heudiconv with custom heuristics

Tutorial: How to create a BIDS dataset

Author

Dr. Lennart Wittkuhn

Published

February 5, 2026

Introduction

This tutorial is based on Dianne Patterson’s University of Arizona tutorials. It was adapted from the heudiconv Quickstart tutorial. This guide demonstrates how to use heudiconv with a provided heuristic.py to convert DICOMS into the BIDS data structure using a basic conversion approach.

Installation

Depending on your environment, paste the installation command here:

# < replace with installation command >

Download the data

Download and extract the example dataset or retrieve it from OSF at https://osf.io/rghtc/files/mqgzh.

curl -L https://nx81903.your-storageshare.de/s/fKw8zSoLwGoDmyE/download -o data.zip
unzip -j -o data.zip -d data
rm -f data.zip
Code Output 
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  694k    0  694k    0     0   451k      0 --:--:--  0:00:01 --:--:--  451k100 24.2M    0 24.2M    0     0  9767k      0 --:--:--  0:00:02 --:--:-- 23.5M100 53.3M    0 53.3M    0     0  14.9M      0 --:--:--  0:00:03 --:--:-- 26.0M100 81.4M    0 81.4M    0     0  17.9M      0 --:--:--  0:00:04 --:--:-- 26.9M100  110M    0  110M    0     0  19.9M      0 --:--:--  0:00:05 --:--:-- 27.3M100  140M    0  140M    0     0  21.3M      0 --:--:--  0:00:06 --:--:-- 27.8M100  169M    0  169M    0     0  22.4M      0 --:--:--  0:00:07 --:--:-- 29.0M100  200M    0  200M    0     0  23.4M      0 --:--:--  0:00:08 --:--:-- 29.5M100  229M    0  229M    0     0  24.1M      0 --:--:--  0:00:09 --:--:-- 29.6M100  240M    0  240M    0     0  24.2M      0 --:--:--  0:00:09 --:--:-- 29.8M
Archive:  data.zip
 extracting: data/sub-219_dicom.zip

Prepare the data

Extract the downloaded archive. This created the folder MRIS.

unzip data/sub-219_dicom.zip
Code Output 
Archive:  data/sub-219_dicom.zip
   creating: MRIS/
   creating: MRIS/dicom/
   creating: MRIS/dicom/219/
   creating: MRIS/dicom/219/itbs/
   creating: MRIS/dicom/219/itbs/Bzero_verify_PA_17/
  inflating: MRIS/dicom/219/itbs/Bzero_verify_PA_17/IM-0005-0001.dcm  
  inflating: MRIS/dicom/219/itbs/Bzero_verify_PA_17/IM-0005-0002.dcm  
  inflating: MRIS/dicom/219/itbs/Bzero_verify_PA_17/IM-0005-0003.dcm  
  inflating: MRIS/dicom/219/itbs/Bzero_verify_PA_17/IM-0005-0004.dcm  
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   creating: MRIS/dicom/219/itbs/DTI_30_DIRs_AP_15/
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  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0070.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0071.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0072.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0073.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0074.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0075.dcm  
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  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0079.dcm  
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  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0082.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0083.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0084.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0085.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0086.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0087.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0088.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0089.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0090.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0091.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0092.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0093.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0094.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0095.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0096.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0097.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0098.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0099.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0100.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0101.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0102.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0103.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0104.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0105.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0106.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0107.dcm  
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  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0110.dcm  
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  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0112.dcm  
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  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0116.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0117.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0118.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0119.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0120.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0121.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0122.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0123.dcm  
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  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0126.dcm  
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  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0135.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0136.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0137.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0138.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0139.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0140.dcm  
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  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0150.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0151.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0152.dcm  
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  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0154.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0155.dcm  
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  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0159.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0160.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0161.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0162.dcm  
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  inflating: MRIS/dicom/219/itbs/MoCoSeries_19/IM-0007-0177.dcm  
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  inflating: MRIS/dicom/219/itbs/MoCoSeries_31/IM-0015-0001.dcm  
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  inflating: MRIS/dicom/219/itbs/MoCoSeries_31/IM-0015-0111.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_31/IM-0015-0112.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_31/IM-0015-0113.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_31/IM-0015-0114.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_31/IM-0015-0115.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_31/IM-0015-0116.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_31/IM-0015-0117.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_31/IM-0015-0118.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_31/IM-0015-0119.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_31/IM-0015-0120.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_31/IM-0015-0121.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_31/IM-0015-0122.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_31/IM-0015-0123.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_31/IM-0015-0124.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_31/IM-0015-0125.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_31/IM-0015-0126.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_31/IM-0015-0127.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_31/IM-0015-0128.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_31/IM-0015-0129.dcm  
  inflating: MRIS/dicom/219/itbs/MoCoSeries_31/IM-0015-0130.dcm  
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Inspect the raw data structure

Let’s examine the directory structure of our dataset. The dataset contains DICOM files organized by subject and session:

tree -L 2 MRIS
Code Output 
MRIS
├── Makefile
├── Nifti
│   └── code
├── dicom
│   └── 219
└── hdc_run.sh

5 directories, 2 files

Create the heuristic file

Let’s examine the provided heuristic file that defines how to organize the DICOM files:

cat MRIS/Nifti/code/heuristic1.py
Code Output 
import os


def create_key(template, outtype=('nii.gz',), annotation_classes=None):
    if template is None or not template:
        raise ValueError('Template must be a valid format string')
    return template, outtype, annotation_classes


def infotodict(seqinfo):
    # Section 1: These key definitions should be revised by the user
    ###################################################################
    # For each sequence, define a key variables (e.g., t1w, dwi etc) and template using the create_key function:
    # key = create_key(output_directory_path_and_name).
    # TIPS
    # If there are sessions, then session must be subfolder name. 
    # Do not prepend the ses key to the session! It will be prepended automatically for the subfolder and the filename.
    # The final value in the filename should be the modality.  It does not have a key, just a value.
    # Otherwise, there is a key for every value. 
    # Filenames always start with subject, optionally followed by session, and end with modality.
    
