Dcm2bids question re: warnings

Software Support
1

Summary of what happened:

Hi all,

I am new to dcm2bids and am trying to convert some Siemens TiM Trio data using dcm2bids v. 3.1.1. I get several warnings and am trying to figure out whether they are critical. The run completes and I get the expected filenames in the anat, dwi, and func directories.

Command used (and if a helper script was used, a link to the helper script or the command generated):

dcm2bids -d sourcedata/sub-1008 -p sub-1008 --auto_extract_entities --bids_validate --force_dcm2bids --clobber -c code/dcm2bids_config.json

Version:

v. 3.1.1

Environment (Docker, Singularity, custom installation):

conda

Data formatted according to a validatable standard? Please provide the output of the validator:

I used the bids-validator website

Relevant log outputs (up to 20 lines):

2024-01-04 10:40:35.878 - INFO     - sidecar.build_acquisitions | No Pairing  <-  001_sub-1008_Localizer_20210406142807_i00007
2024-01-04 10:40:35.879 - INFO     - sidecar.searchDcmTagEntity | Removing entity 'T1w' since it does not fit the basic BIDS specification (Entity-Value)
2024-01-04 10:40:35.879 - INFO     - sidecar.build_acquisitions | sub-1008_T1w  <-  002_sub-1008_MPRAGE_STAN_20210406142807
2024-01-04 10:40:35.880 - WARNING  - sidecar.searchDcmTagEntity | {'task'} have not been found for datatype 'func' and suffix 'bold'.
2024-01-04 10:40:35.880 - INFO     - sidecar.build_acquisitions | sub-1008_task-rest_acq-TR1400_bold  <-  003_sub-1008_REST_1400_20210406142807
2024-01-04 10:40:35.880 - INFO     - sidecar.build_acquisitions | No Pairing  <-  004_sub-1008_set_volume_20210406142807
2024-01-04 10:40:35.880 - WARNING  - sidecar.searchDcmTagEntity | {'task'} have not been found for datatype 'func' and suffix 'bold'.
2024-01-04 10:40:35.881 - INFO     - sidecar.build_acquisitions | sub-1008_task-emoreg1_acq-TR1400_bold  <-  005_sub-1008_emo_reg1_20210406142807
2024-01-04 10:40:35.881 - WARNING  - sidecar.searchDcmTagEntity | {'task'} have not been found for datatype 'func' and suffix 'bold'.
2024-01-04 10:40:35.881 - INFO     - sidecar.build_acquisitions | sub-1008_task-emoreg2_acq-TR1400_bold  <-  006_sub-1008_emo_reg2_20210406142807
2024-01-04 10:40:35.882 - WARNING  - acquisition.setDstFile | Entity "['dwi7']" is not a valid BIDS entity.
2024-01-04 10:40:35.882 - INFO     - sidecar.build_acquisitions | sub-1008_dwi7-AP_dwi  <-  007_sub-1008_DIFF_7_AP_20210406142807
2024-01-04 10:40:35.882 - WARNING  - acquisition.setDstFile | Entity "['dwi7']" is not a valid BIDS entity.
2024-01-04 10:40:35.882 - INFO     - sidecar.build_acquisitions | sub-1008_dwi7-PA_dwi  <-  008_sub-1008_DIFF_7_PA_20210406142807
2024-01-04 10:40:35.883 - INFO     - sidecar.build_acquisitions | sub-1008_dwi  <-  009_sub-1008_DIFF_137_AP_20210406142807
2024-01-04 10:40:35.883 - INFO     - sidecar.build_acquisitions | No Pairing  <-  010_sub-1008_FLAIR_-_ch32_iPAT2_-CLINICAL_20210406142807
2024-01-04 10:40:35.883 - INFO     - dcm2bids_gen.run | Moving acquisitions into BIDS folder "/home/matt/studies/AFSP/sub_1006/rawdicom/new/temp/sub-1008".

