Event type 'neutral_resp' and 'reward_resp' are not found in TSV file. #11
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Thanks for this @HanadS! @AlexBowring and I are looking into it and will get back to you ASAP. |
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@HanadS: Can I make sure: You've downloaded the BIDS data and amended CC: @AlexBowring |
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Yes that's correct.
Hanad
…On Wed, Nov 14, 2018 at 5:44 AM Thomas Nichols ***@***.***> wrote:
@HanadS <https://github.com/HanadS>: Can I make sure: You've downloaded
the BIDS data and amended process_ds120_AFNI.py so that pre_raw_dir, and
raw_dir are set to reflect where your BIDS data is placed?
CC: @AlexBowring <https://github.com/AlexBowring>
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Huh. What happens when you do this command, at the root for your data (for us it is grep neutral_resp ds120_R1.0.0_AMENDED/sub-*/func/*_events.tsv | wc? I get: |
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Hi @HanadS Have you ran the Amendds120tsv.sh script on your raw_data directory: This alters the event files to combine the trial_type and trial_phases columns to make them compatible with the BIDSto3col.sh. i.e. this should give you new event files, where the 'trial_type' and 'trial_phase' columns are combined as one column. In particular this means for 'neutral' trial_type and 'resp' trial_phase events, the new altered event files should just have one column with a 'neutral_resp' event, and then the process_ds120_AFNI.py should work fine. |
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Hi @AlexBowring and @nicholst , This is what I think the issue is. When I run the script the FIRST time I get an error saying Amendds120tsv.sh: not found because I don't provide the full path for the Amendds120tsv.sh on line 31. When I run the script the SECOND time without making any changes the if statement is now false because the shutil.copytree(pre_raw_dir, raw_dir) created the directory from the first execution. So the program continues without ever calling the Amendds120tsv function which is needed as @AlexBowring explains. This results in the error message that I get above. Does this make sense? Perhaps an easy fix would be to call the Amendds120tsv.sh function outside of the if statement? |
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Indeed, the Amendds120tsv.sh script is crucial. @AlexBowring how do you
handle search paths? Is there guidance in the Readme about how shell paths
have to be set? If not we should add it (or create a scripts dir variable
in the python script and call Amendds120tsv.sh with an absolute path.
--
…_________________________________________________________
Thomas Nichols, PhD
Professor of Neuroimaging Statistics
Nuffield Department of Population Health | University of Oxford
Big Data Institute | Li Ka Shing Centre for Health Information and Discovery
Old Road Campus | Headington | Oxford | OX3 7LF | United Kingdom
T: +44 1865 743590 | E: [email protected]
W: http://nisox.org | http://www.bdi.ox.ac.uk
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@HanadS I understand, and agree that is probably exactly what is happening. As a solution for now, I would suggest you delete the raw_dir Thanks for reporting, I will add to the README that the |
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Hi @AlexBowring, That makes sense. Thank you for your help. I followed your instructions and I get another error at the run level analysis. The mask_epi_anat.*.HEAD file is missing from that directory. |
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Oh dear... this looks like an AFNI/R problem. The first error is
Error in library("afex") : there is no package called ‘afex’
which is an R library. R doesn't ship with AFNI maybe you have to install
it? Ideas @AlexBowring?
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Update: @HanadS, AFNI can be a bear to install... did you do this step: |
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Hi @nicholst, I don't believe we have R installed so that may be the issue. I'll install those packages and rerun the analysis and then let you know how it goes. |
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Hi @nicholst, I reran the analysis after installing the R packages and I get a similar error. |
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Huh. Can you send us a listing of what files *are* in /home/hanads/Documents/Nguyen/final_version/Software_Comparison-master/ds120/output/ds120/AFNI/LEVEL1/sub-*/sub*/ (for a subject or two)
@AlexBowring - actually is that path right? Looks like there’s an extra sub*
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@nicholst @AlexBowring Thank you for your replies. I will update afni and run the pipeline again. |
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Hello, sorry for the delay. I updated AFNI and this is the error I am getting now |
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Hi @HanadS, Sorry for the delay with this reply. Can you please tell me which version of AFNI you are using now. Then can you try putting |
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Hi @AlexBowring! The afni version I am using is 18.3.16. The @SSwarper apears to be working. Here is what is in the script. |
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Hello!
I am trying to rerun the analysis using ds120 for AFNI. I ran the script process_ds120_AFNI.py and here is the output from the terminal.
I tried changing the conditions variable in process_ds120_AFNI.py to 'neutral' and 'reward' instead of 'neutral_resp' and 'reward_resp'. Is this the correct fix?
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