    # The "data" key creates sequential numbers which can be for naming sequences.
    # This is especially valuable if you run the same sequence multiple times at the scanner.
    data = create_key('run-{item:03d}')
    
    t1w = create_key('sub-{subject}/{session}/anat/sub-{subject}_{session}_T1w')
    
    dwi = create_key('sub-{subject}/{session}/dwi/sub-{subject}_{session}_acq-AP_dwi')
    
    # Save the RPE (reverse phase-encode) B0 image as a fieldmap (fmap).  It will be used to correct
    # the distortion in the DWI
    fmap_rev_phase =  create_key('sub-{subject}/{session}/fmap/sub-{subject}_{session}_dir-PA_epi')
    
    fmap_mag =  create_key('sub-{subject}/{session}/fmap/sub-{subject}_{session}_magnitude')
    
    fmap_phase = create_key('sub-{subject}/{session}/fmap/sub-{subject}_{session}_phasediff')
    
    # Even if this is resting state, you still need a task key
    func_rest = create_key('sub-{subject}/{session}/func/sub-{subject}_{session}_task-rest_run-01_bold')
    func_rest_post = create_key('sub-{subject}/{session}/func/sub-{subject}_{session}_task-rest_run-02_bold')

    # Section 1b: This data dictionary (below) should be revised by the user.
    ########################################################################### 
    # info is a Python dictionary containing the following keys from the infotodict defined above.
    # This list should contain all and only the sequences you want to export from the dicom directory.
    info = {t1w: [], dwi: [], fmap_rev_phase: [], fmap_mag: [], fmap_phase: [], func_rest: [], func_rest_post: []}

    # The following line does no harm, but it is not part of the dictionary.
    last_run = len(seqinfo)

    # Section 2: These criteria should be revised by the user.
    ##########################################################
    # Define test criteria to check that each DICOM sequence is correct
    # seqinfo (s) refers to information in dicominfo.tsv. Consult that file for
    # available criteria.
    # Each sequence to export must have been defined in Section 1 and included in Section 1b.
    # The following illustrates the use of multiple criteria:
    for idx, s in enumerate(seqinfo):
        # Dimension 3 must equal 176 and the string 'mprage' must appear somewhere in the protocol_name
        if (s.dim3 == 176) and ('mprage' in s.protocol_name):
            info[t1w].append(s.series_id)
        
        # Dimension 3 must equal 74 and dimension 4 must equal 32, and the string 'DTI' must appear somewhere in the protocol_name
        if (s.dim3 == 74) and (s.dim4 == 32) and ('DTI' in s.protocol_name):
            info[dwi].append(s.series_id)
        
        # The string 'verify_P-A' must appear somewhere in the protocol_name    
        if ('verify_P-A' in s.protocol_name):
            info[fmap_rev_phase] = [s.series_id]
        
        # Dimension 3 must equal 64, and the string 'field_mapping' must appear somewhere in the protocol_name    
        if (s.dim3 == 64) and ('field_mapping' in s.protocol_name):
            info[fmap_mag] = [s.series_id]
        
        # Dimension 3 must equal 32, and the string 'field_mapping' must appear somewhere in the protocol_name      
        if (s.dim3 == 32) and ('field_mapping' in s.protocol_name):
            info[fmap_phase] = [s.series_id]
        
        # The string 'resting_state' must appear somewhere in the protocol_name and the boolean field is_motion_corrected must be False (i.e. not motion corrected) 
        
        # This ensures I do NOT get the motion corrected MOCO series instead of the raw series!
        if ('restingstate' == s.protocol_name) and (not s.is_motion_corrected):
            info[func_rest].append(s.series_id) 
        
        # The string 'Post_TMS_resting_state' must appear somewhere in the protocol_name and the boolean field is_motion_corrected must be False (i.e. not motion corrected) 
        # This ensures I do NOT get the motion corrected MOCO series instead of the raw series.
        if ('Post_TMS_restingstate' == s.protocol_name) and (not s.is_motion_corrected):
            info[func_rest_post].append(s.series_id)

    # Section 3: Optional Report
    ###################################
    # Populate the msg list IF the wrong number of files is created (!= means not equal) 
    # and exit the program with an error (No BIDS files are generated)
    msg = []

    if len(info[t1w]) != 1: msg.append('WARNING: Missing correct number of T1w runs')
    if len(info[dwi]) != 1: msg.append('WARNING: Missing correct number of dwi runs')
    if len(info[fmap_rev_phase]) != 1: msg.append('WARNING: Missing correct number of RPE runs')
    if len(info[fmap_mag]) != 1: msg.append('WARNING: Missing correct number of magnitude runs')
    if len(info[fmap_phase]) != 1: msg.append('WARNING: Missing correct number of phasediff runs')
    if len(info[func_rest]) != 1: msg.append('WARNING: Missing correct number of resting_state runs')
    if len(info[func_rest_post]) != 1: msg.append('WARNING: Missing correct number of resting_state_post runs')

    # If there is an error, a message will be generated and no NIfTI files will be generated for the subject.
    if msg:
      raise ValueError('\n'.join(msg))

    return info

Run basic heudiconv conversion

Now we’ll use heudiconv to convert DICOMS into the BIDS data structure using the custom heuristic.

Here’s an explanation of the flags and arguments:

