Dcm2bids not working running sif file through shell script--need to convert dcm to BIDS

abore · June 26, 2024, 7:16pm

No need to share it I think I know the next step.
Please make sure your config.file follow the new dcm2bids convention.
Use this link.
Then try again

MadhavanSubhashini · June 26, 2024, 7:25pm

Hi,

So I have several folders that don’t actually need to be converted to BIDS format that is within the SCANS folder. After the SCANS folder there are multiple subfolders then within each of those subfolders there is a DICOM folder. I just need to convert the folders that have a subfolder of DICOM within SCANS. There are several warning that are printing:

2024-06-26 15:22:08.555 - WARNING - sidecar.isLink | This key contains is not allowed.
2024-06-26 15:22:08.555 - WARNING - sidecar.isLink | This key contains is not allowed.
2024-06-26 15:22:08.555 - WARNING - sidecar.isLink | This key contains is not allowed.
2024-06-26 15:22:08.555 - WARNING - sidecar.isLink | This key contains is not allowed.
2024-06-26 15:22:08.555 - WARNING - sidecar.isLink | This key contains is not allowed.
2024-06-26 15:22:08.555 - WARNING - sidecar.isLink | This key contains is not allowed.
2024-06-26 15:22:08.555 - WARNING - sidecar.isLink | This key contains is not allowed.
2024-06-26 15:22:08.555 - WARNING - sidecar.isLink | This key contains is not allowed.
2024-06-26 15:22:08.555 - WARNING - sidecar.isLink | This key contains is not allowed.
2024-06-26 15:22:08.555 - WARNING - sidecar.isLink | This key contains is not allowed.
2024-06-26 15:22:08.594 - WARNING - sidecar.build_acquisitions | → _bold
2024-06-26 15:22:08.594 - WARNING - sidecar.build_acquisitions | Several Pairing ← 1001_SCANS_104C_B0_map-AP_20240430110520_fieldmaphz
2024-06-26 15:22:08.594 - WARNING - sidecar.build_acquisitions | → _T1w
2024-06-26 15:22:08.594 - WARNING - sidecar.build_acquisitions | → _T2w
2024-06-26 15:22:08.595 - WARNING - sidecar.build_acquisitions | → _bold
2024-06-26 15:22:08.595 - WARNING - sidecar.build_acquisitions | → _bold
2024-06-26 15:22:08.595 - WARNING - sidecar.build_acquisitions | → _bold
2024-06-26 15:22:08.595 - WARNING - sidecar.build_acquisitions | Several Pairing ← 1101_SCANS_104D_B0_map-PA_20240430110520
2024-06-26 15:22:08.618 - WARNING - dcm2bids_gen.run | NO PAIRING WAS FOUND. BIDS FOLDER “/FS/ESS/PAS2302/SUBBI/TURBO/TERBO/DATA/YT/DICOM/BIDS/SUB-YT0691035I/SES-1” WON’T BE CREATED. CHECK YOUR CONFIG FILE.

2024-06-26 15:22:08.618 - INFO - dcm2bids.main | Logs saved in /fs/ess/PAS2302/Subbi/TURBO/TERBO/data/YT/DICOM/BIDS/tmp_dcm2bids/log/sub-YT0691035i_ses-1_20240626-152155.log
2024-06-26 15:22:08.618 - INFO - dcm2bids.main | — dcm2bids end —

