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preprocessed-connectomes-project / quality-assessment-protocol

Scripts and documentation for the PCP's protocol for assessing data quality.
BSD 3-Clause "New" or "Revised" License
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[BUG] CSV file for anatomical measures not created - part 2 #55

Closed hebbianloop closed 8 years ago

hebbianloop commented 8 years ago

Hi,

I followed the advice for setting absolute paths in the previous bug resolution but this did not fix the bug:

File "pandas/parser.pyx", line 353, in pandas.parser.TextReader.cinit (pandas/parser.c:3246) File "pandas/parser.pyx", line 591, in pandas.parser.TextReader._setup_parser_source (pandas/parser.c:6111) IOError: File /Volumes/Archive.ADS/ADS/analysis/ads.qap/qap_anatomical_spatial.csv does not exist

the configuration file is as below

num_cores_per_subject: 4

num_subjects_at_once: 6

output_directory: /Volumes/Archive.ADS/ADS/analysis/ads.qap

working_directory: /Volumes/Archive.ADS/ADS/analysis/ads.qap/working

write_all_outputs: True

template_brain_for_anat: /usr/local/fsl/data/standard/MNI152_T1_2mm_brain.nii.gz

template_skull_for_anat: /usr/local/fsl/data/standard/MNI152_T1_2mm.nii.gz

write_report: True

write_graph: True

jpellman commented 8 years ago

Hi @seldamat ,

Are there any files being generated in the output directory that end in '.pklz'? These are nipype crash files that might be able to aid us in narrowing down what might have caused the crash.

hebbianloop commented 8 years ago

Hi John,

Thank you for your quick attention. There are no files in the output directory that end in .pklz.

shad@foo:/Volumes/Archive.ADS/ADS/analysis/ads.qap 👾 ls -al total 64K drwxr-xr-x 8 shad 272 Aug 2 16:06 . drwxr-xr-x 11 shad 374 Aug 2 16:02 .. -rw-r--r-- 1 shad 6.1K Aug 2 15:49 .DS_Store drwxr-xr-x 134 shad 4.5K Aug 2 15:50 qap_config_ADS_spatial -rwxr-xr-x 1 shad 377 Aug 2 16:06 qap_config_ADS_spatial.yml -rw-r--r-- 1 shad 18K Aug 2 16:06 w1-list.yml -rw-r--r-- 1 shad 18K Aug 2 16:02 w1-list.yml-old drwxr-xr-x 134 shad 4.5K Aug 2 15:50 working

jpellman commented 8 years ago

Hi @seldamat ,

Just to verify, does the pipeline execution work after switching 'num_cores_per_subject' to just one core? Or does that cause the 'qap_mosaic' error you posted earlier?

hebbianloop commented 8 years ago

Hi @jpellman

I ran the pipeline again with 1 core per subject and 24 subjects at once and it appears to have advanced to the skull stripping stage. Hopefully it won't crash out again!

Just so you know, I've also followed the pull request to fix the duplicate problem when running multiple cores.

sgiavasis commented 8 years ago

Closing this issue! Re-open if we see recurrence.