  • --files specifies the DICOM files to convert
  • -f provides the heuristic file path
  • -o tells heudiconv where to place output (Nifti directory)
  • -s specifies the subject ID
  • -ss specifies the session
  • -c dcm2niix uses dcm2niix converter
  • -b indicates BIDS format output
  • --minmeta prevents overflow of meta-information in JSON files
  • --overwrite overwrites existing converted files
heudiconv --files MRIS/dicom/219/itbs/*/*.dcm -o MRIS/Nifti -f MRIS/Nifti/code/heuristic1.py -s 219 -ss itbs -c dcm2niix -b --minmeta --overwrite
Code Output 
WARNING: Could not check for version updates: Connection to server could not be made
INFO: Running heudiconv version 1.3.4 latest Unknown
INFO: Analyzing 1716 dicoms
INFO: Generated sequence info for 1 studies with 25 entries total
INFO: Heuristic is missing an `infotoids` method, assigning empty method and using provided subject id 219. Provide `session` and `locator` fields for best results.
INFO: Study session for StudySessionInfo(locator=None, session='itbs', subject='219')
INFO: Need to process 1 study sessions
INFO: PROCESSING STARTS: {'subject': '219', 'outdir': '/app/MRIS/Nifti/', 'session': 'itbs'}
INFO: Processing 25 pre-sorted seqinfo entries
INFO: Doing conversion using dcm2niix
INFO: Converting /app/MRIS/Nifti/sub-219/ses-itbs/anat/sub-219_ses-itbs_T1w (176 DICOMs) -> /app/MRIS/Nifti/sub-219/ses-itbs/anat . Converter: dcm2niix . Output types: ('nii.gz',)
260205-18:29:30,660 nipype.workflow INFO:
     [Node] Setting-up "convert" in "/tmp/dcm2niixlm5axg0c/convert".
INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixlm5axg0c/convert".
260205-18:29:30,703 nipype.workflow INFO:
     [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
INFO: [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
260205-18:29:30,881 nipype.interface INFO:
     stdout 2026-02-05T18:29:30.881924:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
INFO: stdout 2026-02-05T18:29:30.881924:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
260205-18:29:30,882 nipype.interface INFO:
     stdout 2026-02-05T18:29:30.881924:Found 176 DICOM file(s)
INFO: stdout 2026-02-05T18:29:30.881924:Found 176 DICOM file(s)
260205-18:29:30,882 nipype.interface INFO:
     stdout 2026-02-05T18:29:30.881924:Convert 176 DICOM as /app/MRIS/Nifti/sub-219/ses-itbs/anat/sub-219_ses-itbs_T1w_heudiconv746 (256x256x176x1)
INFO: stdout 2026-02-05T18:29:30.881924:Convert 176 DICOM as /app/MRIS/Nifti/sub-219/ses-itbs/anat/sub-219_ses-itbs_T1w_heudiconv746 (256x256x176x1)
260205-18:29:33,422 nipype.interface INFO:
     stdout 2026-02-05T18:29:33.422542:Conversion required 2.595486 seconds (2.593593 for core code).
INFO: stdout 2026-02-05T18:29:33.422542:Conversion required 2.595486 seconds (2.593593 for core code).
260205-18:29:33,448 nipype.workflow INFO:
     [Node] Finished "convert", elapsed time 2.658454s.
INFO: [Node] Finished "convert", elapsed time 2.658454s.
INFO: Post-treating /app/MRIS/Nifti/sub-219/ses-itbs/anat/sub-219_ses-itbs_T1w.json file
INFO: Converting /app/MRIS/Nifti/sub-219/ses-itbs/dwi/sub-219_ses-itbs_acq-AP_dwi (32 DICOMs) -> /app/MRIS/Nifti/sub-219/ses-itbs/dwi . Converter: dcm2niix . Output types: ('nii.gz',)
260205-18:29:33,465 nipype.workflow INFO:
     [Node] Setting-up "convert" in "/tmp/dcm2niixtz8t88lp/convert".
INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixtz8t88lp/convert".
260205-18:29:33,473 nipype.workflow INFO:
     [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
INFO: [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
260205-18:29:33,550 nipype.interface INFO:
     stdout 2026-02-05T18:29:33.550716:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
INFO: stdout 2026-02-05T18:29:33.550716:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
260205-18:29:33,550 nipype.interface INFO:
     stdout 2026-02-05T18:29:33.550716:Found 32 DICOM file(s)
INFO: stdout 2026-02-05T18:29:33.550716:Found 32 DICOM file(s)
260205-18:29:33,551 nipype.interface INFO:
     stdout 2026-02-05T18:29:33.550716:Convert 32 DICOM as /app/MRIS/Nifti/sub-219/ses-itbs/dwi/sub-219_ses-itbs_acq-AP_dwi_heudiconv786 (128x128x74x32)
INFO: stdout 2026-02-05T18:29:33.550716:Convert 32 DICOM as /app/MRIS/Nifti/sub-219/ses-itbs/dwi/sub-219_ses-itbs_acq-AP_dwi_heudiconv786 (128x128x74x32)
260205-18:29:40,766 nipype.interface INFO:
     stdout 2026-02-05T18:29:40.766174:Conversion required 7.255900 seconds (7.255090 for core code).
INFO: stdout 2026-02-05T18:29:40.766174:Conversion required 7.255900 seconds (7.255090 for core code).
260205-18:29:40,795 nipype.workflow INFO:
     [Node] Finished "convert", elapsed time 7.321301s.
INFO: [Node] Finished "convert", elapsed time 7.321301s.
INFO: Post-treating /app/MRIS/Nifti/sub-219/ses-itbs/dwi/sub-219_ses-itbs_acq-AP_dwi.json file
INFO: Converting /app/MRIS/Nifti/sub-219/ses-itbs/fmap/sub-219_ses-itbs_dir-PA_epi (148 DICOMs) -> /app/MRIS/Nifti/sub-219/ses-itbs/fmap . Converter: dcm2niix . Output types: ('nii.gz',)
260205-18:29:40,806 nipype.workflow INFO:
     [Node] Setting-up "convert" in "/tmp/dcm2niixjd6ga02g/convert".
INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixjd6ga02g/convert".
260205-18:29:40,841 nipype.workflow INFO:
     [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
INFO: [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
260205-18:29:40,922 nipype.interface INFO:
     stdout 2026-02-05T18:29:40.922479:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
INFO: stdout 2026-02-05T18:29:40.922479:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
260205-18:29:40,922 nipype.interface INFO:
     stdout 2026-02-05T18:29:40.922479:Found 148 DICOM file(s)
INFO: stdout 2026-02-05T18:29:40.922479:Found 148 DICOM file(s)
260205-18:29:40,922 nipype.interface INFO:
     stdout 2026-02-05T18:29:40.922479:Convert 148 DICOM as /app/MRIS/Nifti/sub-219/ses-itbs/fmap/sub-219_ses-itbs_dir-PA_epi_heudiconv841 (128x128x74x2)
INFO: stdout 2026-02-05T18:29:40.922479:Convert 148 DICOM as /app/MRIS/Nifti/sub-219/ses-itbs/fmap/sub-219_ses-itbs_dir-PA_epi_heudiconv841 (128x128x74x2)
260205-18:29:41,352 nipype.interface INFO:
     stdout 2026-02-05T18:29:41.352273:Conversion required 0.473840 seconds (0.473729 for core code).
INFO: stdout 2026-02-05T18:29:41.352273:Conversion required 0.473840 seconds (0.473729 for core code).
260205-18:29:41,377 nipype.workflow INFO:
     [Node] Finished "convert", elapsed time 0.535248s.
INFO: [Node] Finished "convert", elapsed time 0.535248s.
INFO: Post-treating /app/MRIS/Nifti/sub-219/ses-itbs/fmap/sub-219_ses-itbs_dir-PA_epi.json file
INFO: Converting /app/MRIS/Nifti/sub-219/ses-itbs/fmap/sub-219_ses-itbs_magnitude (64 DICOMs) -> /app/MRIS/Nifti/sub-219/ses-itbs/fmap . Converter: dcm2niix . Output types: ('nii.gz',)
260205-18:29:41,392 nipype.workflow INFO:
     [Node] Setting-up "convert" in "/tmp/dcm2niixmw4_cwya/convert".
INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixmw4_cwya/convert".
260205-18:29:41,408 nipype.workflow INFO:
     [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
INFO: [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
260205-18:29:41,465 nipype.interface INFO:
     stdout 2026-02-05T18:29:41.465355:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
INFO: stdout 2026-02-05T18:29:41.465355:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
