6.2_nuis1-3a-lower-thresh.yml without error in a Singularity image on Habanero with full dataset.
C-PAC on Habanero
C-PAC is the main product of the Computational Neuroimaging Lab. Habanero is a cluster server at Columbia University.
Specification Documents
Log
Wednesday, 2020 December 2
C-PAC • C-PAC on Habanero
| our copy of niworkflows v0.10.2 | niworkflows v1.3.2 | ||
|---|---|---|---|
| ANTs v2.1.0 | Docker | cpac-docker-image.tar.gz | cpac-docker-image.tar.gz |
| Singularity | cpac-singularity-image.simg | cpac-singularity-image.simg | |
| ANTs v2.3.4 | Docker | cpac-docker-image.tar.gz | cpac-docker-image.tar.gz |
| Singularity | cpac-singularity-image.simg | cpac-singularity-image.simg | |
Monday, 2020 November 30 ‒ Wednesday, 2020 December 2
C-PAC on Habanero
i am attaching a few more slurm files here from participants who i tried to re-run. got the same error for all, didn’t seem to run at all.
i submitted 14 pipelines using the strategies ryan suggested (i.e. each run its own singularity instance; running on 1 core; and using 2min delays for each instance). this went much more smoothly - only 2 came up with errors, which I am attaching here with teh slurm.out files and the data_config.yml file referenced in the slurm files. any thoughts on what the issues are here? i tried rerunning anyways to see if there was a glitch.
attached is the zipped crash directory.
- in addition, for all subjects who did get the full output on their first session, they did not have any output for their second session despite having very lot motion estimates as well. do i need to turn on the longitudinal setting for this to work?
I see ses-2 and ses-3 in the data config files, so I think these sessions are just being blocked by C-PAC crashing/dying before getting to them. You could try running a single post-ses-1 session by providing C-PAC with a --data_config_file with just that session, e.g., sub-181_ses-3.
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Crash files with reasons
FileNotFoundError
📎 crash-20201112-221527-av2902-check_func_scan.b7-9537c246-2f20-476d-8ca9-7ba142667aed.pklz
📎 crash-20201112-220558-av2902-select_scan_params.b1-958ca922-e993-42c3-aced-57c4db76ebd5.pklz
📎 crash-20201112-221314-av2902-anat_template_edge_0-03101fbf-8369-4057-9708-df43daac041d.pklz
📎 crash-20201112-221529-av2902-selectrest.b4-998f56dc-9a7c-49b5-a610-35dfb87cabba.pklz
📎 crash-20201112-221315-av2902-anat_template_edge_0-4cfa398f-0746-4018-8a6f-36d4bca6d962.pklz
📎 crash-20201112-220558-av2902-check_func_scan.b2-cda0c324-1b35-4f7f-92f1-a0fb43c6eaf2.pklz
📎 crash-20201112-221526-av2902-select_scan_params.b7-9caa04b0-5111-4da8-9d00-b27387e8ad59.pklz
📎 crash-20201112-220556-av2902-select_scan_params.b4-a4b8846b-91d9-4b22-99c8-daa8b573813f.pklz
📎 crash-20201112-221529-av2902-select_scan_params.b4-3140b40b-e151-4fce-ac92-5067e8877b8e.pklz
📎 crash-20201112-221532-av2902-check_func_scan.b1-0b84fb07-d153-49e0-8943-62f830a7786d.pklz
📎 crash-20201112-221530-av2902-check_func_scan.b3-760e09f1-163f-445d-b9f2-ddf27a39fceb.pklz
📎 crash-20201112-221527-av2902-select_scan_params.b6-50adcc1d-4260-4a58-8f4c-43b203b0ab52.pklz