2024-01-04 10:40:35.884 - INFO     - utils.run_shell_command | Running: pydeface --force --verbose --outfile /home/matt/studies/AFSP/sub_1006/rawdicom/new/temp/sub-1008/anat/sub-1008_T1w.nii.gz /home/matt/studies/AFSP/sub_1006/rawdicom/new/temp/tmp_dcm2bids/sub-1008/002_sub-1008_MPRAGE_STAN_20210406142807.nii.gz
2024-01-04 10:49:42.741 - ERROR    - dcm2bids_gen.run | The bids-validator does not seem to work properly. The bids-validator may not be installed on your computer. Please check: https://github.com/bids-standard/bids-validator.
2024-01-04 10:49:42.742 - INFO     - dcm2bids.main | Logs saved in /home/matt/studies/AFSP/sub_1006/rawdicom/new/temp/tmp_dcm2bids/log/sub-1008_20240104-104014.log
2024-01-04 10:49:42.742 - INFO     - dcm2bids.main | --- dcm2bids end ---

Screenshots / relevant information:

I am running ubuntu 16.04.1. The error message from the online bids validator was:
File Path: Quick validation failed - the general folder structure does not resemble a BIDS dataset. Have you chosen the right folder (with "sub-*/" subfolders)? Check for structural/naming issues and presence of at least one subject.

Type:		Error
File:		sub-1008_task-emoreg1_acq-TR1400_bold.json
Reason:		Quick validation failed - the general folder structure does not resemble a BIDS dataset. Have you chosen the right folder (with "sub-*/" subfolders)? Check for structural/naming issues and presence of at least one subject.

======================================================

2

Hi @hoptman,

Sounds like you input the wrong directory in to the BIDS validator. You should input the root of the BIDS directory (that is the folder that contains the subject folders).

Also,

Sounds like you do not have BIDS validator installed (or if you do, it is not in your environment PATH). If you want dcm2bids to run BIDS validation, you should install the validator and put it in your path (GitHub - bids-standard/bids-validator: Validator for the Brain Imaging Data Structure).

Best,
Steven

3

Hi Steven,
I realized that after I uploaded the data, but that is why I ended up using the website.
Best wishes,
Matt

PS. I also had an error in my config file (“custom-entities” for “custom_entities” for my defaced T1w. But now I get the warning “Entity “[‘T1w’]” is not a valid BIDS entity.”

4

Hi @hoptman

It would help if you could share the contents of your config file.

Best,
Steven

5

Hi Steven,
Sure. Sorry about that.

Here it is:

{
	"post_op": [
		{
			"cmd": "pydeface --force --verbose --outfile dst_file src_file",
			"datatype": "anat",
			"suffix": "T1w",
			"custom_entities": "T1w-defaced" 
		}
		],
	"descriptions": [
		{
			"datatype": "func",
			"suffix": "bold",
			"custom_entities": ["task", "task-rest_acq-TR1400"],
			"criteria": {
				"SeriesDescription": "REST_1400"
			},
			"sidecar_changes": {
				"TaskName": "task-rest"
			}
		},
		{
			"datatype": "func",
			"suffix": "bold",
			"custom_entities": ["task", "task-emoreg1_acq-TR1400"],
			"criteria": {
				"SeriesDescription": "emo_reg1"
			}		
		},
		{
			"datatype": "func",
			"suffix": "bold",
			"custom_entities": ["task", "task-emoreg2_acq-TR1400"],
			"criteria": {
				"SeriesDescription": "emo_reg2"
			}		
		},
		{
			"datatype": "anat",
			"suffix": "T1w",
			"custom_entities": "T1w",
			"criteria": {
				"SeriesDescription": "MPRAGE_STAN",
				"EchoTime": 0.00226
			}		
		},
		{
			"datatype": "dwi",
			"suffix": "dwi",
			"criteria": {
				"SeriesDescription": "DIFF_137_AP",
				"EchoTime": 0.087
			}		
		},
		{
			"datatype": "dwi",
			"suffix": "dwi",
			"custom_entities": "dwi7-AP",
			"criteria": {
				"SeriesDescription": "DIFF_7_AP",
				"EchoTime": 0.087
			},
			"sidecarChanges": {
			"ProtocolName": "AP"
			}	
		},
		{
			"datatype": "dwi",
			"suffix": "dwi",
			"custom_entities": "dwi7-PA",
			"criteria": {
				"SeriesDescription": "DIFF_7_PA",
				"EchoTime": 0.087
			},
			"sidecarChanges": {
			"ProtocolName": "PA"
			}
		}
	]
}
6

Hi @hoptman,

Thanks for sharing.