260205-18:29:41,465 nipype.interface INFO:
     stdout 2026-02-05T18:29:41.465355:Found 64 DICOM file(s)
INFO: stdout 2026-02-05T18:29:41.465355:Found 64 DICOM file(s)
260205-18:29:41,465 nipype.interface INFO:
     stdout 2026-02-05T18:29:41.465355:Slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1). Use 'merge 2D slices' option to force stacking
INFO: stdout 2026-02-05T18:29:41.465355:Slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1). Use 'merge 2D slices' option to force stacking
260205-18:29:41,465 nipype.interface INFO:
     stdout 2026-02-05T18:29:41.465355:Convert 32 DICOM as /app/MRIS/Nifti/sub-219/ses-itbs/fmap/sub-219_ses-itbs_magnitude_heudiconv445_e2 (80x80x32x1)
INFO: stdout 2026-02-05T18:29:41.465355:Convert 32 DICOM as /app/MRIS/Nifti/sub-219/ses-itbs/fmap/sub-219_ses-itbs_magnitude_heudiconv445_e2 (80x80x32x1)
260205-18:29:41,498 nipype.interface INFO:
     stdout 2026-02-05T18:29:41.498568:Convert 32 DICOM as /app/MRIS/Nifti/sub-219/ses-itbs/fmap/sub-219_ses-itbs_magnitude_heudiconv445_e1 (80x80x32x1)
INFO: stdout 2026-02-05T18:29:41.498568:Convert 32 DICOM as /app/MRIS/Nifti/sub-219/ses-itbs/fmap/sub-219_ses-itbs_magnitude_heudiconv445_e1 (80x80x32x1)
260205-18:29:41,530 nipype.interface INFO:
     stdout 2026-02-05T18:29:41.530683:Conversion required 0.085686 seconds (0.085644 for core code).
INFO: stdout 2026-02-05T18:29:41.530683:Conversion required 0.085686 seconds (0.085644 for core code).
260205-18:29:41,559 nipype.workflow INFO:
     [Node] Finished "convert", elapsed time 0.150102s.
INFO: [Node] Finished "convert", elapsed time 0.150102s.
WARNING: For now not embedding BIDS and info generated .nii.gz itself since sequence produced multiple files
INFO: Converting /app/MRIS/Nifti/sub-219/ses-itbs/fmap/sub-219_ses-itbs_phasediff (32 DICOMs) -> /app/MRIS/Nifti/sub-219/ses-itbs/fmap . Converter: dcm2niix . Output types: ('nii.gz',)
260205-18:29:41,571 nipype.workflow INFO:
     [Node] Setting-up "convert" in "/tmp/dcm2niixnl7eeayv/convert".
INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixnl7eeayv/convert".
260205-18:29:41,580 nipype.workflow INFO:
     [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
INFO: [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
260205-18:29:41,629 nipype.interface INFO:
     stdout 2026-02-05T18:29:41.629019:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
INFO: stdout 2026-02-05T18:29:41.629019:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
260205-18:29:41,629 nipype.interface INFO:
     stdout 2026-02-05T18:29:41.629019:Found 32 DICOM file(s)
INFO: stdout 2026-02-05T18:29:41.629019:Found 32 DICOM file(s)
260205-18:29:41,629 nipype.interface INFO:
     stdout 2026-02-05T18:29:41.629019:Convert 32 DICOM as /app/MRIS/Nifti/sub-219/ses-itbs/fmap/sub-219_ses-itbs_phasediff_heudiconv934_e2_ph (80x80x32x1)
INFO: stdout 2026-02-05T18:29:41.629019:Convert 32 DICOM as /app/MRIS/Nifti/sub-219/ses-itbs/fmap/sub-219_ses-itbs_phasediff_heudiconv934_e2_ph (80x80x32x1)
260205-18:29:41,648 nipype.interface INFO:
     stdout 2026-02-05T18:29:41.648306:Conversion required 0.032712 seconds (0.032709 for core code).
INFO: stdout 2026-02-05T18:29:41.648306:Conversion required 0.032712 seconds (0.032709 for core code).
260205-18:29:41,677 nipype.workflow INFO:
     [Node] Finished "convert", elapsed time 0.096651s.
INFO: [Node] Finished "convert", elapsed time 0.096651s.
INFO: Post-treating /app/MRIS/Nifti/sub-219/ses-itbs/fmap/sub-219_ses-itbs_phasediff.json file
INFO: Converting /app/MRIS/Nifti/sub-219/ses-itbs/func/sub-219_ses-itbs_task-rest_run-01_bold (177 DICOMs) -> /app/MRIS/Nifti/sub-219/ses-itbs/func . Converter: dcm2niix . Output types: ('nii.gz',)
260205-18:29:41,689 nipype.workflow INFO:
     [Node] Setting-up "convert" in "/tmp/dcm2niixf0rlqtbf/convert".
INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixf0rlqtbf/convert".
260205-18:29:41,726 nipype.workflow INFO:
     [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
INFO: [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
260205-18:29:41,842 nipype.interface INFO:
     stdout 2026-02-05T18:29:41.842904:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
INFO: stdout 2026-02-05T18:29:41.842904:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
260205-18:29:41,843 nipype.interface INFO:
     stdout 2026-02-05T18:29:41.842904:Found 177 DICOM file(s)
INFO: stdout 2026-02-05T18:29:41.842904:Found 177 DICOM file(s)
260205-18:29:41,843 nipype.interface INFO:
     stdout 2026-02-05T18:29:41.842904:Convert 177 DICOM as /app/MRIS/Nifti/sub-219/ses-itbs/func/sub-219_ses-itbs_task-rest_run-01_bold_heudiconv079 (88x84x32x177)
INFO: stdout 2026-02-05T18:29:41.842904:Convert 177 DICOM as /app/MRIS/Nifti/sub-219/ses-itbs/func/sub-219_ses-itbs_task-rest_run-01_bold_heudiconv079 (88x84x32x177)
260205-18:29:49,953 nipype.interface INFO:
     stdout 2026-02-05T18:29:49.953659:Conversion required 8.191842 seconds (8.191081 for core code).
INFO: stdout 2026-02-05T18:29:49.953659:Conversion required 8.191842 seconds (8.191081 for core code).
260205-18:29:49,984 nipype.workflow INFO:
     [Node] Finished "convert", elapsed time 8.257005s.
INFO: [Node] Finished "convert", elapsed time 8.257005s.
INFO: Post-treating /app/MRIS/Nifti/sub-219/ses-itbs/func/sub-219_ses-itbs_task-rest_run-01_bold.json file
INFO: Converting /app/MRIS/Nifti/sub-219/ses-itbs/func/sub-219_ses-itbs_task-rest_run-02_bold (177 DICOMs) -> /app/MRIS/Nifti/sub-219/ses-itbs/func . Converter: dcm2niix . Output types: ('nii.gz',)
260205-18:29:50,1 nipype.workflow INFO:
     [Node] Setting-up "convert" in "/tmp/dcm2niixhn_yfyif/convert".
INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixhn_yfyif/convert".
260205-18:29:50,43 nipype.workflow INFO:
     [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
INFO: [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
260205-18:29:50,158 nipype.interface INFO:
     stdout 2026-02-05T18:29:50.158797:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
INFO: stdout 2026-02-05T18:29:50.158797:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
260205-18:29:50,159 nipype.interface INFO:
     stdout 2026-02-05T18:29:50.158797:Found 177 DICOM file(s)
INFO: stdout 2026-02-05T18:29:50.158797:Found 177 DICOM file(s)
260205-18:29:50,159 nipype.interface INFO:
     stdout 2026-02-05T18:29:50.158797:Convert 177 DICOM as /app/MRIS/Nifti/sub-219/ses-itbs/func/sub-219_ses-itbs_task-rest_run-02_bold_heudiconv367 (88x84x32x177)
INFO: stdout 2026-02-05T18:29:50.158797:Convert 177 DICOM as /app/MRIS/Nifti/sub-219/ses-itbs/func/sub-219_ses-itbs_task-rest_run-02_bold_heudiconv367 (88x84x32x177)
260205-18:29:58,181 nipype.interface INFO:
     stdout 2026-02-05T18:29:58.180954:Conversion required 8.101576 seconds (8.100701 for core code).
INFO: stdout 2026-02-05T18:29:58.180954:Conversion required 8.101576 seconds (8.100701 for core code).
260205-18:29:58,209 nipype.workflow INFO:
     [Node] Finished "convert", elapsed time 8.1659s.
INFO: [Node] Finished "convert", elapsed time 8.1659s.
INFO: Post-treating /app/MRIS/Nifti/sub-219/ses-itbs/func/sub-219_ses-itbs_task-rest_run-02_bold.json file
INFO: Populating template files under /app/MRIS/Nifti/
INFO: PROCESSING DONE: {'subject': '219', 'outdir': '/app/MRIS/Nifti/', 'session': 'itbs'}

