Summary of what happened:
I ran fmripost-aroma and got an HTML report that says there are no errors. However, SLURM returned Slurm Job_id=4651398 Name=runfmripost-aroma-2026 Failed, Run time 00:26:24, FAILED, ExitCode 1
The tree of directories looks fine to me (there is one resting state fmri scan and a T1w anatomical image in the original BIDS directory):
$ cd fmripost-aroma
$ ls
dataset_description.json logs sub-CAM003 sub-CAM003.html
$ tree
.
|-- dataset_description.json
|-- logs
| |-- CITATION.bib
| |-- CITATION.html
| |-- CITATION.md
| `-- CITATION.tex
|-- sub-CAM003
| |-- log
| | `-- 20260218-183830_b21830d7-ce05-4245-a427-c800cd056c04
| | `-- fmripost_aroma.toml
| `-- ses-01brain
| |-- figures
| | |-- sub-CAM003_ses-01brain_task-rest_run-01_space-MNI152NLin6Asym_desc-aroma_bold.svg
| | |-- sub-CAM003_ses-01brain_task-rest_run-01_space-MNI152NLin6Asym_desc-metrics_bold.svg
| | |-- sub-CAM003_ses-01brain_task-rest_run-01_space-MNI152NLin6Asym_desc-nonaggrCarpetplot_bold.svg
| | |-- sub-CAM003_ses-01brain_task-rest_run-01_space-MNI152NLin6Asym_desc-preprocCarpetplot_bold.svg
| | |-- sub-CAM003_ses-01brain_task-rest_run-01_space-MNI152NLin6Asym_res-2_desc-about_bold.html
| | |-- sub-CAM003_ses-01brain_task-rest_run-01_space-MNI152NLin6Asym_res-2_desc-normalization_bold.svg
| | `-- sub-CAM003_ses-01brain_task-rest_run-01_space-MNI152NLin6Asym_res-2_desc-summary_bold.html
| `-- func
| |-- sub-CAM003_ses-01brain_task-rest_run-01_desc-aroma_metrics.json
| |-- sub-CAM003_ses-01brain_task-rest_run-01_desc-aroma_metrics.tsv
| |-- sub-CAM003_ses-01brain_task-rest_run-01_desc-aroma_timeseries.tsv
| |-- sub-CAM003_ses-01brain_task-rest_run-01_space-MNI152NLin6Asym_res-2_desc-melodic_mixing.tsv
| |-- sub-CAM003_ses-01brain_task-rest_run-01_space-MNI152NLin6Asym_res-2_desc-nonaggrDenoised_bold.nii.gz
| `-- sub-CAM003_ses-01brain_task-rest_run-01_space-MNI152NLin6Asym_res-2_thresh-0p5_desc-melodic_components.nii.gz
`-- sub-CAM003.html
7 directories, 20 files
Command used (and if a helper script was used, a link to the helper script or the command generated):
apptainer run \
--cleanenv \
--bind ${DATA}:/data \
--bind ${FMRIPREP_DERIV_DIR}:/fmriprep:ro \
--bind ${WORK_DIR}:/work \
--bind ${AROMA_DERIV_DIR}:/out \
${APP} \
/fmriprep /out participant \
--participant_label ${Subject} \
--stop-on-first-crash \
--denoising-method nonaggr \
-w /work
Versions:
$ apptainer run fmripost_aroma.sif --version
fMRIPost-AROMA v0.1.dev1+gc69585a (this was from 2024)
and replicated with
$ apptainer run fmripost_aroma_v0.0.12plus.sif --version
fMRIPost-AROMA v0.1.dev1+g96a89a22b (this was main, downloaded today)
Environment (Docker, Singularity / Apptainer, custom installation):
Apptainer on HPC
Data formatted according to a validatable standard? Please provide the output of the validator. (I use this dataset for testing and teaching, it has some warnings, but has always behaved well with other BIDS tools):
{
"issues": {
"issues": [
{
"code": "README_FILE_SMALL",
"severity": "warning",
"location": "/README",
"rule": "rules.checks.general.ReadmeFileSmall"
},
{
"code": "JSON_KEY_RECOMMENDED",
"subCode": "HEDVersion",
"severity": "warning",
"location": "/dataset_description.json",
"issueMessage": "Field description: If HED tags are used:\nThe version of the HED schema used to validate HED tags for study.\nMay include a single schema or a base schema and one or more library schema.\n",
"rule": "rules.dataset_metadata.dataset_description"
},
{
"code": "JSON_KEY_RECOMMENDED",
"subCode": "GeneratedBy",
"severity": "warning",
"location": "/dataset_description.json",
"issueMessage": "Field description: Used to specify provenance of the dataset.\n",
"rule": "rules.dataset_metadata.dataset_description"
},
{
"code": "JSON_KEY_RECOMMENDED",
"subCode": "SourceDatasets",
"severity": "warning",
"location": "/dataset_description.json",