You are not using the "custom_entities" argument correctly. Each input should correspond to a label-<value> pair as defined by the BIDS specification (e.g., dir-PA). So things like "custom_entities": "dwi7-AP" and "custom_entities": "T1w-defaced" are not valid. I have corrected your json below:

{
    "post_op": [
        {
            "cmd": "pydeface --force --verbose --outfile dst_file src_file",
            "datatype": "anat",
            "suffix": "T1w",
            "custom_entities": "rec-defaced"
        }
    ],
    "descriptions": [
        {
            "datatype": "func",
            "suffix": "bold",
            "custom_entities": "task-rest_acq-TR1400",
            "criteria": {
                "SeriesDescription": "REST_1400"
            },
            "sidecar_changes": {
                "TaskName": "rest"
            }
        },
        {
            "datatype": "func",
            "suffix": "bold",
            "custom_entities": "task-emoreg1_acq-TR1400",
            "criteria": {
                "SeriesDescription": "emo_reg1"
            },
            "sidecar_changes": {
                "TaskName": "emoreg1"
            }
        },
        {
            "datatype": "func",
            "suffix": "bold",
            "custom_entities": "task-emoreg2_acq-TR1400",
            "criteria": {
                "SeriesDescription": "emo_reg2"
            },
            "sidecar_changes": {
                "TaskName": "emoreg2"
            }
        },
        {
            "datatype": "anat",
            "suffix": "T1w",
            "custom_entities": "acq-MPRAGE",
            "criteria": {
                "SeriesDescription": "MPRAGE_STAN",
                "EchoTime": 0.00226
            }
        },
        {
            "datatype": "dwi",
            "suffix": "dwi",
            "custom_entities": "acq-DIFF137_dir-AP",
            "criteria": {
                "SeriesDescription": "DIFF_137_AP",
                "EchoTime": 0.087
            }
        },
        {
            "datatype": "dwi",
            "suffix": "dwi",
            "custom_entities": "acq-DIFF7_dir-AP",
            "criteria": {
                "SeriesDescription": "DIFF_7_AP",
                "EchoTime": 0.087
            },
            "sidecarChanges": {
                "ProtocolName": "AP"
            }
        },
        {
            "datatype": "dwi",
            "suffix": "dwi",
            "custom_entities": "acq-DIFF7_dir-PA",
            "criteria": {
                "SeriesDescription": "DIFF_7_PA",
                "EchoTime": 0.087
            },
            "sidecarChanges": {
                "ProtocolName": "PA"
            }
        }
    ]
}
7

Hi Steven,
That’s great!! Thanks so much! Like I said, I’m a newbie :slight_smile:
Best wishes,
Matt

8

Hi @hoptman,

No problem, please let me know if it works or not! I also noticed there wasn’t an entry for DIFF137 in PA direction, is that intended?

Best,
Steven

9

Hi again,
I still get warnings like this:
WARNING | {‘task’} have not been found for datatype ‘func’ and suffix ‘bold’.

Are these inconsequential?
Thanks,
Matt

10

May you share the full log please? As well as the output of tree run on a subject output folder so I can see what the output structure and file names are?

11

Hi Steven,
Still running. Will send when the command finishes.
Best wishes,
Matt

12

Hi Steven,
Here is the tree:

sub-1008/
├── anat
│   ├── sub-1008_acq-MPRAGE_rec-defaced_T1w.json
│   ├── sub-1008_acq-MPRAGE_rec-defaced_T1w.nii.gz
│   ├── sub-1008_acq-MPRAGE_T1w.json
│   └── sub-1008_acq-MPRAGE_T1w.nii.gz
├── dwi
│   ├── sub-1008_acq-DIFF137_dir-AP_dwi.bval
│   ├── sub-1008_acq-DIFF137_dir-AP_dwi.bvec
│   ├── sub-1008_acq-DIFF137_dir-AP_dwi.json
│   ├── sub-1008_acq-DIFF137_dir-AP_dwi.nii.gz
│   ├── sub-1008_acq-DIFF7_dir-AP_dwi.bval
│   ├── sub-1008_acq-DIFF7_dir-AP_dwi.bvec
│   ├── sub-1008_acq-DIFF7_dir-AP_dwi.json
│   ├── sub-1008_acq-DIFF7_dir-AP_dwi.nii.gz
│   ├── sub-1008_acq-DIFF7_dir-PA_dwi.bval
│   ├── sub-1008_acq-DIFF7_dir-PA_dwi.bvec
│   ├── sub-1008_acq-DIFF7_dir-PA_dwi.json
│   └── sub-1008_acq-DIFF7_dir-PA_dwi.nii.gz
└── func
    ├── sub-1008_task-emoreg1_acq-TR1400_bold.json
    ├── sub-1008_task-emoreg1_acq-TR1400_bold.nii.gz
    ├── sub-1008_task-emoreg2_acq-TR1400_bold.json
    ├── sub-1008_task-emoreg2_acq-TR1400_bold.nii.gz
    ├── sub-1008_task-rest_acq-TR1400_bold.json
    └── sub-1008_task-rest_acq-TR1400_bold.nii.gz

And here is the log:

2024-01-04 12:27:06.677 - INFO     - dcm2bids.main | --- dcm2bids start ---
2024-01-04 12:27:06.677 - INFO     - dcm2bids.main | Running the following command: /var/share/software/miniconda2/envs/dcm2bids/bin/dcm2bids -d sourcedata/sub-1008 -p sub-1008 --auto_extract_entities --force_dcm2bids --bids_validate --clobber -c code/dcm2bids_config.json
2024-01-04 12:27:06.680 - INFO     - dcm2bids.main | OS version: Linux-4.15.0-142-generic-x86_64-with-glibc2.23
2024-01-04 12:27:06.680 - INFO     - dcm2bids.main | Python version: 3.12.1 | packaged by conda-forge | (main, Dec 23 2023, 08:03:24) [GCC 12.3.0]
2024-01-04 12:27:06.680 - INFO     - dcm2bids.main | dcm2bids version: 3.1.1
2024-01-04 12:27:06.683 - INFO     - dcm2bids.main | dcm2niix version: v1.0.20230411
2024-01-04 12:27:06.683 - INFO     - dcm2bids.main | Checking for software update
2024-01-04 12:27:06.866 - INFO     - tools.check_latest | Currently using the latest version of dcm2bids.
2024-01-04 12:27:06.967 - INFO     - tools.check_latest | Currently using the latest version of dcm2niix.
2024-01-04 12:27:06.968 - INFO     - dcm2bids.main | participant: sub-1008
2024-01-04 12:27:06.968 - INFO     - dcm2bids.main | config: /home/matt/studies/AFSP/sub_1006/rawdicom/new/temp/code/dcm2bids_config.json
2024-01-04 12:27:06.968 - INFO     - dcm2bids.main | BIDS directory: /home/matt/studies/AFSP/sub_1006/rawdicom/new/temp
2024-01-04 12:27:06.968 - INFO     - dcm2bids.main | Auto extract entities: True
2024-01-04 12:27:06.969 - INFO     - dcm2bids.main | Validate BIDS: True