Inspect the BIDS dataset

Let’s see what was created in the Nifti directory:

tree MRIS/Nifti
Code Output 
MRIS/Nifti
├── CHANGES
├── README
├── code
│   ├── __pycache__
│   │   └── heuristic1.cpython-313.pyc
│   ├── heuristic1.py
│   └── heuristic2.py
├── dataset_description.json
├── participants.json
├── participants.tsv
├── scans.json
├── sub-219
│   └── ses-itbs
│       ├── anat
│       │   ├── sub-219_ses-itbs_T1w.json
│       │   └── sub-219_ses-itbs_T1w.nii.gz
│       ├── dwi
│       │   ├── sub-219_ses-itbs_acq-AP_dwi.bval
│       │   ├── sub-219_ses-itbs_acq-AP_dwi.bvec
│       │   ├── sub-219_ses-itbs_acq-AP_dwi.json
│       │   └── sub-219_ses-itbs_acq-AP_dwi.nii.gz
│       ├── fmap
│       │   ├── sub-219_ses-itbs_dir-PA_epi.json
│       │   ├── sub-219_ses-itbs_dir-PA_epi.nii.gz
│       │   ├── sub-219_ses-itbs_magnitude1.json
│       │   ├── sub-219_ses-itbs_magnitude1.nii.gz
│       │   ├── sub-219_ses-itbs_magnitude2.json
│       │   ├── sub-219_ses-itbs_magnitude2.nii.gz
│       │   ├── sub-219_ses-itbs_phasediff.json
│       │   └── sub-219_ses-itbs_phasediff.nii.gz
│       ├── func
│       │   ├── sub-219_ses-itbs_task-rest_run-01_bold.json
│       │   ├── sub-219_ses-itbs_task-rest_run-01_bold.nii.gz
│       │   ├── sub-219_ses-itbs_task-rest_run-01_events.tsv
│       │   ├── sub-219_ses-itbs_task-rest_run-02_bold.json
│       │   ├── sub-219_ses-itbs_task-rest_run-02_bold.nii.gz
│       │   └── sub-219_ses-itbs_task-rest_run-02_events.tsv
│       └── sub-219_ses-itbs_scans.tsv
└── task-rest_bold.json

9 directories, 31 files

The output should contain:

  • A BIDS-compliant subject directory (sub-219/ses-itbs/)
  • Subdirectories for different data types (anat, dwi, fmap, func)
  • Required BIDS text files (CHANGES, README, dataset_description.json, etc.)