My updated config file looks like this:
{
“descriptions”: [
{
“datatype”: “anat”,
“suffix”: “T1w”,
“criteria”: {
“SeriesDescription”: {
“contains”: “T1W”
}
}
},
{
“datatype”: “anat”,
“suffix”: “T2w”,
“criteria”: {
“SeriesDescription”: {
“contains”: “T2”
}
}
},
{
“datatype”: “func”,
“suffix”: “bold”,
“custom_entities”: “task-sst_dir-PA”,
“criteria”: {
“SeriesDescription”: {
“contains”: “STT2”
}
}
},
{
“datatype”: “func”,
“suffix”: “bold”,
“custom_entities”: “task-sst_dir-AP”,
“criteria”: {
“SeriesDescription”: {
“contains”: “STT1”
}
}
},
{
“datatype”: “func”,
“suffix”: “bold”,
“custom_entities”: “task-mid_dir-PA”,
“criteria”: {
“SeriesDescription”: {
“contains”: “MID2”
}
}
}
]
}

abore · June 26, 2024, 7:33pm

This is not something dcm2bids allows:

“criteria”: {
    “SeriesDescription”: {
        “contains”: “MID2”}
}

If you found this somewhere in the documentation please tell so I can fix it.

Check here to find the correct way to write your config file.

The option -d should point to the folder containing the dicoms you want to convert. You can also be more specific with your criteria in the config file, it will convert your dicom into nifti files but it will reorder only the files you need.

MadhavanSubhashini · June 26, 2024, 7:37pm

Hi @abore Okay. Thanks. I’ll update my config file, and re-run it latest by tomorrow. I’ll let you know if there are any issues.

Thanks.

–Subbi M.

MadhavanSubhashini · June 26, 2024, 7:39pm

Hi,

Separate question. If I want the folder structure to be sub-{subject}/ses-{session} instead of sub-{subject}_ses-{session} is that a change in the Shell script or the config file?

Thanks.

–Subbi M.

abore · June 26, 2024, 7:43pm

The output structure created by dcm2bids is: sub-{subject}/ses-{session}/
Once you fixed your config file it should work as expected.

MadhavanSubhashini · June 26, 2024, 7:43pm

Hi @abore

Thanks! Will touch base tomorrow.

–Subbi M.

MadhavanSubhashini · June 27, 2024, 8:28pm

Hi @abore

How do I make this more specific:

    {
        "dataType": "func",
        "modalityLabel": "bold",
        "customLabels": "task-sst",
        "criteria": {
            "SeriesDescription": "*STT1*"
        }
    },

Let’s say I have 2 runs of task-sst. Ignore that the seriesdescription says STT-they misspelled it in the scanner. STT1 is run-01 and STT2 is run-02.

I want my end .nii.gz file and .json file to look like this:

sub-YT7060217L_ses-1_task-sst_dir-AP_run-01_bold.nii.gz

Also where do I put acq-label if I want to customize the above further?

Please advice on how to edit the config file so my BIDS data looks like the naming convention above.

Thanks.

*Also I know I’m working of an older version will revise it to fit newer config.json file standard labels at the end. Thanks.

–Subbi M.

abore · June 27, 2024, 9:02pm

Hello,

You can hardcode the run and its number in the custom entities like this “run-01” for this description and add another one with STT2.
You can add more custom entities. Check this link.

Arnaud

MadhavanSubhashini · June 28, 2024, 8:01pm

Hi,

Is there a way to modify the config file so it doesn’t hard code the runs. So for example in heudiconv doing the heuristic:

mid = create_key(‘sub-{subject}/{session}/func/sub-{subject}_{session}_task-mid_run-{item:02d}_bold’)

The run-{item:02d}_bold takes the first occurrence of a task and labels it as run-01 and the second occurrence of a task and labels it as run-02 automatically.

Is there a way to do that with the newest version of dcm2bids so I don’t have to hard-code it. I don’t know for certain how many runs there are of a task. Sometimes in a scanner if run-01 is partial they will sometimes re-do it.

I don’t want to hardcode it.

Thanks.

–Subbi M.

abore · June 29, 2024, 12:23am

Hello,

It’s exactly how dcm2bids works but you don’t have to do anything.
Change your config file like this:

"SeriesDescription": "*STT*"

Then the first iteration will be named run-01 and the second one run-02.