2024-01-04 12:27:06.970 - WARNING  - dcm2niix_gen.run | Previous dcm2bids temporary directory output found:
2024-01-04 12:27:06.970 - WARNING  - dcm2niix_gen.run | /home/matt/studies/AFSP/sub_1006/rawdicom/new/temp/tmp_dcm2bids/sub-1008
2024-01-04 12:27:06.970 - WARNING  - dcm2niix_gen.run | 'force' argument is set to True
2024-01-04 12:27:06.970 - WARNING  - dcm2niix_gen.run | Cleaning the previous directory and running dcm2bids
2024-01-04 12:27:07.148 - INFO     - utils.run_shell_command | Running: dcm2niix -b y -ba y -z y -f %3s_%f_%p_%t -o /home/matt/studies/AFSP/sub_1006/rawdicom/new/temp/tmp_dcm2bids/sub-1008 sourcedata/sub-1008
2024-01-04 12:27:27.855 - DEBUG    - dcm2niix_gen.execute | 
Chris Rorden's dcm2niiX version v1.0.20230411  GCC12.2.0 x86-64 (64-bit Linux)
Found 1559 DICOM file(s)
Convert 18 DICOM as /home/matt/studies/AFSP/sub_1006/rawdicom/new/temp/tmp_dcm2bids/sub-1008/004_sub-1008_set_volume_20210406142807 (112x112x64x18)
Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/home/matt/studies/AFSP/sub_1006/rawdicom/new/temp/tmp_dcm2bids/sub-1008/004_sub-1008_set_volume_20210406142807.nii"
Convert 7 DICOM as /home/matt/studies/AFSP/sub_1006/rawdicom/new/temp/tmp_dcm2bids/sub-1008/007_sub-1008_DIFF_7_AP_20210406142807 (106x90x64x7)
Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/home/matt/studies/AFSP/sub_1006/rawdicom/new/temp/tmp_dcm2bids/sub-1008/007_sub-1008_DIFF_7_AP_20210406142807.nii"
Convert 383 DICOM as /home/matt/studies/AFSP/sub_1006/rawdicom/new/temp/tmp_dcm2bids/sub-1008/006_sub-1008_emo_reg2_20210406142807 (112x112x64x383)
Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/home/matt/studies/AFSP/sub_1006/rawdicom/new/temp/tmp_dcm2bids/sub-1008/006_sub-1008_emo_reg2_20210406142807.nii"
Warning: Instance Number (0020,0013) order is not spatial.
Warning: Interslice distance varies in this volume (incompatible with NIfTI format).
Convert 5 DICOM as /home/matt/studies/AFSP/sub_1006/rawdicom/new/temp/tmp_dcm2bids/sub-1008/001_sub-1008_Localizer_20210406142807_i00005 (256x256x5x1)
Compress: "/usr/bin/pigz" -n -f -6 "/home/matt/studies/AFSP/sub_1006/rawdicom/new/temp/tmp_dcm2bids/sub-1008/001_sub-1008_Localizer_20210406142807_i00005.nii"
Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/home/matt/studies/AFSP/sub_1006/rawdicom/new/temp/tmp_dcm2bids/sub-1008/001_sub-1008_Localizer_20210406142807_i00005_Eq_1.nii"
Convert 1 DICOM as /home/matt/studies/AFSP/sub_1006/rawdicom/new/temp/tmp_dcm2bids/sub-1008/001_sub-1008_Localizer_20210406142807_i00006 (256x256x1x1)
