Load preset paired t-test with CPAC

Software Support
1

Hello everyone!

I’m using C-PAC (v1.8.7.dev1) on a HPC (singularity v3.11.5). I want to run an analysis comparing two groups pre-post, for which I’m trying to get the paired-two preset from the command line.

These are the arguments that cpac asks for:

Usage: cpac group feat load-preset paired-two [OPTIONS] PIPELINE_DIR Z_THRESH
                                              P_THRESH CONDITIONS
                                              CONDITION_TYPE MODEL_NAME

So I’m entering:

singularity exec c-pac.sif \
cpac group feat load-preset paired-two /path/to/pipeline_cpac-ost-fix 2.3 0.05 [pre, post] session --output-dir /path/to/output

For which I get this error message:

INFO:    Converting SIF file to temporary sandbox...
/usr/share/fsl/6.0/bin/cpac:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
  __import__('pkg_resources').require('CPAC==1.8.7.dev1')
Traceback (most recent call last):
  File "/code/CPAC/utils/create_fsl_flame_preset.py", line 998, in run
    keys = pd.read_csv(keys_csv)
  File "/usr/share/fsl/6.0/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
  File "/usr/share/fsl/6.0/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
  File "/usr/share/fsl/6.0/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
  File "/usr/share/fsl/6.0/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
  File "/usr/share/fsl/6.0/lib/python3.10/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
FileNotFoundError: [Errno 2] No such file or directory: '/code/CPAC/resources/cpac_outputs.csv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/share/fsl/6.0/bin/cpac", line 7, in <module>
    exec(compile(f.read(), __file__, 'exec'))
  File "/code/scripts/cpac", line 5, in <module>
    main()
  File "/usr/share/fsl/6.0/lib/python3.10/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
  File "/usr/share/fsl/6.0/lib/python3.10/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
  File "/usr/share/fsl/6.0/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/usr/share/fsl/6.0/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/usr/share/fsl/6.0/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  [Previous line repeated 1 more time]
  File "/usr/share/fsl/6.0/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/usr/share/fsl/6.0/lib/python3.10/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "/code/CPAC/__main__.py", line 258, in paired_two
    create_fsl_flame_preset.run(pipeline_dir, 'all', z_thresh, p_thresh,
  File "/code/CPAC/utils/create_fsl_flame_preset.py", line 1002, in run
    raise Exception(err)
Exception: 
[!] Could not access or read the cpac_outputs.csv resource file:
/code/CPAC/resources/cpac_outputs.csv

Error details [Errno 2] No such file or directory: '/code/CPAC/resources/cpac_outputs.csv'

I have tried changing PIPELINE_DIR to the group_analysis_participants.txt file, different combinations of singularity run and singularity exec, as well as different inputs for pre and post with the same result.
I was checking C-PAC’s GitHub and it seems that cpac_outputs is a .tsv file (~/CPAC/resources/cpac_outputs.tsv), which I’m not sure if could be the issue?

Thanks in advance!!

~L

2

Hi @luisagulleiro, thanks for reaching out!

That is a strange error.

I know you said you’re using v1.8.7.dev1, but could you triple-check that this is actually the version that’s running? Will be in log/.../pypeline.log next to C-PAC version: .

3

Hi @tamsinrogers, thanks for your reply!

I’ve checked log/.../pypeline.log from the previous preprocessing run and it says C-PAC version: 1.8.7.dev1.

Just to confirm, I ran singularity exec c-pac.sif cpac version, which returned:

Environment
===========
AFNI: 23.3.09:linux_universal
ldd: (Ubuntu GLIBC 2.35-0ubuntu3.1) 2.35
Python: 3.10.6 | packaged by conda-forge | (main, Aug 22 2022, 20:36:39) [GCC 10.4.0]
  Python packages
  ---------------

[...long list of packages...]

C-PAC version: 1.8.7.dev1
4

Hi @luisagulleiro,

Thanks for checking! As it turns out, cpac_outputs.csv was in fact changed to cpac_outputs.tsv in v1.8.1, but it was not updated in some places - the group-level builder hasn’t been updated/supported for quite some time.

Our team is working on a fix and I’ll get back to you shortly.

Thank you for bringing this to our attention!

5

Hi @luisagulleiro,

This update has just been merged to dev - should work as expected now when using the nightly image. Please let me know if you run into any additional issues!

6

Hi @tamsinrogers,

Thanks for your help! I’ve pulled the nightly image and now the command is able to run, but I found a new error message.