Arnaud

MadhavanSubhashini · July 3, 2024, 9:32pm

Hi,

When I run the singularity command it generates the nii.gz and json sidecar files but its not generating the BIDS tree structure.

scaffold_directory/
├── CHANGES
├── code/
├── dataset_description.json
├── derivatives/
├── participants.json
├── participants.tsv
├── README
├── .bidsignore
└── sourcedata/


How do I generate the participants.tsv and other json files. It says dcm2bids generates this automatically but its not generating the files I need to run MRIQC. Do I need to add something to my config.json?

Thanks.

--Subbi M.

Steven · July 3, 2024, 9:59pm

Hi @MadhavanSubhashini

Without seeing your most recent config, command, and log, there’s not much we can do to help.

Best,
Steven

MadhavanSubhashini · July 3, 2024, 10:02pm

Hi,

Here is my config.json

{
“descriptions”: [
{
“datatype”: “anat”,
“suffix”: “T1w”,
“custom_entities”: “run-01”,
“criteria”: {
“SeriesDescription”: “T1W_3D_TFE”
}
},
{
“datatype”: “anat”,
“suffix”: “T2w”,
“custom_entities”: “run-01”,
“criteria”: {
“SeriesDescription”: “T2”
}
},
{
“datatype”: “fmap”,
“suffix”: “epi”,
“custom_entities”: “dir-AP”,
“criteria”: {
“SeriesDescription”: “*B0 map-AP”
}
},
{
“datatype”: “fmap”,
“suffix”: “epi”,
“custom_entities”: “dir-PA”,
“criteria”: {
“SeriesDescription”: “*B0 map-PA”
}
},
{
“datatype”: “fmap”,
“suffix”: “fieldmap”,
“custom_entities”: “acq-B0map”,
“criteria”: {
“SeriesDescription”: “*B0 map”,
“ImageType”: [“ORIGINAL”, “PRIMARY”, “T1”, “MIXED”, “REAL”, “FIELDMAPHZ”]
}
},
{
“datatype”: “fmap”,
“suffix”: “magnitude”,
“custom_entities”: “acq-B0map”,
“criteria”: {
“SeriesDescription”: “*B0 map”,
“ImageType”: [“ORIGINAL”, “PRIMARY”, “T1”, “MIXED”, “FIELDMAPHZ”]
}
},
{
“datatype”: “func”,
“suffix”: “bold”,
“custom_entities”: [“task-gamb”, “dir-AP”],
“criteria”: {
“SeriesDescription”: {
“any”: [“*HCP_fMRIgamb-AP”, “*1NX_fMRI_gamb-AP”]
}
}
},
{
“datatype”: “func”,
“suffix”: “bold”,
“custom_entities”: [“task-gamb”, “dir-PA”],
“criteria”: {
“SeriesDescription”: {
“any”: [“*HCP_fMRIgamb-PA”, “*1NX_fMRI_gamb-PA”]
}
}
},
{
“datatype”: “func”,
“suffix”: “bold”,
“custom_entities”: [“task-wm”, “dir-AP”],
“criteria”: {
“SeriesDescription”: {
“any”: [“*HCP_fMRI_wm-AP”, “*1NX_fMRI_wm-AP”]
}
}
},
{
“datatype”: “func”,
“suffix”: “bold”,
“custom_entities”: [“task-wm”, “dir-PA”],
“criteria”: {
“SeriesDescription”: {
“any”: [“*HCP_fMRI_wm-PA”, “*1NX_fMRI_wm-PA”]
}
}
},
{
“datatype”: “func”,
“suffix”: “bold”,
“custom_entities”: [“task-rest”, “dir-AP”],
“criteria”: {
“SeriesDescription”: {
“any”: [“*HCP_fMRI_rs-AP”, “*1NX_fMRI_rest-AP”]
}
}
},
{
“datatype”: “func”,
“suffix”: “bold”,
“custom_entities”: [“task-rest”, “dir-PA”],
“criteria”: {
“SeriesDescription”: {
“any”: [“*HCP_fMRI_rs-PA”, “*1NX_fMRI_rest-PA”]
}
}
},
{
“datatype”: “func”,
“suffix”: “bold”,
“custom_entities”: [“task-ep”, “dir-AP”],
“criteria”: {
“SeriesDescription”: {
“any”: [“*HCP_fMRI_ep-AP”, “*1NX_fMRI_ep-AP”]
}
}
},
{
“datatype”: “func”,
“suffix”: “bold”,
“custom_entities”: [“task-ep”, “dir-PA”],
“criteria”: {
“SeriesDescription”: {
“any”: [“*HCP_fMRI_ep-PA”, “*1NX_fMRI_ep-PA”]
}
}
},
{
“datatype”: “dwi”,
“suffix”: “dwi”,
“custom_entities”: [“acq-dti”, “dir-PA”],
“criteria”: {
“SeriesDescription”: “MB4_102d_PA”
}
},
{
“datatype”: “dwi”,
“suffix”: “dwi”,
“custom_entities”: [“acq-B0”, “dir-PA”],
“criteria”: {
“SeriesDescription”: “DTI B0 PA”,
“ImageType”: [“ORIGINAL”, “PRIMARY”, “DIFFUSION”, “NONE”]
}
},
{
“datatype”: “dwi”,
“suffix”: “dwi”,
“custom_entities”: [“acq-B0”, “dir-AP”],
“criteria”: {
“SeriesDescription”: “DTI B0 AP”,
“ImageType”: [“ORIGINAL”, “PRIMARY”, “DIFFUSION”, “NONE”]
}
}
]
}