"issueMessage": "Field description: Used to specify the locations and relevant attributes of all source datasets (BIDS or not).\nValid keys in each object include `\"URL\"`, `\"DOI\"` (see\n[URI](SPEC_ROOT/common-principles.md#uniform-resource-indicator)), and\n`\"Version\"` with\n[string](https://www.w3schools.com/js/js_json_datatypes.asp)\nvalues.\n",
"rule": "rules.dataset_metadata.dataset_description"
},
{
"code": "SIDECAR_KEY_RECOMMENDED",
"subCode": "SpoilingType",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/dwi/sub-CAM003_ses-01brain_dir-AP_dwi.bvec",
"issueMessage": "Field description: Specifies which spoiling method(s) are used by a spoiled sequence.\n",
"rule": "rules.sidecars.mri.SpoilingType"
},
{
"code": "SIDECAR_KEY_RECOMMENDED",
"subCode": "MatrixCoilMode",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/dwi/sub-CAM003_ses-01brain_dir-AP_dwi.nii.gz",
"issueMessage": "Field description: (If used)\nA method for reducing the number of independent channels by combining in\nanalog the signals from multiple coil elements.\nThere are typically different default modes when using un-accelerated or\naccelerated (for example, `\"GRAPPA\"`, `\"SENSE\"`) imaging.\n",
"rule": "rules.sidecars.mri.MRIHardware"
},
{
"code": "SIDECAR_KEY_RECOMMENDED",
"subCode": "PulseSequenceType",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/dwi/sub-CAM003_ses-01brain_dir-AP_dwi.nii.gz",
"issueMessage": "Field description: A general description of the pulse sequence used for the scan.\n",
"rule": "rules.sidecars.mri.MRISequenceSpecifics"
},
{
"code": "SIDECAR_KEY_RECOMMENDED",
"subCode": "SpoilingType",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/dwi/sub-CAM003_ses-01brain_dir-AP_dwi.nii.gz",
"issueMessage": "Field description: Specifies which spoiling method(s) are used by a spoiled sequence.\n",
"rule": "rules.sidecars.mri.SpoilingType"
},
{
"code": "SIDECAR_KEY_RECOMMENDED",
"subCode": "PartialFourierDirection",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/dwi/sub-CAM003_ses-01brain_dir-AP_dwi.nii.gz",
"issueMessage": "Field description: The direction where only partial Fourier information was collected.\nCorresponds to [DICOM Tag 0018, 9036](https://dicomlookup.com/dicomtags/(0018,9036)) `Partial Fourier Direction`.\n",
"rule": "rules.sidecars.mri.MRIPartialFourier"
},
{
"code": "SIDECAR_KEY_RECOMMENDED",
"subCode": "SpoilingType",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/dwi/sub-CAM003_ses-01brain_dir-AP_dwi.bval",
"issueMessage": "Field description: Specifies which spoiling method(s) are used by a spoiled sequence.\n",
"rule": "rules.sidecars.mri.SpoilingType"
},
{
"code": "B0_FIELD_IDENTIFIER_RECOMMENDED",
"subCode": "B0FieldIdentifier",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/fmap/sub-CAM003_ses-01brain_magnitude2.nii.gz",
"issueMessage": "Field description: The presence of this key states that this particular 3D or 4D image MAY be\nused for fieldmap estimation purposes.\nEach `\"B0FieldIdentifier\"` MUST be a unique string within one participant's tree,\nshared only by the images meant to be used as inputs for the estimation of a\nparticular instance of the *B<sub>0</sub> field* estimation.\nIt is RECOMMENDED to derive this identifier from DICOM Tags, for example,\nDICOM tag 0018, 1030 `Protocol Name`, or DICOM tag 0018, 0024 `Sequence Name`\nwhen the former is not defined (for example, in GE devices.)\n",
"rule": "rules.sidecars.fmap.MRIFieldmapB0FieldIdentifier"
},
{
"code": "SIDECAR_KEY_RECOMMENDED",
"subCode": "PulseSequenceType",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/fmap/sub-CAM003_ses-01brain_magnitude2.nii.gz",
"issueMessage": "Field description: A general description of the pulse sequence used for the scan.\n",
"rule": "rules.sidecars.mri.MRISequenceSpecifics"
},
{
"code": "SIDECAR_KEY_RECOMMENDED",
"subCode": "PartialFourierDirection",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/fmap/sub-CAM003_ses-01brain_magnitude2.nii.gz",