Let’s look at the subject structure in more detail:

tree MRIS/Nifti/sub-219
Code Output 
MRIS/Nifti/sub-219
└── ses-itbs
    ├── anat
    │   ├── sub-219_ses-itbs_T1w.json
    │   └── sub-219_ses-itbs_T1w.nii.gz
    ├── dwi
    │   ├── sub-219_ses-itbs_acq-AP_dwi.bval
    │   ├── sub-219_ses-itbs_acq-AP_dwi.bvec
    │   ├── sub-219_ses-itbs_acq-AP_dwi.json
    │   └── sub-219_ses-itbs_acq-AP_dwi.nii.gz
    ├── fmap
    │   ├── sub-219_ses-itbs_dir-PA_epi.json
    │   ├── sub-219_ses-itbs_dir-PA_epi.nii.gz
    │   ├── sub-219_ses-itbs_magnitude1.json
    │   ├── sub-219_ses-itbs_magnitude1.nii.gz
    │   ├── sub-219_ses-itbs_magnitude2.json
    │   ├── sub-219_ses-itbs_magnitude2.nii.gz
    │   ├── sub-219_ses-itbs_phasediff.json
    │   └── sub-219_ses-itbs_phasediff.nii.gz
    ├── func
    │   ├── sub-219_ses-itbs_task-rest_run-01_bold.json
    │   ├── sub-219_ses-itbs_task-rest_run-01_bold.nii.gz
    │   ├── sub-219_ses-itbs_task-rest_run-01_events.tsv
    │   ├── sub-219_ses-itbs_task-rest_run-02_bold.json
    │   ├── sub-219_ses-itbs_task-rest_run-02_bold.nii.gz
    │   └── sub-219_ses-itbs_task-rest_run-02_events.tsv
    └── sub-219_ses-itbs_scans.tsv

6 directories, 21 files

Check BIDS files

Let’s examine the required BIDS files that were created:

ls MRIS/Nifti/*.json
Code Output 
MRIS/Nifti/dataset_description.json  MRIS/Nifti/scans.json
MRIS/Nifti/participants.json         MRIS/Nifti/task-rest_bold.json
cat MRIS/Nifti/participants.tsv
Code Output 
participant_id  age sex group
sub-219 54  F   control
cat MRIS/Nifti/participants.json
Code Output 
{
  "participant_id": {
    "Description": "Participant identifier"
  },
  "age": {
    "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions"
  },
  "sex": {
    "Description": "self-rated by participant, M for male/F for female (TODO: verify)"
  },
  "group": {
    "Description": "(TODO: adjust - by default everyone is in control group)"
  }
}
cat MRIS/Nifti/README
Code Output 
TODO: Provide description for the dataset -- basic details about the study, possibly pointing to pre-registration (if public or embargoed)
cat MRIS/Nifti/CHANGES
Code Output 
0.0.1  Initial data acquired
TODOs:
    - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208)
    - fill out dataset_description.json, README, sourcedata/README (if present)
    - provide _events.tsv file for each _bold.nii.gz with onsets of events (see  '8.5 Task events'  of BIDS specification)

View the dataset description:

cat MRIS/Nifti/dataset_description.json
Code Output 
{
  "Acknowledgements": "TODO: whom you want to acknowledge",
  "Authors": [
    "TODO:",
    "First1 Last1",
    "First2 Last2",
    "..."
  ],
  "BIDSVersion": "1.8.0",
  "DatasetDOI": "TODO: eventually a DOI for the dataset",
  "Funding": [
    "TODO",
    "GRANT #1",
    "GRANT #2"
  ],
  "HowToAcknowledge": "TODO: describe how to acknowledge -- either cite a corresponding paper, or just in acknowledgement section",
  "License": "TODO: choose a license, e.g. PDDL (http://opendatacommons.org/licenses/pddl/)",
  "Name": "TODO: name of the dataset",
  "ReferencesAndLinks": [
    "TODO",
    "List of papers or websites"
  ]
}

Validate the BIDS dataset

Validate the dataset using the BIDS Validator to ensure everything is according to specification:

bids-validator-deno MRIS/Nifti
Code Output 
   [WARNING] JSON_KEY_RECOMMENDED A JSON file is missing a key listed as recommended.

        GeneratedBy

        /dataset_description.json - Field description: Used to specify provenance of the dataset.



        SourceDatasets

        /dataset_description.json - Field description: Used to specify the locations and relevant attributes of all source datasets.

Valid keys in each object include "URL", "DOI" (see

URI (https://bids-specification.readthedocs.io/en/stable/common-principles.md#uniform-resource-indicator)), and

"Version" with

string (https://www.w3schools.com/js/js_json_datatypes.asp)

values.



 Please visit https://neurostars.org/search?q=JSON_KEY_RECOMMENDED for existing conversations about this issue.



    [WARNING] SIDECAR_FIELD_OVERRIDE Sidecar files should not override values assigned at a higher level.

        ImageType

        /sub-219/ses-itbs/func/sub-219_ses-itbs_task-rest_run-01_bold.json - Sidecar key defined in /task-rest_bold.json overrides previous value (ORIGINAL,PRIMARY,M,ND,NORM,MOSAIC,MAGNITUDE) from /sub-219/ses-itbs/func/sub-219_ses-itbs_task-rest_run-01_bold.json

        /sub-219/ses-itbs/func/sub-219_ses-itbs_task-rest_run-02_bold.json - Sidecar key defined in /task-rest_bold.json overrides previous value (ORIGINAL,PRIMARY,M,ND,NORM,MOSAIC,MAGNITUDE) from /sub-219/ses-itbs/func/sub-219_ses-itbs_task-rest_run-02_bold.json



        TablePosition

        /sub-219/ses-itbs/func/sub-219_ses-itbs_task-rest_run-01_bold.json - Sidecar key defined in /task-rest_bold.json overrides previous value (0,0,0) from /sub-219/ses-itbs/func/sub-219_ses-itbs_task-rest_run-01_bold.json

        /sub-219/ses-itbs/func/sub-219_ses-itbs_task-rest_run-02_bold.json - Sidecar key defined in /task-rest_bold.json overrides previous value (0,0,0) from /sub-219/ses-itbs/func/sub-219_ses-itbs_task-rest_run-02_bold.json



        TaskName

        /sub-219/ses-itbs/func/sub-219_ses-itbs_task-rest_run-01_bold.json - Sidecar key defined in /task-rest_bold.json overrides previous value (TODO: full task name for rest) from /sub-219/ses-itbs/func/sub-219_ses-itbs_task-rest_run-01_bold.json

        /sub-219/ses-itbs/func/sub-219_ses-itbs_task-rest_run-02_bold.json - Sidecar key defined in /task-rest_bold.json overrides previous value (TODO: full task name for rest) from /sub-219/ses-itbs/func/sub-219_ses-itbs_task-rest_run-02_bold.json



 Please visit https://neurostars.org/search?q=SIDECAR_FIELD_OVERRIDE for existing conversations about this issue.



    [WARNING] README_FILE_SMALL The recommended file '/README' is very small.

Please consider expanding it with additional information about the dataset.

        /README



 Please visit https://neurostars.org/search?q=README_FILE_SMALL for existing conversations about this issue.



    [WARNING] SIDECAR_KEY_RECOMMENDED A data file's JSON sidecar is missing a key listed as recommended.