I ran the following:

singularity exec --bind /path/to/ost_fix:/path/to/ost_fix c-pac:nightly.sif \
cpac group feat load-preset paired-two \
/path/to/ost_fix/output/pipeline_cpac-ost-fix 2.3 0.05 \
[ses-pre,ses-post] session grp_analysis \
--output-dir /path/to/ost_fix/output

Which returns this error:

INFO:    Converting SIF file to temporary sandbox...
/usr/share/fsl/6.0/bin/cpac:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
  __import__('pkg_resources').require('CPAC==1.8.8.dev1')
Traceback (most recent call last):
  File "/usr/share/fsl/6.0/bin/cpac", line 7, in <module>
    exec(compile(f.read(), __file__, 'exec'))
  File "/code/scripts/cpac", line 5, in <module>
    main()
  File "/usr/share/fsl/6.0/lib/python3.10/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
  File "/usr/share/fsl/6.0/lib/python3.10/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
  File "/usr/share/fsl/6.0/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/usr/share/fsl/6.0/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/usr/share/fsl/6.0/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  [Previous line repeated 1 more time]
  File "/usr/share/fsl/6.0/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/usr/share/fsl/6.0/lib/python3.10/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "/code/CPAC/__main__.py", line 318, in paired_two
    create_fsl_flame_preset.run(
  File "/code/CPAC/utils/create_fsl_flame_preset.py", line 1291, in run
    design_df, contrasts_df, group_config_update = preset_paired_two_group(
  File "/code/CPAC/utils/create_fsl_flame_preset.py", line 695, in preset_paired_two_group
    design_df = create_design_matrix_df(group_list, ses_id=sesflag)
  File "/code/CPAC/utils/create_fsl_flame_preset.py", line 224, in create_design_matrix_df
    sess = part_ses.split("_")[1]
IndexError: list index out of range
INFO:    Cleaning up image...

I modified the names of the directories to not include underscores (ie, ost-fix, pipeline-cpac-ost-fix), but it returns the same error. I also tried a variation of the session string as [pre,post] only, with the same result.

7

Hi @luisagulleiro,

Looking at /utils/create_fsl_flame_preset.py/create_design_matrix, group_list needs to look something like this:

["sub-01_ses-pre", "sub-01_ses-post", ...]

I know you said you tried without underscores, and looks like in your initial run command you’re giving it ses-pre,ses-post. Can you try rerunning with your group list in the above format? If that doesn’t work I can dig deeper.

8

Hi @tamsinrogers,

I’ve tried the following command:

singularity exec --bind /path/to/ost_fix:/path/to/ost_fix c-pac:nightly.sif \
cpac group feat load-preset paired-two \
/path/to/ost_fix/output/pipeline_cpac-ost-fix \ #This is PIPELINE_DIR, where all the preprocessed files and derivatives are. Structure looks like ~/pipeline_cpac-ost-fix/678301/ses-pre/func/
2.3 0.05 \ #Z_THRESH and P_THRESH
["sub-678301_ses-post","sub-678301_ses-pre","sub-678311_ses-post","sub-678311_ses-pre", ...] \ # I've also tried "678301_pre" (this is how the group_analysis_participants.txt names them) and "678301_ses-pre" (to match the naming of PIPELINE_DIR) with the same result
session grp_analysis \
--output-dir /path/to/ost_fix/output

But I get this error message:

/usr/share/fsl/6.0/bin/cpac:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
  __import__('pkg_resources').require('CPAC==1.8.8.dev1')
Traceback (most recent call last):
  File "/usr/share/fsl/6.0/bin/cpac", line 7, in <module>
    exec(compile(f.read(), __file__, 'exec'))
  File "/code/scripts/cpac", line 5, in <module>
    main()
  File "/usr/share/fsl/6.0/lib/python3.10/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
  File "/usr/share/fsl/6.0/lib/python3.10/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
  File "/usr/share/fsl/6.0/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/usr/share/fsl/6.0/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/usr/share/fsl/6.0/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  [Previous line repeated 1 more time]
  File "/usr/share/fsl/6.0/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/usr/share/fsl/6.0/lib/python3.10/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "/code/CPAC/__main__.py", line 318, in paired_two
    create_fsl_flame_preset.run(
  File "/code/CPAC/utils/create_fsl_flame_preset.py", line 1291, in run
    design_df, contrasts_df, group_config_update = preset_paired_two_group(
  File "/code/CPAC/utils/create_fsl_flame_preset.py", line 686, in preset_paired_two_group
    raise Exception
Exception

Thanks for your help!!

9

Hi @luisagulleiro ,

We stopped actively supporting the C-PAC group model builder several years ago. It’s likely you are seeing issues because there are most likely certain things that have drifted in terms of data organization since then.

What the builder needs is a small refresher, but as we currently don’t have bandwidth, any fixes or refactoring would be slow at best.

However, we are currently in the process of transitioning much of our products to maintenance, and there is a possibility we will need to invest in the group model builder to some degree to separate it out into its own tool.

In the meantime, can you tell us a little more about your original C-PAC run and what kind of model you’re looking to build? How many participants and scans, and also how large your phenotypic/EV matrix is, and how much of it you wish to include? I can glean some of this info from your group config but would like to know more so we can better update the code if/when we can.