"issueMessage": "Field description: The direction where only partial Fourier information was collected.\nCorresponds to [DICOM Tag 0018, 9036](https://dicomlookup.com/dicomtags/(0018,9036)) `Partial Fourier Direction`.\n",
"rule": "rules.sidecars.mri.MRIPartialFourier"
},
{
"code": "B0_FIELD_IDENTIFIER_RECOMMENDED",
"subCode": "B0FieldIdentifier",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/fmap/sub-CAM003_ses-01brain_phasediff.nii.gz",
"issueMessage": "Field description: The presence of this key states that this particular 3D or 4D image MAY be\nused for fieldmap estimation purposes.\nEach `\"B0FieldIdentifier\"` MUST be a unique string within one participant's tree,\nshared only by the images meant to be used as inputs for the estimation of a\nparticular instance of the *B<sub>0</sub> field* estimation.\nIt is RECOMMENDED to derive this identifier from DICOM Tags, for example,\nDICOM tag 0018, 1030 `Protocol Name`, or DICOM tag 0018, 0024 `Sequence Name`\nwhen the former is not defined (for example, in GE devices.)\n",
"rule": "rules.sidecars.fmap.MRIFieldmapB0FieldIdentifier"
},
{
"code": "SIDECAR_KEY_RECOMMENDED",
"subCode": "PulseSequenceType",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/fmap/sub-CAM003_ses-01brain_phasediff.nii.gz",
"issueMessage": "Field description: A general description of the pulse sequence used for the scan.\n",
"rule": "rules.sidecars.mri.MRISequenceSpecifics"
},
{
"code": "SIDECAR_KEY_RECOMMENDED",
"subCode": "PartialFourierDirection",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/fmap/sub-CAM003_ses-01brain_phasediff.nii.gz",
"issueMessage": "Field description: The direction where only partial Fourier information was collected.\nCorresponds to [DICOM Tag 0018, 9036](https://dicomlookup.com/dicomtags/(0018,9036)) `Partial Fourier Direction`.\n",
"rule": "rules.sidecars.mri.MRIPartialFourier"
},
{
"code": "B0_FIELD_IDENTIFIER_RECOMMENDED",
"subCode": "B0FieldIdentifier",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/fmap/sub-CAM003_ses-01brain_dir-PA_epi.nii.gz",
"issueMessage": "Field description: The presence of this key states that this particular 3D or 4D image MAY be\nused for fieldmap estimation purposes.\nEach `\"B0FieldIdentifier\"` MUST be a unique string within one participant's tree,\nshared only by the images meant to be used as inputs for the estimation of a\nparticular instance of the *B<sub>0</sub> field* estimation.\nIt is RECOMMENDED to derive this identifier from DICOM Tags, for example,\nDICOM tag 0018, 1030 `Protocol Name`, or DICOM tag 0018, 0024 `Sequence Name`\nwhen the former is not defined (for example, in GE devices.)\n",
"rule": "rules.sidecars.fmap.MRIFieldmapB0FieldIdentifier"
},
{
"code": "SIDECAR_KEY_RECOMMENDED",
"subCode": "MatrixCoilMode",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/fmap/sub-CAM003_ses-01brain_dir-PA_epi.nii.gz",
"issueMessage": "Field description: (If used)\nA method for reducing the number of independent channels by combining in\nanalog the signals from multiple coil elements.\nThere are typically different default modes when using un-accelerated or\naccelerated (for example, `\"GRAPPA\"`, `\"SENSE\"`) imaging.\n",
"rule": "rules.sidecars.mri.MRIHardware"
},
{
"code": "SIDECAR_KEY_RECOMMENDED",
"subCode": "PulseSequenceType",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/fmap/sub-CAM003_ses-01brain_dir-PA_epi.nii.gz",
"issueMessage": "Field description: A general description of the pulse sequence used for the scan.\n",
"rule": "rules.sidecars.mri.MRISequenceSpecifics"
},
{
"code": "SIDECAR_KEY_RECOMMENDED",
"subCode": "SpoilingType",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/fmap/sub-CAM003_ses-01brain_dir-PA_epi.nii.gz",
"issueMessage": "Field description: Specifies which spoiling method(s) are used by a spoiled sequence.\n",
"rule": "rules.sidecars.mri.SpoilingType"
},
{
"code": "SIDECAR_KEY_RECOMMENDED",
"subCode": "PartialFourierDirection",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/fmap/sub-CAM003_ses-01brain_dir-PA_epi.nii.gz",
