I have encountered a problem in converting multi echo anatomical SPGR dicoms to BIDS format using dcm2bids (version 2.1.5, on Ubuntu 16.04).
Specifically, there is no pairing for the different echoes:
:No Pairing <- 015_S003_t1_fl3d_FA10_20210105111149_e1
INFO:dcm2bids.sidecar:No Pairing <- 015_S003_t1_fl3d_FA10_20210105111149_e2
INFO:dcm2bids.sidecar:No Pairing <- 015_S003_t1_fl3d_FA10_20210105111149_e3
I attempted to fix this by adding the customLabels key-value, following this suggestion, but the problem persists.
My bids_config.json file has entries such as:
It seems that others have been able to complete such conversions successfully.
Any idea what I may be doing wrong?
Any help would be greatly appreciated!
Can you share with me the json files of your anatomical images ?
I will check, why your bids config file is not grabbing this.
"SidecarFilename": "*_e1" doesn’t catch anything since it’s not a key in your json file.
To catch the different echoes you have two options.
- Option 1:
- Option 2:
Option 2 can be tricky if you don’t have the exact same echo time for each participant.
The order should stay the same so I would suggest you to use option 1.
Obviously, change the number of the echo for each image.
Thank you so much. This makes perfect sense (I was under the impression that SiecarFilename was not a key in the json file, but rather the actual name of the json file). Now the conversion works smoothly.
Many thanks for your kind help,
Hi @roeysc ,
Can you tag this discussion as solved ? It helps us to sort the different threads.
I think, you just need to click on the button response under my response.
Absolutely. Thanks for pointing that out!