📎 crash-20201112-221534-av2902-check_for_s3.a1-f13a93ea-5c6d-4d45-a8f9-657771feb81b.pklz
📎 crash-20201112-221259-av2902-lap_tmpl-6cea2816-eca3-43dc-96c3-ee9463bfe78c.pklz
📎 crash-20201112-221304-av2902-lap_tmpl-1950dcd9-381c-41a8-8515-db864a7f96f1.pklz
📎 crash-20201112-220556-av2902-select_scan_params.b4-eddd7b41-dca1-476d-b513-068ce63b1a04.pklz
📎 crash-20201112-220556-av2902-selectrest.b4-56363e91-6774-4f3f-9ede-47491f74ca47.pklz
📎 crash-20201112-220558-av2902-select_scan_params.b2-bc8bc608-6276-4627-807f-d0cedea5a893.pklz
📎 crash-20201112-221539-av2902-lap_tmpl-363cbf2f-65d4-4c06-a9c9-51b95d378023.pklz
📎 crash-20201112-221524-av2902-func_get_idx.b8-da1401b1-67e9-436d-82f7-93ba38731f95.pklz
📎 crash-20201112-221531-av2902-select_scan_params.b2-4e960093-33b1-49fd-9522-d9fb9e26e636.pklz
📎 crash-20201112-221524-av2902-func_get_idx.b8-edb2497f-6fc7-46db-8476-7a215dbf6ace.pklz
📎 crash-20201112-220557-av2902-select_scan_params.b3-a0a89daf-2aee-47cb-ab8f-f0a4889e8e93.pklz
📎 crash-20201112-221528-av2902-check_func_scan.b6-43fe4cfa-74e7-4415-a567-270a3eececcc.pklz
📎 crash-20201112-221531-av2902-selectrest.b2-3ebcd5e1-1d2b-4d3a-a7f1-5669f8b2ba9b.pklz
📎 crash-20201112-220556-av2902-selectrest.b4-b7833ce1-4cd6-40bb-9586-01870e6f9ba8.pklz
📎 crash-20201112-220557-av2902-selectrest.b3-b598b339-a138-411c-bfb9-86095f27a209.pklz
📎 crash-20201112-221530-av2902-check_func_scan.b3-7796b93f-e8cd-4d85-8232-dc16d6107c5e.pklz
📎 crash-20201112-221529-av2902-select_scan_params.b3-6dfc51af-99f1-411d-9a8e-d71e9e8b70fb.pklz
📎 crash-20201112-221525-av2902-check_func_scan.b8-e80d5b77-4845-4d23-9753-6bfaf4e76e3d.pklz
📎 crash-20201112-221530-av2902-check_for_s3.b3-20a366da-bb5c-451d-a09d-5606b754e8c3.pklz
📎 crash-20201112-221554-av2902-anat_template_edge_0-3207c2f7-5843-422d-ae2f-f04450b1ff48.pklz
📎 crash-20201112-221532-av2902-select_scan_params.b1-4e657ff7-a236-45a1-bb12-86c568604436.pklz
📎 crash-20201112-221525-av2902-sinker_0_raw_functional.b8-d3fc8914-590e-4da7-87a4-812e835bf4a2.pklz
📎 crash-20201112-220557-av2902-check_func_scan.b4-06250430-a644-4cda-b5d6-ae9716a497e3.pklz
📎 crash-20201112-221532-av2902-selectrest.b1-4bb19ae1-ddb5-4908-80ed-c561c8b4d20b.pklz
📎 crash-20201112-221534-av2902-check_for_s3.a0-02d9f09b-3705-456d-a534-e5e80bcd16ab.pklz
📎 crash-20201112-220557-av2902-check_func_scan.b3-3796764b-f33f-4bfd-97b7-e769776ed018.pklz
📎 crash-20201112-221528-av2902-selectrest.b5-d1536989-050e-4304-8a7c-2143a2e8417b.pklz
📎 crash-20201112-221532-av2902-selectrest.b1-698f15c9-eea7-49f8-b361-30c76e975951.pklz
📎 crash-20201112-221531-av2902-selectrest.b2-d7b39c6b-7a78-4a80-864c-d1ad7fa8d8cd.pklz
📎 crash-20201112-221531-av2902-check_func_scan.b2-97a54684-a9af-446a-a7bb-affbc0323a30.pklz
📎 crash-20201112-221529-av2902-check_func_scan.b4-093fc426-2f93-4825-959c-29c42731462c.pklz
📎 crash-20201112-220558-av2902-check_func_scan.b2-c5685c6b-3d44-4fa6-8de1-18c48222d8dd.pklz
📎 crash-20201112-220557-av2902-check_func_scan.b3-045770fb-5513-489c-8485-63277f569b78.pklz
📎 crash-20201112-221533-av2902-selectrest.b0-2d29da64-fd9b-4de0-a448-87b5d4f6cd43.pklz
📎 crash-20201112-220556-av2902-check_func_scan.b4-637714e9-3fe8-4d01-9b33-06db525822ca.pklz