"issueMessage": "Field description: The direction where only partial Fourier information was collected.\nCorresponds to [DICOM Tag 0018, 9036](https://dicomlookup.com/dicomtags/(0018,9036)) `Partial Fourier Direction`.\n",
"rule": "rules.sidecars.mri.MRIPartialFourier"
},
{
"code": "B0_FIELD_IDENTIFIER_RECOMMENDED",
"subCode": "B0FieldIdentifier",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/fmap/sub-CAM003_ses-01brain_magnitude1.nii.gz",
"issueMessage": "Field description: The presence of this key states that this particular 3D or 4D image MAY be\nused for fieldmap estimation purposes.\nEach `\"B0FieldIdentifier\"` MUST be a unique string within one participant's tree,\nshared only by the images meant to be used as inputs for the estimation of a\nparticular instance of the *B<sub>0</sub> field* estimation.\nIt is RECOMMENDED to derive this identifier from DICOM Tags, for example,\nDICOM tag 0018, 1030 `Protocol Name`, or DICOM tag 0018, 0024 `Sequence Name`\nwhen the former is not defined (for example, in GE devices.)\n",
"rule": "rules.sidecars.fmap.MRIFieldmapB0FieldIdentifier"
},
{
"code": "SIDECAR_KEY_RECOMMENDED",
"subCode": "PulseSequenceType",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/fmap/sub-CAM003_ses-01brain_magnitude1.nii.gz",
"issueMessage": "Field description: A general description of the pulse sequence used for the scan.\n",
"rule": "rules.sidecars.mri.MRISequenceSpecifics"
},
{
"code": "SIDECAR_KEY_RECOMMENDED",
"subCode": "PartialFourierDirection",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/fmap/sub-CAM003_ses-01brain_magnitude1.nii.gz",
"issueMessage": "Field description: The direction where only partial Fourier information was collected.\nCorresponds to [DICOM Tag 0018, 9036](https://dicomlookup.com/dicomtags/(0018,9036)) `Partial Fourier Direction`.\n",
"rule": "rules.sidecars.mri.MRIPartialFourier"
},
{
"code": "SIDECAR_KEY_RECOMMENDED",
"subCode": "PulseSequenceType",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/anat/sub-CAM003_ses-01brain_FLAIR.nii.gz",
"issueMessage": "Field description: A general description of the pulse sequence used for the scan.\n",
"rule": "rules.sidecars.mri.MRISequenceSpecifics"
},
{
"code": "SIDECAR_KEY_RECOMMENDED",
"subCode": "SpoilingType",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/anat/sub-CAM003_ses-01brain_FLAIR.nii.gz",
"issueMessage": "Field description: Specifies which spoiling method(s) are used by a spoiled sequence.\n",
"rule": "rules.sidecars.mri.SpoilingType"
},
{
"code": "SIDECAR_KEY_RECOMMENDED",
"subCode": "PartialFourierDirection",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/anat/sub-CAM003_ses-01brain_FLAIR.nii.gz",
"issueMessage": "Field description: The direction where only partial Fourier information was collected.\nCorresponds to [DICOM Tag 0018, 9036](https://dicomlookup.com/dicomtags/(0018,9036)) `Partial Fourier Direction`.\n",
"rule": "rules.sidecars.mri.MRIPartialFourier"
},
{
"code": "SIDECAR_KEY_RECOMMENDED",
"subCode": "PulseSequenceType",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/anat/sub-CAM003_ses-01brain_T1w.nii.gz",
"issueMessage": "Field description: A general description of the pulse sequence used for the scan.\n",
"rule": "rules.sidecars.mri.MRISequenceSpecifics"
},
{
"code": "SIDECAR_KEY_RECOMMENDED",
"subCode": "SpoilingType",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/anat/sub-CAM003_ses-01brain_T1w.nii.gz",
"issueMessage": "Field description: Specifies which spoiling method(s) are used by a spoiled sequence.\n",
"rule": "rules.sidecars.mri.SpoilingType"
},
{
"code": "SIDECAR_KEY_RECOMMENDED",
"subCode": "PartialFourierDirection",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/anat/sub-CAM003_ses-01brain_T1w.nii.gz",
"issueMessage": "Field description: The direction where only partial Fourier information was collected.\nCorresponds to [DICOM Tag 0018, 9036](https://dicomlookup.com/dicomtags/(0018,9036)) `Partial Fourier Direction`.\n",