Compress: "/usr/bin/pigz" -n -f -6 "/home/matt/studies/AFSP/sub_1006/rawdicom/new/temp/tmp_dcm2bids/sub-1008/001_sub-1008_Localizer_20210406142807_i00006.nii"
Convert 1 DICOM as /home/matt/studies/AFSP/sub_1006/rawdicom/new/temp/tmp_dcm2bids/sub-1008/001_sub-1008_Localizer_20210406142807_i00007 (256x256x1x1)
Compress: "/usr/bin/pigz" -n -f -6 "/home/matt/studies/AFSP/sub_1006/rawdicom/new/temp/tmp_dcm2bids/sub-1008/001_sub-1008_Localizer_20210406142807_i00007.nii"
Convert 176 DICOM as /home/matt/studies/AFSP/sub_1006/rawdicom/new/temp/tmp_dcm2bids/sub-1008/002_sub-1008_MPRAGE_STAN_20210406142807 (256x256x176x1)
Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/home/matt/studies/AFSP/sub_1006/rawdicom/new/temp/tmp_dcm2bids/sub-1008/002_sub-1008_MPRAGE_STAN_20210406142807.nii"
Convert 404 DICOM as /home/matt/studies/AFSP/sub_1006/rawdicom/new/temp/tmp_dcm2bids/sub-1008/003_sub-1008_REST_1400_20210406142807 (112x112x64x404)
Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/home/matt/studies/AFSP/sub_1006/rawdicom/new/temp/tmp_dcm2bids/sub-1008/003_sub-1008_REST_1400_20210406142807.nii"
Convert 137 DICOM as /home/matt/studies/AFSP/sub_1006/rawdicom/new/temp/tmp_dcm2bids/sub-1008/009_sub-1008_DIFF_137_AP_20210406142807 (106x90x64x137)
Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/home/matt/studies/AFSP/sub_1006/rawdicom/new/temp/tmp_dcm2bids/sub-1008/009_sub-1008_DIFF_137_AP_20210406142807.nii"
Convert 44 DICOM as /home/matt/studies/AFSP/sub_1006/rawdicom/new/temp/tmp_dcm2bids/sub-1008/010_sub-1008_FLAIR_-_ch32_iPAT2_-CLINICAL_20210406142807 (192x256x44x1)
Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/home/matt/studies/AFSP/sub_1006/rawdicom/new/temp/tmp_dcm2bids/sub-1008/010_sub-1008_FLAIR_-_ch32_iPAT2_-CLINICAL_20210406142807.nii"
Convert 376 DICOM as /home/matt/studies/AFSP/sub_1006/rawdicom/new/temp/tmp_dcm2bids/sub-1008/005_sub-1008_emo_reg1_20210406142807 (112x112x64x376)
Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/home/matt/studies/AFSP/sub_1006/rawdicom/new/temp/tmp_dcm2bids/sub-1008/005_sub-1008_emo_reg1_20210406142807.nii"
Convert 7 DICOM as /home/matt/studies/AFSP/sub_1006/rawdicom/new/temp/tmp_dcm2bids/sub-1008/008_sub-1008_DIFF_7_PA_20210406142807 (106x90x64x7)
Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/home/matt/studies/AFSP/sub_1006/rawdicom/new/temp/tmp_dcm2bids/sub-1008/008_sub-1008_DIFF_7_PA_20210406142807.nii"
Conversion required 20.698498 seconds (6.712206 for core code).