Script I’m running:
#!/bin/bash
#SBATCH --time=01:00:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=2
#SBATCH --account=PAS2302

folder=$1
subject=$2
session=$3
echo “Starting BIDS conversion for subject” $folder $subject $session

singularity exec
/fs/ess/PAS2302/Subbi/TURBO/TERBO/Scripts/dcm2bids_dev.sif
dcm2bids
-d /fs/ess/PAS2302/Subbi/TURBO/TERBO/data/YA/DICOM/$folder/SCANS/*
-p $subject
-s $session
-o /fs/ess/PAS2302/Subbi/TURBO/TERBO/data/YA/DICOM/BIDS
-c /fs/ess/PAS2302/Subbi/TURBO/TERBO/Scripts/study_config_YA.json
–clobber

echo “Finished subject” $subject $session

This is the log:

2024-07-03 15:01:29.679 - INFO - dcm2niix_gen.execute | Check log file for dcm2niix output

2024-07-03 15:01:29.721 - INFO 2024-07-03 15:01:29.721 - INFO 2024-07-03 15:01:29.721 - INFO 2024-07-03 15:01:29.721 - INFO 2024-07-03 15:01:29.721 - INFO 2024-07-03 15:01:29.722 - INFO 2024-07-03 15:01:29.722 - INFO 2024-07-03 15:01:29.722 - INFO 2024-07-03 15:01:29.722 - INFO 2024-07-03 15:01:29.722 - INFO 2024-07-03 15:01:29.722 - INFO 2024-07-03 15:01:29.724 - INFO 2024-07-03 15:01:29.724 - INFO 2024-07-03 15:01:29.724 - INFO 2024-07-03 15:01:29.725 - INFO 2024-07-03 15:01:29.725 - INFO 2024-07-03 15:01:29.725 - INFO 2024-07-03 15:01:29.725 - INFO 2024-07-03 15:01:29.725 - INFO 2024-07-03 15:01:29.725 - INFO 2024-07-03 15:01:29.725 - INFO 2024-07-03 15:01:29.725 - INFO 2024-07-03 15:01:29.726 - INFO 2024-07-03 15:01:29.726 - INFO 2024-07-03 15:01:29.726 - INFO 2024-07-03 15:01:29.726 - INFO 2024-07-03 15:01:29.728 - INFO 2024-07-03 15:01:29.728 - INFO 2024-07-03 15:01:29.728 - INFO 2024-07-03 15:01:29.729 - INFO 2024-07-03 15:01:29.729 - INFO 2024-07-03 15:01:29.729 - INFO - sidecar.build_acquisitions | SIDECAR PAIRING
- sidecar.build_acquisitions | No Pairing ← 101_101_199_SURVEY_MST_199_SURVEY_MST_20231121100251
- sidecar.build_acquisitions | sub-YA0690246B_ses-1_run-01_T1w ← 201_201_198_3min_T1W_3D_TFE_198_3min_T1W_3D_TFE_20231121100251
- sidecar.build_acquisitions | No Pairing ← 203_203_SAGITTAL_SAGITTAL_20231121100251
- sidecar.build_acquisitions | No Pairing ← 204_204_CORONAL_CORONAL_20231121100251
- sidecar.build_acquisitions | sub-YA0690246B_ses-1_dir-AP_epi ← 301_301_197_B0_map-AP_197_B0_map-AP_20231121100251
- sidecar.build_acquisitions | sub-YA0690246B_ses-1_dir-AP_epi ← 301_301_197_B0_map-AP_197_B0_map-AP_20231121100251_fieldmaphz
- sidecar.build_acquisitions | sub-YA0690246B_ses-1_dir-PA_epi ← 401_401_101_B0_map-PA_101_B0_map-PA_20231121100251
- sidecar.build_acquisitions | sub-YA0690246B_ses-1_dir-PA_epi ← 401_401_101_B0_map-PA_101_B0_map-PA_20231121100251_fieldmaphz