📎 crash-20201112-221534-av2902-check_for_s3.a0-07a80d16-cbb6-4642-a686-566bde7c572f.pklz
📎 crash-20201112-221555-av2902-anat_template_edge_0-2d2933db-4629-444c-9b55-46982405d5c1.pklz
📎 crash-20201112-221526-av2902-check_for_s3.b7-2d078c4e-7134-4c2e-bbde-5a9f7fb02da3.pklz
📎 crash-20201112-221525-av2902-check_func_scan.b8-ad7897ae-a1d8-48d9-935a-93f6a93dbc18.pklz
📎 crash-20201112-221533-av2902-check_func_scan.b1-a4f55769-6b2a-45aa-bff7-8273c7cac44e.pklz
📎 crash-20201112-221529-av2902-selectrest.b4-f3a3525c-85bd-44a4-8ec2-00776e49b56c.pklz
📎 crash-20201112-220558-av2902-select_scan_params.b2-56b9681b-6399-4b4c-be3c-87e4421ff524.pklz
📎 crash-20201112-221527-av2902-select_scan_params.b6-9e911b35-cdcd-45cb-bf58-4a765e32f161.pklz
📎 crash-20201112-221532-av2902-select_scan_params.b1-26aa62ad-bb89-430f-b9ad-ac6549644387.pklz
📎 crash-20201112-221531-av2902-check_func_scan.b2-40fe4a59-5f18-40d2-ac01-c5cf36d95d9b.pklz
📎 crash-20201112-221531-av2902-select_scan_params.b2-7d6acfb9-e592-4510-a1df-31a2b0e11008.pklz
📎 crash-20201112-221456-av2902-lap_tmpl-76a1462f-3be0-4e5a-9588-180e2fd65129.pklz
📎 crash-20201112-221530-av2902-check_for_s3.b3-6b4c7668-0bf8-4599-bbf6-f557c63ab310.pklz
📎 crash-20201112-221528-av2902-select_scan_params.b5-38d8b4fe-89af-4623-a133-53ae1599e3da.pklz
📎 crash-20201112-221548-av2902-resample_o-142589a2-d388-4425-b6cd-ec04bf1dd8f1.pklz
📎 crash-20201112-221527-av2902-check_func_scan.b7-3fe9020c-c9b0-4209-bb44-5d28971fa04e.pklz
📎 crash-20201112-221525-av2902-sinker_0_raw_functional.b8-dcc67a78-7222-47ad-96a1-8242b82933c9.pklz
📎 crash-20201112-221544-av2902-lap_tmpl-d667fd47-bddf-4296-8776-65c7020565e5.pklz
📎 crash-20201112-221505-av2902-lap_tmpl-22267029-acb1-4a68-80e6-73a7a33f2b7c.pklz
Directory not empty
📎 crash-20201112-221528-av2902-select_scan_params.b4-c3ac09c3-7ffc-4e0d-b072-f67489ba9e03.pklz
📎 crash-20201112-220559-av2902-check_for_s3.b1-0402782f-c3bb-4161-b2c7-9b6857c8ff78.pklz
📎 crash-20201112-221533-av2902-check_func_scan.b0-d411de0f-b4c1-4cb0-aa01-7050b12b25c2.pklz
📎 crash-20201112-221528-av2902-select_scan_params.b5-ea2ac5ac-61c4-4d34-8a0b-83248db84a48.pklz
📎 crash-20201112-221529-av2902-check_func_scan.b4-0997fc0b-2917-4300-81bd-c376d78462ee.pklz
📎 crash-20201112-221533-av2902-select_scan_params.b0-95cba77b-fae9-42ed-b4bf-c9d1315d076e.pklz
📎 crash-20201112-221527-av2902-check_func_scan.b6-643a6816-0e8e-47da-a7af-09b54165d575.pklz
📎 crash-20201112-221527-av2902-selectrest.b6-88e73345-9cbe-4b9d-89a9-4b938fc7fc99.pklz
📎 crash-20201112-220558-av2902-selectrest.b2-89ed0d45-af9e-48e8-a889-53266c1c7861.pklz
📎 crash-20201112-221528-av2902-check_func_scan.b5-f9e1de15-1c2a-40ef-bfdd-be2e4d56ffa9.pklz
📎 crash-20201112-221528-av2902-selectrest.b5-d346b001-545d-4fb8-aabc-521c980e8f2b.pklz
OSError: .proc-* not found
📎 crash-20201112-221527-av2902-selectrest.b6-ba51562a-5103-4f05-9438-8724f88e9ec7.pklz
📎 crash-20201112-220558-av2902-selectrest.b2-2b2da5a9-1594-4dd7-b3a6-cde8a368d367.pklz
📎 crash-20201112-221528-av2902-check_func_scan.b5-80b76d16-b43c-4684-8aa4-294fd683da4d.pklz
📎 crash-20201112-221533-av2902-check_func_scan.b0-051245a2-7e1c-427f-94b9-07b3b089ba7c.pklz
