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Group-level command shown in tutorial runs into error

See original GitHub issue

Both the below commands run into errror: mriqc ~/INTRuST_BIDS_tb571/ ~/mriqc-out/ group

mriqc ~/INTRuST_BIDS_tb571/ ~/mriqc-out/ group --participant-label 003GNX007 003GNX012 003GNX021

Error:

2020-03-10 09:49:41,149 mriqc:IMPORTANT
    Running MRIQC version 0.15.2rc1+36.gf6c7066:
      * BIDS dataset path: ~/INTRuST_BIDS_tb571.
      * Output folder: /home/ek520/mriqc-out.
      * Analysis levels: group.

Traceback (most recent call last):
  File "/rfanfs/pnl-zorro/software/pnlpipe3/miniconda3/envs/pnlpipe3/bin/mriqc", line 11, in <module>
    load_entry_point('mriqc==0.15.2rc1+36.gf6c7066', 'console_scripts', 'mriqc')()
  File "/rfanfs/pnl-zorro/software/pnlpipe3/miniconda3/envs/pnlpipe3/lib/python3.6/site-packages/mriqc-0.15.2rc1+36.gf6c7066-py3.6.egg/mriqc/bin/mriqc_run.py", line 295, in main
Exception: No data found. No group level reports were generated.

However, participant level analysis runs fine:

mriqc ~/INTRuST_BIDS_tb571/ ~/mriqc-out/ participant --participant-label 003GNX007 003GNX012 003GNX021

So, am I not running group-level analysis right? I am following the commands shown here: https://mriqc.readthedocs.io/en/stable/running.html#running-mriqc

Issue Analytics

State:
Created 4 years ago
Comments:8 (1 by maintainers)

Top GitHub Comments

2reactions

tashrifbillahcommented, Mar 25, 2020

While trying to find a way around, the following seems to perform group level analysis:

mriqc ~/INTRuST_BIDS_tb571/ ~/mriqc-out/ participant

2020-03-24 22:54:56,030 mriqc:IMPORTANT 
    Running MRIQC version 0.15.2rc1+36.gf6c7066:
      * BIDS dataset path: /home/tb571/Downloads/INTRuST_BIDS/rawdata.
      * Output folder: /tmp/mriqc-ica.
      * Analysis levels: group, participant.
    
...
...

1reaction

tashrifbillahcommented, Mar 24, 2020

Maybe MRIQC is not expanding the user shortcuts (~/) from some paths?

And it is expanding for participant level?

Tried again with expanded paths, didn’t help.

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