Bidsmapper skips a folder

[paradeisios]

Describe the bug

I am trying to run bidsmapper for the following folder

Each folder contains dicom files. The gre field mapping folders contain magniture and phase diff for run 2 and run 3 respectively. When I run bidsmapper ima ., the command completely skips folders 46,47.

INFO                                                                                                                           
INFO     -------------- START BIDSmapper ------------                                                                          
INFO     >>> bidsmapper sourcefolder=/media/veracrypt1/datasets/WM-ORDER/s04601/ima                                            
         bidsfolder=/media/veracrypt1/datasets/WM-ORDER/s04601 bidsmap=bidsmap.yaml                                            
         template=/home/paradeisios/.bidscoin/4.6.2/templates/bidsmap_dccn.yaml plugins=[] subprefix=None sesprefix=None       
         store=False force=False                                                                                               
INFO     No bidsmap file found: /media/veracrypt1/datasets/WM-ORDER/s04601/code/bidscoin/bidsmap.yaml                          
INFO     Reading: /home/paradeisios/.bidscoin/4.6.2/templates/bidsmap_dccn.yaml                                                
INFO     Checking the bidsmap run-items:                                                                                       
SUCCESS  All datatypes and options in the template bidsmap are valid                                                           
INFO     Mapping: /media/veracrypt1/datasets/WM-ORDER/s04601/ima/sub-pil001 (subject 1/1)                                      
WARNING  Not all .dcm-files in '/media/veracrypt1/datasets/WM-ORDER/s04601/ima/sub-pil001/cmrr_ep2d_mb3_3mm_1s_Task_run1_11_MR'
         have the same size. This may be OK but can also be indicative of a truncated acquisition or file corruption(s)        
INFO     Discovered sample: [DICOM]                                                                                            
         /media/veracrypt1/datasets/WM-ORDER/s04601/ima/sub-pil001/cmrr_ep2d_mb3_3mm_1s_Task_run1_11_MR/1.dcm                  
WARNING  Not all .dcm-files in '/media/veracrypt1/datasets/WM-ORDER/s04601/ima/sub-pil001/cmrr_ep2d_mb3_3mm_1s_Task_run2_19_MR'
         have the same size. This may be OK but can also be indicative of a truncated acquisition or file corruption(s)        
INFO     Discovered sample: [DICOM]                                                                                            
         /media/veracrypt1/datasets/WM-ORDER/s04601/ima/sub-pil001/cmrr_ep2d_mb3_3mm_1s_Task_run2_19_MR/1.dcm                  
WARNING  Not all .dcm-files in '/media/veracrypt1/datasets/WM-ORDER/s04601/ima/sub-pil001/cmrr_ep2d_mb3_3mm_1s_Task_run3_38_MR'
         have the same size. This may be OK but can also be indicative of a truncated acquisition or file corruption(s)        
INFO     Discovered sample: [DICOM]                                                                                            
         /media/veracrypt1/datasets/WM-ORDER/s04601/ima/sub-pil001/cmrr_ep2d_mb3_3mm_1s_Task_run3_38_MR/1.dcm                  
INFO     Discovered sample: [DICOM] /media/veracrypt1/datasets/WM-ORDER/s04601/ima/sub-pil001/gre_field_mapping_27_MR/1.dcm    
INFO     Discovered sample: [DICOM] /media/veracrypt1/datasets/WM-ORDER/s04601/ima/sub-pil001/gre_field_mapping_28_MR/1.dcm    
INFO     Discovered sample: [DICOM] /media/veracrypt1/datasets/WM-ORDER/s04601/ima/sub-pil001/t1_mpr_sag_p2_iso_2_MR/1.dcm     
INFO     Opening the bidseditor  

BIDS-version:		1.10.0
BIDScoin-version:	4.6.2, Your BIDScoin version is up-to-date :-)
No LSB modules are available.
Distributor ID:	Ubuntu
Description:	Ubuntu 24.04.3 LTS
Release:	24.04
Codename:	noble

Am I doing something wrong in the specification ?

[FocusMode-coder]

Hey! I may be able to help with this bug.

I build custom fixes for Python projects and automation systems.

If you'd like help resolving this issue quickly feel free to reach out.

Happy to take a look 👍

[marcelzwiers]

Are you sure that folders 46,47 are different from the other folders? The bidsmapper make a map of the unique scan protocols (i.e. a shortlist), it doesn't make an entry for every folder (a long-list), as that would make it very labourious to make edits.

[marcelzwiers]

Btw, that warning about the truncated scans is important, as it will probably result in dcm2niix not being able to convert the data (because of dimension mismatch). So I woul either remove those truncated scans or make them hidden by prepending a dot (.)