Closed thomshaw92 closed 1 year ago
Thanks for reporting this, I will look into it when I am back from my holidays (the 10th of August)...
Sent from my phone
Op vr 28 jul. 2023 04:30 schreef Thom Shaw @.***>:
Describe the bug
Re-running Bidscoiner from a new filesystem/directory structure. Bidsmap.yaml stays the same, but new participants added to my raw data directory. When I finish running the bidscoiner, there is a "sub-" subject folder, but no subject folders. e.g.:
INFO | --> Coining: /30days/uqtshaw/BeLong_processing/raw_all_dicomsorted_zips/sub-011/ses-01/020-T2star_2d_bipolar-inphase_GRE_16ME_aspire_p7.p7.2 INFO | Running: dcm2niix -b y -z y -i n -l n -f "sub-_acq-2dbipolarinphaseGRE16MEaspirep7p72_run-1_mod-T2star2dbipolarinphaseGRE16MEaspirep7p72_echo-16_GR" -o "/30days/uqtshaw/BeLong_processing/BeLong_brain_BIDS_20230529/sub-/extra_data" "/30days/uqtshaw/BeLong_processing/raw_all_dicomsorted_zips/sub-011/ses-01/020-T2star_2d_bipolar-inphase_GRE_16ME_aspire_p7.p7.2" INFO | Output: Chris Rorden's dcm2niiX version v1.0.20220505 GCC11.3.0 x86-64 (64-bit Linux) Found 15 DICOM file(s) Warning: Assuming mosaics saved in reverse order due to 'sSliceArray.ucImageNumb' Convert 15 DICOM as /30days/uqtshaw/BeLong_processing/BeLong_brain_BIDS_20230529/sub-/extra_data/sub-_acq-2dbipolarinphaseGRE16MEaspirep7p72_run-1_mod-T2star2dbipolarinphaseGRE16MEaspirep7p72_echo-16_GR_e16 (336x336x15x1) Conversion required 0.555997 seconds (0.293178 for core code).
INFO | ------------------- Subject 2/28 ------------------- ERROR | Could not parse required sub- information from /30days/uqtshaw/BeLong_processing/raw_all_dicomsorted_zips/sub-013/ses-01/001-Localizer/SUB-013.MR.RESEARCH_TOM.0001.0001.2021.12.01.09.54.12.76178.258127961.IMA using: <filepath:/raw_all_dicomsorted/sub-(.?)/> -> 'sub-' INFO | >>> Skipping processed session: /30days/uqtshaw/BeLong_processing/BeLong_brain_BIDS_20230529/sub- already has ['anat', 'dwi', 'extra_data'] data (you can carefully use the -f option to overrule) INFO | ------------------- Subject 3/28 ------------------- ERROR | Could not parse required sub- information from /30days/uqtshaw/BeLong_processing/raw_all_dicomsorted_zips/sub-014/ses-01/001-Localizer/SUB-014.MR.RESEARCH_21034_BELONG.0001.0001.2022.02.18.11.23.29.958454.276314191.IMA using: <filepath:/raw_all_dicomsorted/sub-(.?)/> -> 'sub-' INFO | >>> Skipping processed session: /30days/uqtshaw/BeLong_processing/BeLong_brain_BIDS_20230529/sub- already has ['anat', 'dwi', 'extra_data'] data (you can carefully use the -f option to overrule)
Expected behavior New participants to be converted to nifti, old ones tro remain the same
I ran bidscoiner ./raw ./bids
Screenshots If applicable, add screenshots to help explain your problem.
Software version
- BIDScoin version 4.0
- OS (Linux)
— Reply to this email directly, view it on GitHub https://github.com/Donders-Institute/bidscoin/issues/194, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADTUGL4XNCK6BNHPARDXXTTXSMP3ZANCNFSM6AAAAAA224KHBQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>
The map file would help.
I see the error:
ERROR | Could not parse required sub- information from /30days/uqtshaw/BeLong_processing/raw_all_dicomsorted_zips/sub-013/ses-01/001-Localizer/SUB-013.MR.RESEARCH_TOM.0001.0001.2021.12.01.09.54.12.76178.258127961.IMA using: <filepath:/raw_all_dicomsorted/sub-(.*?)/> -> 'sub-'
Shouldn't the subject pattern be surrounded with double
<< >>
? This is how I'm using it.
I see that your new data is in raw_all_dicomsorted_zips
but your bidsmap subject field (<<filepath:/raw_all_dicomsorted/sub-(.*?)/>>
is using a different (older) path, i.e. raw_all_dicomsorted
. I'll see if I can easily add a check for this issue
I had a look and I think it's more complicated and error-prone to programmatically catch use cases where the path of the raw-folder changes between different runs of bidsmapper and/or bidscoiner. The best solution is open the bidsmap in the bidseditor and update the path in the subject and session fields by hand. I'll add some Troubleshooting documentation of this issue...
Alternatively, if you don't want any rawfolder paths in your bidsmap, you can use bidsmapper's --no-update
option (the first time you run it on the raw folder). The downside is that the subject label parsing may be less robust (especially if you have no or a very short subject prefix)
Feel free to reopen this issue if your problem persists
Describe the bug
Re-running Bidscoiner from a new filesystem/directory structure. Bidsmap.yaml stays the same, but new participants added to my raw data directory. When I finish running the bidscoiner, there is a "sub-" subject folder, but no subject folders. e.g.:
INFO | --> Coining: /30days/uqtshaw/BeLong_processing/raw_all_dicomsorted_zips/sub-011/ses-01/020-T2star_2d_bipolar-inphase_GRE_16ME_aspire_p7.p7.2 INFO | Running: dcm2niix -b y -z y -i n -l n -f "sub-_acq-2dbipolarinphaseGRE16MEaspirep7p72_run-1_mod-T2star2dbipolarinphaseGRE16MEaspirep7p72_echo-16_GR" -o "/30days/uqtshaw/BeLong_processing/BeLong_brain_BIDS_20230529/sub-/extra_data" "/30days/uqtshaw/BeLong_processing/raw_all_dicomsorted_zips/sub-011/ses-01/020-T2star_2d_bipolar-inphase_GRE_16ME_aspire_p7.p7.2" INFO | Output: Chris Rorden's dcm2niiX version v1.0.20220505 GCC11.3.0 x86-64 (64-bit Linux) Found 15 DICOM file(s) Warning: Assuming mosaics saved in reverse order due to 'sSliceArray.ucImageNumb' Convert 15 DICOM as /30days/uqtshaw/BeLong_processing/BeLong_brain_BIDS_20230529/sub-/extra_data/sub-_acq-2dbipolarinphaseGRE16MEaspirep7p72_run-1_mod-T2star2dbipolarinphaseGRE16MEaspirep7p72_echo-16_GR_e16 (336x336x15x1) Conversion required 0.555997 seconds (0.293178 for core code).
INFO | ------------------- Subject 2/28 ------------------- ERROR | Could not parse required sub-
Expected behavior New participants to be converted to nifti, old ones tro remain the same
I ran bidscoiner ./raw ./bids
Screenshots If applicable, add screenshots to help explain your problem.
Software version