📎 crash-20201112-221533-av2902-select_scan_params.b0-82199afa-6e43-40f7-9066-d8da60d6952e.pklz
📎 crash-20201112-221533-av2902-selectrest.b0-2dc8e5cb-c2b7-4846-aaee-216c585303fb.pklz
Tuesday, 2020 November 17
C-PAC on Habanero
- kick off run of
| name | description | mri | meg | eeg | ieeg | full data |
|---|---|---|---|---|---|---|
| ds006 | single task, multiple sessions, multiple runs, in-plane T2, events, T1w, BOLD | mri |
Monday, 2020 November 16 ‒ Tuesday, 2020 November 17
C-PAC on Habanero
- […] i ran CPAC:FX on 1.7.2. I ran 10 test subjects at a range of motion estimates (from very low motion to very high motion). 7/10 had outputs but 2 didn’t get all the way through (so 5 did!), and it looks like 3 of the very high motion subjects don’t have any output folders at all. […]
- in addition, for all subjects who did get the full output on their first session, they did not have any output for their second session despite having very lot motion estimates as well. do i need to turn on the longitudinal setting for this to work?
- i’m also not entirely sure what files would be helpful for you in helping me resolve the subjects who didn’t finish complete, but let me know!
I’m glad you’re seeing some success. We’ll do our best to help you get your pipeline working for everything else you want it to do. I’ll probably ask for some more files as I dig in, but to start, can you please share your pipeline configuration and data configuration (if any, or let me know if you’re just giving a BIDS directory)
i’m also happy to be seeing some success! we are feeding in a BIDS directory - most participants have at least 2 sessions and multiple scan runs that we are processing for each session. here is the config file i am using . running on 1 core. only things changed from original that Lei sent was some of the beginning information, turning on despiking, and specifying to extract an ROI time series for 2 atlases.
great, thanks! I’ll dig in more tomorrow
thank you! attached are all the slurm files.
it seems that many of the files are timeouts, so I will just relaunch those particular jobs. but there are some files that did not finish otherwise.
for sub-206_ses-1 (slurm-25509329.out; slurm-22509338.out)- i have these folders in the output;
coordinate_transformation motion_correct frame_wise_displacement_jenkinson motion_params frame_wise_displacement_power movement_parameters functional_brain_mask power_params functional_preprocessed qc functional_preprocessed_mask raw_functional max_displacement slice_time_corrected mean_functional
sub-026_ses-3 (slurm-25509335.out)- have these folders in the output:
qc raw_functional
sub-026_ses-2 (slurm-25509336.out; weird it says sub-303 at the top ….); here are the output files I have:
coordinate_transformation motion_correct frame_wise_displacement_jenkinson motion_params frame_wise_displacement_power movement_parameters functional_brain_mask power_params functional_preprocessed qc functional_preprocessed_mask raw_functional max_displacement slice_time_corrected mean_functional
At the top level of the output directory, could you please share the yaml file with the name that starts with cpac_data_config?