- sidecar.build_acquisitions | sub-YA0690246B_ses-1_task-ep_dir-PA_bold ← 601_601_104_HCP_fMRI_ep-PA_104_HCP_fMRI_ep-PA_20231121100251
- sidecar.build_acquisitions | sub-YA0690246B_ses-1_task-wm_dir-AP_bold ← 801_801_105B_1NX_fMRI_wm-AP_105B_1NX_fMRI_wm-AP_20231121100251
- sidecar.build_acquisitions | sub-YA0690246B_ses-1_task-wm_dir-PA_bold ← 1201_1201_102B_1NX_fMRI_wm-PA_102B_1NX_fMRI_wm-PA_20231121100251
- sidecar.build_acquisitions | sub-YA0690246B_ses-1_task-rest_dir-AP_bold ← 1301_1301_106B0_HCP_fMRI_rs-AP_106B0_HCP_fMRI_rs-AP_20231121100251
- sidecar.build_acquisitions | sub-YA0690246B_ses-1_task-rest_dir-AP_bold ← 1601_1601_106B0_HCP_fMRI_rs-AP_106B0_HCP_fMRI_rs-AP_20231121100251
- sidecar.build_acquisitions | sub-YA0690246B_ses-1_acq-B0map_magnitude ← 1701_1701_107_B0_map_107_B0_map_20231121100251
- sidecar.build_acquisitions | sub-YA0690246B_ses-1_acq-B0map_fieldmap ← 1701_1701_107_B0_map_107_B0_map_20231121100251_fieldmaphz
- sidecar.build_acquisitions | sub-YA0690246B_ses-1_run-01_T2w ← 1801_1801_111_3D_T2_SAG_RAW_111_3D_T2_SAG_RAW_20231121100251
- sidecar.build_acquisitions | No Pairing ← 1803_1803_MPR_COR_0.8_-0.4mm_MPR_COR_0.8_-0.4mm_20231121100251
- sidecar.build_acquisitions | No Pairing ← 1804_1804_MPR_AX_0.8_-0.4mm_MPR_AX_0.8_-0.4mm_20231121100251
- sidecar.build_acquisitions | sub-YA0690246B_ses-1_acq-B0_dir-PA_dwi ← 1901_1901_114_DTI_B0_PA_114_DTI_B0_PA_20231121100251
- sidecar.build_acquisitions | No Pairing ← 1903_1903_DIFF_SAG_DIFF_SAG_20231121100251
- sidecar.build_acquisitions | No Pairing ← 1904_1904_DIFF_COR_DIFF_COR_20231121100251
- sidecar.build_acquisitions | sub-YA0690246B_ses-1_acq-B0_dir-AP_dwi ← 2001_2001_114_DTI_B0_AP_114_DTI_B0_AP_20231121100251
- sidecar.build_acquisitions | No Pairing ← 2003_2003_DIFF_SAG_DIFF_SAG_20231121100251
- sidecar.build_acquisitions | No Pairing ← 2004_2004_DIFF_COR_DIFF_COR_20231121100251
- sidecar.find_runs | sub-YA0690246B/ses-1/fmap/sub-YA0690246B_ses-1_dir-AP_epi has 2 runs
- sidecar.find_runs | Adding run information to the acquisition
- sidecar.find_runs | sub-YA0690246B/ses-1/fmap/sub-YA0690246B_ses-1_dir-PA_epi has 2 runs
- sidecar.find_runs | Adding run information to the acquisition
- sidecar.find_runs | sub-YA0690246B/ses-1/func/sub-YA0690246B_ses-1_task-rest_dir-AP_bold has 2 runs
- sidecar.find_runs | Adding run information to the acquisition
- dcm2bids_gen.run | Moving acquisitions into BIDS folder “/fs/ess/PAS2302/Subbi/TURBO/TERBO/data/YA/DICOM/BIDS/sub-YA0690246B/ses-1”.

