jooh / dcm2bids Goto Github PK

Hi,
I think you wrote the logger for Dcm2bids, right? Thank you for this very useful extension to dcm2bids.
I was wondering if it's possible to write all the output to one log_file that contains all information.
Sometimes it's difficult to figure out which log_file to use to do some parsing for counting of sequences etc...
Is there an easy solution?

Thanks

I haven't managed to get it installed using your instructions. Maybe you could either add more detail or include a pip installer? I think that would help a lot of people. Thanks!

Hi Johan,
I would like to have the tool accept more than one criteria to do the classification. For example, based on the example/config.json file, a run will be classified as T1w if the string "T1W_3D" appears in the "SeriesDescription". However, many times, the T1w file contains "MPRAGE" instead. Is it possible to have a config.json file that will work for both scenarios?
I tried changing the criteria for the T1w to something like:

 {
    "dataType": "anat",
    "suffix": "T1w",
    "criteria": {
        "in": {"SeriesDescription": [ "T1W_3D" ,
                                      "T1w" ,
                                      "MPRAGE" ,
                                      "MP-RAGE"
                                    ]
              }
    }
},

but when I run the code, it doesn't match the criteria.

I also tried:

{
    "dataType": "anat",
    "suffix": "T1w",
    "criteria": [
{
    "in": {"SeriesDescription": "T1W_3D"}
},
{
    "in": {"SeriesDescription": "T1w"}
}
]
},

But, again, it doesn't match.

I assume the code in sidecarparser will need to be changed, but how to do that in a way that it still respect the case in which you have to match several criteria at the same time (like match the series description AND the echotime)?

Thanks!

-Pablo

Just curious on how these two can dovetail with each others

Hello,
I'm having some trouble setting up the config file so that it properly handles the field map images in my data set. One of the magnitude fieldmap images only differs from the phase difference image in one field: ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"] vs "ImageType": ["ORIGINAL", "PRIMARY", "P", "ND"]. I cannot seem to get the config file set up so that these are properly differentiated. I tried including statements such as "in": {"ImageType": "'"P""} for the former and "in": {"ImageType": "'"M""} for the latter in the config file with no luck. The tool is very new to me, so I am probably missing something obvious. Does anyone happen to know where I am going wrong? Thanks very much for any suggestions.
Best regards,
Steve wilson

I'm having a hard time understanding "suffix", "seriesnum" and how these should be entered into the example.json file. It would be really awesome if your example.json file would include exmaples of all possible combinations in the descriptions dictionary. I couldn't figure it out.