2024-01-04 12:27:27.855 - INFO     - dcm2niix_gen.execute | Check log file for dcm2niix output

2024-01-04 12:27:27.861 - INFO     - sidecar.build_acquisitions | SIDECAR PAIRING
2024-01-04 12:27:27.861 - INFO     - sidecar.build_acquisitions | No Pairing  <-  001_sub-1008_Localizer_20210406142807_i00005
2024-01-04 12:27:27.862 - INFO     - sidecar.build_acquisitions | No Pairing  <-  001_sub-1008_Localizer_20210406142807_i00006
2024-01-04 12:27:27.862 - INFO     - sidecar.build_acquisitions | No Pairing  <-  001_sub-1008_Localizer_20210406142807_i00007
2024-01-04 12:27:27.862 - INFO     - sidecar.build_acquisitions | sub-1008_acq-MPRAGE_T1w  <-  002_sub-1008_MPRAGE_STAN_20210406142807
2024-01-04 12:27:27.863 - WARNING  - sidecar.searchDcmTagEntity | {'task'} have not been found for datatype 'func' and suffix 'bold'.
2024-01-04 12:27:27.863 - INFO     - sidecar.build_acquisitions | sub-1008_task-rest_acq-TR1400_bold  <-  003_sub-1008_REST_1400_20210406142807
2024-01-04 12:27:27.863 - INFO     - sidecar.build_acquisitions | No Pairing  <-  004_sub-1008_set_volume_20210406142807
2024-01-04 12:27:27.863 - WARNING  - sidecar.searchDcmTagEntity | {'task'} have not been found for datatype 'func' and suffix 'bold'.
2024-01-04 12:27:27.863 - INFO     - sidecar.build_acquisitions | sub-1008_task-emoreg1_acq-TR1400_bold  <-  005_sub-1008_emo_reg1_20210406142807
2024-01-04 12:27:27.863 - WARNING  - sidecar.searchDcmTagEntity | {'task'} have not been found for datatype 'func' and suffix 'bold'.
2024-01-04 12:27:27.864 - INFO     - sidecar.build_acquisitions | sub-1008_task-emoreg2_acq-TR1400_bold  <-  006_sub-1008_emo_reg2_20210406142807
2024-01-04 12:27:27.864 - WARNING  - acquisition.setDstFile | ✅ Filename was reordered according to BIDS entity table order:
                from:   sub-1008_dir-AP_acq-DIFF7_dwi
                to:     sub-1008_acq-DIFF7_dir-AP_dwi
2024-01-04 12:27:27.864 - INFO     - sidecar.build_acquisitions | sub-1008_acq-DIFF7_dir-AP_dwi  <-  007_sub-1008_DIFF_7_AP_20210406142807
2024-01-04 12:27:27.864 - WARNING  - acquisition.setDstFile | ✅ Filename was reordered according to BIDS entity table order:
                from:   sub-1008_dir-PA_acq-DIFF7_dwi
                to:     sub-1008_acq-DIFF7_dir-PA_dwi
2024-01-04 12:27:27.864 - INFO     - sidecar.build_acquisitions | sub-1008_acq-DIFF7_dir-PA_dwi  <-  008_sub-1008_DIFF_7_PA_20210406142807
2024-01-04 12:27:27.865 - WARNING  - acquisition.setDstFile | ✅ Filename was reordered according to BIDS entity table order:
                from:   sub-1008_dir-AP_acq-DIFF137_dwi
                to:     sub-1008_acq-DIFF137_dir-AP_dwi
2024-01-04 12:27:27.865 - INFO     - sidecar.build_acquisitions | sub-1008_acq-DIFF137_dir-AP_dwi  <-  009_sub-1008_DIFF_137_AP_20210406142807
2024-01-04 12:27:27.865 - INFO     - sidecar.build_acquisitions | No Pairing  <-  010_sub-1008_FLAIR_-_ch32_iPAT2_-CLINICAL_20210406142807
2024-01-04 12:27:27.865 - INFO     - dcm2bids_gen.run | Moving acquisitions into BIDS folder "/home/matt/studies/AFSP/sub_1006/rawdicom/new/temp/sub-1008".

2024-01-04 12:27:27.866 - WARNING  - acquisition.setExtraDstFile | ✅ Filename was reordered according to BIDS entity table order:
                from:   sub-1008_acq-MPRAGE_rec-defaced_acq-MPRAGE_T1w
                to:     sub-1008_acq-MPRAGE_rec-defaced_T1w
2024-01-04 12:27:27.867 - INFO     - utils.run_shell_command | Running: pydeface --force --verbose --outfile /home/matt/studies/AFSP/sub_1006/rawdicom/new/temp/sub-1008/anat/sub-1008_acq-MPRAGE_rec-defaced_T1w.nii.gz /home/matt/studies/AFSP/sub_1006/rawdicom/new/temp/tmp_dcm2bids/sub-1008/002_sub-1008_MPRAGE_STAN_20210406142807.nii.gz
2024-01-04 12:36:32.290 - ERROR    - dcm2bids_gen.run | The bids-validator does not seem to work properly. The bids-validator may not be installed on your computer. Please check: https://github.com/bids-standard/bids-validator.
2024-01-04 12:36:32.290 - INFO     - dcm2bids.main | Logs saved in /home/matt/studies/AFSP/sub_1006/rawdicom/new/temp/tmp_dcm2bids/log/sub-1008_20240104-122706.log
2024-01-04 12:36:32.290 - INFO     - dcm2bids.main | --- dcm2bids end ---
13

Hi @hoptman,

Looks great! At least from a file naming perspective, that should be BIDS valid (but only the validator can confirm that and also make sure metadata are in line).

Apologies it looks like I mixed up some custom_entities orders (e.g., acq comes before dir), but dcm2bids fixed it automatically (might still be good to correct it in the config though). I doubt those warnings you get are consequential, but running the BIDS validator should bring any issues to light.

Best,
Steven

14

Hi Steven,
That’s great! Thanks so much!! :smiley:
Best wishes,
Matt

15

No problem! (I just edited the config to fix the order issues I mentioned earlier).