        PulseSequenceType

        /sub-219/ses-itbs/anat/sub-219_ses-itbs_T1w.nii.gz - Field description: A general description of the pulse sequence used for the scan.

        /sub-219/ses-itbs/dwi/sub-219_ses-itbs_acq-AP_dwi.nii.gz - Field description: A general description of the pulse sequence used for the scan.



        6 more files with the same issue



        SpoilingType

        /sub-219/ses-itbs/anat/sub-219_ses-itbs_T1w.nii.gz - Field description: Specifies which spoiling method(s) are used by a spoiled sequence.

        /sub-219/ses-itbs/dwi/sub-219_ses-itbs_acq-AP_dwi.bvec - Field description: Specifies which spoiling method(s) are used by a spoiled sequence.



        3 more files with the same issue



        PartialFourierDirection

        /sub-219/ses-itbs/anat/sub-219_ses-itbs_T1w.nii.gz - Field description: The direction where only partial Fourier information was collected.

Corresponds to DICOM Tag 0018, 9036 (https://dicomlookup.com/dicomtags/(0018,9036)) Partial Fourier Direction.

        /sub-219/ses-itbs/dwi/sub-219_ses-itbs_acq-AP_dwi.nii.gz - Field description: The direction where only partial Fourier information was collected.

Corresponds to DICOM Tag 0018, 9036 (https://dicomlookup.com/dicomtags/(0018,9036)) Partial Fourier Direction.



        6 more files with the same issue



        Instructions

        /sub-219/ses-itbs/func/sub-219_ses-itbs_task-rest_run-01_bold.nii.gz - Field description: Text of the instructions given to participants before the recording.

        /sub-219/ses-itbs/func/sub-219_ses-itbs_task-rest_run-02_bold.nii.gz - Field description: Text of the instructions given to participants before the recording.



        TaskDescription

        /sub-219/ses-itbs/func/sub-219_ses-itbs_task-rest_run-01_bold.nii.gz - Field description: Longer description of the task.

        /sub-219/ses-itbs/func/sub-219_ses-itbs_task-rest_run-02_bold.nii.gz - Field description: Longer description of the task.



        CogPOID

        /sub-219/ses-itbs/func/sub-219_ses-itbs_task-rest_run-01_bold.nii.gz - Field description: URI (https://bids-specification.readthedocs.io/en/stable/common-principles.md#uniform-resource-indicator)

of the corresponding CogPO (http://www.cogpo.org/) term.

        /sub-219/ses-itbs/func/sub-219_ses-itbs_task-rest_run-02_bold.nii.gz - Field description: URI (https://bids-specification.readthedocs.io/en/stable/common-principles.md#uniform-resource-indicator)

of the corresponding CogPO (http://www.cogpo.org/) term.



        StimulusPresentation

        /sub-219/ses-itbs/func/sub-219_ses-itbs_task-rest_run-01_events.tsv - Field description: Object containing key-value pairs related to the software used to present

the stimuli during the experiment.

        /sub-219/ses-itbs/func/sub-219_ses-itbs_task-rest_run-02_events.tsv - Field description: Object containing key-value pairs related to the software used to present

the stimuli during the experiment.



 Please visit https://neurostars.org/search?q=SIDECAR_KEY_RECOMMENDED for existing conversations about this issue.



    [WARNING] SUSPICIOUSLY_SHORT_EVENT_DESIGN The onset of the last event is less than half the total duration of the corresponding scan.

This design is suspiciously short.

        /sub-219/ses-itbs/func/sub-219_ses-itbs_task-rest_run-01_bold.nii.gz

        /sub-219/ses-itbs/func/sub-219_ses-itbs_task-rest_run-02_bold.nii.gz



 Please visit https://neurostars.org/search?q=SUSPICIOUSLY_SHORT_EVENT_DESIGN for existing conversations about this issue.



    [WARNING] TSV_ADDITIONAL_COLUMNS_UNDEFINED A TSV file has extra columns which are not defined in its associated JSON sidecar

        TODO -- fill in rows and add more tab-separated columns if desired

        /sub-219/ses-itbs/func/sub-219_ses-itbs_task-rest_run-01_events.tsv

        /sub-219/ses-itbs/func/sub-219_ses-itbs_task-rest_run-02_events.tsv



 Please visit https://neurostars.org/search?q=TSV_ADDITIONAL_COLUMNS_UNDEFINED for existing conversations about this issue.



    [WARNING] B0_FIELD_IDENTIFIER_RECOMMENDED File is missing B0FieldIdentifier metadata and IntendedFor metadata,

so it will not be possible to use to perform susceptibility distortion correction.

B0FieldIdentifier metadata permits the flexible selection of images

for estimating B0 inhomogeneity fields, and B0FieldSource permits EPI

images to indicate the identifier of the estimated field to use.

        B0FieldIdentifier

        /sub-219/ses-itbs/fmap/sub-219_ses-itbs_magnitude2.nii.gz - Field description: The presence of this key states that this particular 3D or 4D image MAY be

used for fieldmap estimation purposes.

Each "B0FieldIdentifier" MUST be a unique string within one participant's tree,

shared only by the images meant to be used as inputs for the estimation of a

particular instance of the B<sub>0</sub> field estimation.

It is RECOMMENDED to derive this identifier from DICOM Tags, for example,

DICOM tag 0018, 1030 Protocol Name, or DICOM tag 0018, 0024 Sequence Name

when the former is not defined (for example, in GE devices.)

        /sub-219/ses-itbs/fmap/sub-219_ses-itbs_dir-PA_epi.nii.gz - Field description: The presence of this key states that this particular 3D or 4D image MAY be

used for fieldmap estimation purposes.

Each "B0FieldIdentifier" MUST be a unique string within one participant's tree,

shared only by the images meant to be used as inputs for the estimation of a

particular instance of the B<sub>0</sub> field estimation.

It is RECOMMENDED to derive this identifier from DICOM Tags, for example,

DICOM tag 0018, 1030 Protocol Name, or DICOM tag 0018, 0024 Sequence Name

when the former is not defined (for example, in GE devices.)



        2 more files with the same issue



 Please visit https://neurostars.org/search?q=B0_FIELD_IDENTIFIER_RECOMMENDED for existing conversations about this issue.





          Summary:                         Available Tasks:                     Available Modalities:

          28 Files, 120 MB                 TODO: full task name for rest        MRI                  

          1 - Subjects 1 - Sessions        rest

The validation should show no errors, though there might be a couple of warnings.

