Doesn't really do the conversion? about bidskit HOT 12 CLOSED

@rnair07 great!
it works now! Thanks a lot!
This is the fastest response I ever had online!

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Hi @rnair07 - let me fix #29 before you update the Docker image. Should have a fix today.

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Perfect - good to know! I'll be creating an updated docker image with additional features as per the new convertor script, so do keep an eye out for that! :)

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Yes, post first pass conversion, the files are in the conversion folder. You then need to edit the protocol translator as per BIDS conventions and run a second pass. More info. here: https://github.com/jmtyszka/bidskit#second-pass-conversion and here :https://github.com/jmtyszka/bidskit#edit-translator-dictionary
That puts the files in the BIDS folder.

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Hi Chuan-Peng,

Thanks for the detailed breakdown of the issue - really appreciate the screencaps. Do you see a conversion/ subfolder in analysis/work/ and does it contain any .json or nii.gz files? Trying to work out if the dcm2niix conversion failed somehow. I've tagged @nair-r on this too - she's our container expert.

So far we've tested under Centos/Linux and OS X, but I'll extend this to Windows 7/8/10 asap to see if I can reproduce this behaviour (and fix it).

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Hi @hcp4715 - let me look into this and update soon. There have been several new fixes and updates to the bids converter over the last few days which I'd like to incorporate into the new docker image as well. In the meantime, same question as Mike : did it create any interim files whatsoever, such as the protocol translator in the derivatives folder?

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Hi @hcp4715 - could you confirm this as well: Your command mounts the path that includes 'raw_dicom' whereas your folder structure shows only '../../analysis/dicom' and not raw_dicom. Does raw_dicom contain all the same files as dicom folder? Could you re-check/change the path and retry - just want to rule out path errors.

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@hcp4715 Sorry for spamming :) Try this command: specifies the path correctly:
docker run -it -v G:\Data\coiltest\analysis:/mnt rnair07/bidskit --indir=/mnt/dicom --outdir=/mnt/BIDS

This assumes all your subjects dicom are in the 'dicom' folder which is a sub-folder of 'analysis'.

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Thanks so much for the quick response!

@jmtyszka in the analysis/work/ folder, there is a folder called conversion, but the conversion folder is empty; the analysis/derivative/conversion contain a .json file called "Protocol_Translator.json", but it is empty too.

@rnair07 , thanks for pointing that out, I put my raw data in analysis/dicom, tried

docker run -it -v G:\Data\coiltest\analysis\dicom:/mnt rnair07/bidskit --indir=/mnt/dicom --outd
ir=/mnt/BIDS
the results is the same.

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Hi @hcp4715 you don't actually need to specify the dicom folder when mounting, only need to specify it in the --indir flag. Use the command docker run -it -v G:\Data\coiltest\analysis:/mnt rnair07/bidskit --indir=/mnt/dicom --outdir=/mnt/BIDS instead of docker run -it -v G:\Data\coiltest\analysis\dicom:/mnt rnair07/bidskit --indir=/mnt/dicom --outdir=/mnt/BIDS

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update: the converted file was in 'work/conversion', not in BIDS

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Hi, @nair-r ,
I two addition minor issues:
first, the code for the second pass was as below on the website :

docker run -it -v /PATH_TO_YOUR_RAW_DICOM_FOLDER/:/mnt rnair07/bidskit --indir=/mnt/dicom --outdir=/mnt/source

If I understand correctly, the final BIDS file should be in the BIDS folder, instead of the source folder, so the 'outdir=/mnt/source' should change to 'outdir=/mnt/BIDS' if I hope to put the converted files in BIDS folder. Am I right?

Second, after I delete all the folders generated by the first pass ( because I trying to do the whole process again), and tried to run the first pass conversion again, the output showed that the protocol dictionary already exists. Only after restart docker could I re-run the first-pass.

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