2024-07-03 15:01:29.784 - INFO - dcm2bids.main | Logs saved in /fs/ess/PAS2302/Subbi/TURBO/TERBO/data/YA/DICOM/BIDS/tmp_dcm2bids/log/sub-YA0690246B_ses-1_20240703-150111.log
2024-07-03 15:01:29.784 - INFO - dcm2bids.main | — dcm2bids end —

Steven · July 3, 2024, 10:16pm

Apologies I read your post too fast. You need the dcm2bids_scaffold command to generate all of the BIDS files and folders. But in future if your are going to be pasting lots of text from the command line please use tick marks so the text is nicely formatted like this or

Like this

Best,
Steven

MadhavanSubhashini · July 3, 2024, 10:43pm

Hi,

If I’m using a singularity dcm2bids sif command do I add the scaffold before it?

singularity exec
/fs/ess/PAS2302/Subbi/TURBO/TERBO/Scripts/dcm2bids_dev.sif
dcm2bids \

Add dcm2bids_scaffold before dcm2bids or does it need to be done separately beforehand?

Also you text suggestion formatting is not coming up. Do I click the blockquote to reformat my text when replying?

–Subbi M.

Steven · July 3, 2024, 10:49pm

Hi @MadhavanSubhashini

singularity exec \
-e --containall -B $bids \
/fs/ess/PAS2302/Subbi/TURBO/TERBO/Scripts/dcm2bids_dev.sif \
dcm2bids_scaffold $bids

It’s the </> button in the text editor (or use the ` button on your keyboard)

Best,
Steven

MadhavanSubhashini · July 3, 2024, 11:20pm

Hi,

I ran it for the initial subject and it worked but then when I tried running dcm2bids for a second subject
I got an error for scaffolding. Do I have to use the force button?

Is this right?


Command in command line: ./osc_convert2nifti_TERBO_YA_Bronx.sh $foldername $subject_id $session_id.

Thanks.

--Subbi M.

MadhavanSubhashini · July 3, 2024, 11:22pm

Hi,

Entire code:

Steven · July 3, 2024, 11:40pm

Hi @MadhavanSubhashini,

You only need to scaffold once.

Best,
Steven