Understanding the conversion process

Let’s examine what types of data were converted by looking at the different modality folders:

Anatomical data

ls MRIS/Nifti/sub-219/ses-itbs/anat/
Code Output 
sub-219_ses-itbs_T1w.json  sub-219_ses-itbs_T1w.nii.gz

Functional data

ls MRIS/Nifti/sub-219/ses-itbs/func/
Code Output 
sub-219_ses-itbs_task-rest_run-01_bold.json
sub-219_ses-itbs_task-rest_run-01_bold.nii.gz
sub-219_ses-itbs_task-rest_run-01_events.tsv
sub-219_ses-itbs_task-rest_run-02_bold.json
sub-219_ses-itbs_task-rest_run-02_bold.nii.gz
sub-219_ses-itbs_task-rest_run-02_events.tsv

Diffusion data

ls MRIS/Nifti/sub-219/ses-itbs/dwi/
Code Output 
sub-219_ses-itbs_acq-AP_dwi.bval  sub-219_ses-itbs_acq-AP_dwi.json
sub-219_ses-itbs_acq-AP_dwi.bvec  sub-219_ses-itbs_acq-AP_dwi.nii.gz

Diffusion data

ls MRIS/Nifti/sub-219/ses-itbs/fmap/
Code Output 
sub-219_ses-itbs_dir-PA_epi.json    sub-219_ses-itbs_magnitude2.json
sub-219_ses-itbs_dir-PA_epi.nii.gz  sub-219_ses-itbs_magnitude2.nii.gz
sub-219_ses-itbs_magnitude1.json    sub-219_ses-itbs_phasediff.json
sub-219_ses-itbs_magnitude1.nii.gz  sub-219_ses-itbs_phasediff.nii.gz

Examining JSON sidecars

BIDS requires JSON sidecar files alongside NIfTI files. Let’s examine one:

cat MRIS/Nifti/sub-219/ses-itbs/func/sub-219_ses-itbs_task-rest_run-01_bold.json
Code Output 
{
  "AcquisitionMatrixPE": 84,
  "AcquisitionNumber": 1,
  "AcquisitionTime": "11:27:49.575000",
  "BandwidthPerPixelPhaseEncode": 42.017,
  "BaseResolution": 88,
  "BidsGuess": [
    "func",
    "_acq-epfid2p2_dir-AP_run-18_bold"
],
  "BodyPart": "BRAIN",
  "CoilCombinationMethod": "Sum of Squares",
  "ConsistencyInfo": "N4_VE11A_LATEST_20140830",
  "ConversionSoftware": "dcm2niix",
  "ConversionSoftwareVersion": "v1.0.20250505",
  "DerivedVendorReportedEchoSpacing": 0.000566664,
  "DeviceSerialNumber": "45424",
  "DwellTime": 2.7e-06,
  "EchoTime": 0.025,
  "EchoTrainLength": 43,
  "EffectiveEchoSpacing": 0.000283332,
  "FlipAngle": 90,
  "HeudiconvVersion": "1.3.4",
  "ImageOrientationPatientDICOM": [1, 0, 0, 0, 1, 0],
  "ImageOrientationText": "Tra",
  "ImageType": [
    "ORIGINAL",
    "PRIMARY",
    "M",
    "ND",
    "NORM",
    "MOSAIC",
    "MAGNITUDE"
],
  "ImagingFrequency": 123.238644,
  "InPlanePhaseEncodingDirectionDICOM": "COL",
  "InstitutionAddress": "North Warren Ave 1609,Tucson,Denver,US,85719",
  "InstitutionName": "University of Arizona",
  "InstitutionalDepartmentName": "Department",
  "MRAcquisitionType": "2D",
  "MagneticFieldStrength": 3,
  "Manufacturer": "Siemens",
  "ManufacturersModelName": "Skyra",
  "MatrixCoilMode": "GRAPPA",
  "Modality": "MR",
  "NonlinearGradientCorrection": false,
  "ParallelReductionFactorInPlane": 2,
  "PartialFourier": 1,
  "PatientPosition": "HFS",
  "PercentPhaseFOV": 95.4545,
  "PercentSampling": 100,
  "PhaseEncodingDirection": "j-",
  "PhaseEncodingSteps": 85,
  "PhaseResolution": 1,
  "PixelBandwidth": 2105,
  "ProcedureStepDescription": "Kielar^TMS",
  "ProtocolName": "restingstate",
  "PulseSequenceDetails": "%SiemensSeq%\\ep2d_bold",
  "ReceiveCoilActiveElements": "HEA;HEP",
  "ReceiveCoilName": "Head_32",
  "ReconMatrixPE": 84,
  "RefLinesPE": 24,
  "RepetitionTime": 2,
  "SAR": 0.152693,
  "ScanOptions": "FS",
  "ScanningSequence": "EP",
  "SequenceName": "*epfid2d1_84",
  "SequenceVariant": "SK\\OSP",
  "SeriesDescription": "restingstate",
  "SeriesNumber": 18,
  "ShimSetting": [7564, -13886, 14785, -92, 361, -404, -317, -108],
  "SliceThickness": 2.5,
  "SliceTiming": [0.99, 0, 1.0525, 0.0625, 1.115, 0.125, 1.175, 0.185, 1.2375, 0.2475, 1.3, 0.31, 1.3625, 0.3725, 1.4225, 0.4325, 1.485, 0.495, 1.5475, 0.5575, 1.6075, 0.62, 1.67, 0.68, 1.7325, 0.7425, 1.795, 0.805, 1.855, 0.8675, 1.9175, 0.9275],
  "SoftwareVersions": "syngo MR E11",
  "SpacingBetweenSlices": 3.5,
  "StationName": "AWP45424",
  "StudyDescription": "Kielar^TMS",
  "TablePosition": [0, 0, 0],
  "TaskName": "rest",
  "TotalReadoutTime": 0.0235166,
  "TxRefAmp": 336.357}

Summary

You have successfully converted DICOM files to BIDS format using a custom heuristic file!

Key differences from Exercise 1 (ReproIn approach):

  • Used a custom heuristic1.py file instead of the built-in ReproIn heuristic
  • Required manual specification of subject and session parameters
  • Provides more control over the conversion process
  • Suitable for datasets that don’t follow ReproIn naming conventions

In future tutorials, you can:

  • Learn how to create and modify custom heuristic files for your own data
  • Understand how to handle more complex dataset structures
  • Explore advanced heudiconv options for specific use cases

Once you have a BIDS-compatible dataset, you can run BIDS Apps for further analysis!

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