"rule": "rules.sidecars.mri.MRIPartialFourier"
},
{
"code": "SIDECAR_KEY_RECOMMENDED",
"subCode": "PulseSequenceType",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/anat/sub-CAM003_ses-01brain_acq-hippo_T2w.nii.gz",
"issueMessage": "Field description: A general description of the pulse sequence used for the scan.\n",
"rule": "rules.sidecars.mri.MRISequenceSpecifics"
},
{
"code": "SIDECAR_KEY_RECOMMENDED",
"subCode": "SpoilingType",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/anat/sub-CAM003_ses-01brain_acq-hippo_T2w.nii.gz",
"issueMessage": "Field description: Specifies which spoiling method(s) are used by a spoiled sequence.\n",
"rule": "rules.sidecars.mri.SpoilingType"
},
{
"code": "SIDECAR_KEY_RECOMMENDED",
"subCode": "PartialFourierDirection",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/anat/sub-CAM003_ses-01brain_acq-hippo_T2w.nii.gz",
"issueMessage": "Field description: The direction where only partial Fourier information was collected.\nCorresponds to [DICOM Tag 0018, 9036](https://dicomlookup.com/dicomtags/(0018,9036)) `Partial Fourier Direction`.\n",
"rule": "rules.sidecars.mri.MRIPartialFourier"
},
{
"code": "SIDECAR_KEY_RECOMMENDED",
"subCode": "PulseSequenceType",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/anat/sub-CAM003_ses-01brain_T2w.nii.gz",
"issueMessage": "Field description: A general description of the pulse sequence used for the scan.\n",
"rule": "rules.sidecars.mri.MRISequenceSpecifics"
},
{
"code": "SIDECAR_KEY_RECOMMENDED",
"subCode": "SpoilingType",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/anat/sub-CAM003_ses-01brain_T2w.nii.gz",
"issueMessage": "Field description: Specifies which spoiling method(s) are used by a spoiled sequence.\n",
"rule": "rules.sidecars.mri.SpoilingType"
},
{
"code": "SIDECAR_KEY_RECOMMENDED",
"subCode": "PartialFourierDirection",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/anat/sub-CAM003_ses-01brain_T2w.nii.gz",
"issueMessage": "Field description: The direction where only partial Fourier information was collected.\nCorresponds to [DICOM Tag 0018, 9036](https://dicomlookup.com/dicomtags/(0018,9036)) `Partial Fourier Direction`.\n",
"rule": "rules.sidecars.mri.MRIPartialFourier"
},
{
"code": "SIDECAR_FIELD_OVERRIDE",
"subCode": "ImageOrientationPatientDICOM",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/func/sub-CAM003_ses-01brain_task-rest_run-01_bold.json",
"issueMessage": "Sidecar key defined in /task-rest_bold.json overrides previous value (1,0,0,0,1,0) from /sub-CAM003/ses-01brain/func/sub-CAM003_ses-01brain_task-rest_run-01_bold.json"
},
{
"code": "SIDECAR_FIELD_OVERRIDE",
"subCode": "ImageType",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/func/sub-CAM003_ses-01brain_task-rest_run-01_bold.json",
"issueMessage": "Sidecar key defined in /task-rest_bold.json overrides previous value (ORIGINAL,PRIMARY,M,ND,NORM,MOSAIC) from /sub-CAM003/ses-01brain/func/sub-CAM003_ses-01brain_task-rest_run-01_bold.json"
},
{
"code": "SIDECAR_FIELD_OVERRIDE",
"subCode": "ShimSetting",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/func/sub-CAM003_ses-01brain_task-rest_run-01_bold.json",
"issueMessage": "Sidecar key defined in /task-rest_bold.json overrides previous value (8151,-13726,15044,134,89,-369,-362,-415) from /sub-CAM003/ses-01brain/func/sub-CAM003_ses-01brain_task-rest_run-01_bold.json"
},
{
"code": "SIDECAR_FIELD_OVERRIDE",
"subCode": "SliceTiming",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/func/sub-CAM003_ses-01brain_task-rest_run-01_bold.json",
"issueMessage": "Sidecar key defined in /task-rest_bold.json overrides previous value (0,1.035,0.0925,1.13,0.1875,1.225,0.2825,1.32,0.375,1.4125,0.47,1.5075,0.565,1.6025,0.66,1.695,0.7525,1.79,0.8475,1.885,0.9425,0,1.035,0.0925,1.13,0.1875,1.225,0.2825,1.32,0.375,1.4125,0.47,1.5075,0.565,1.6025,0.66,1.695,0.7525,1.79,0.8475,1.885,0.9425,0,1.035,0.0925,1.13,0.1875,1.225,0.2825,1.32,0.375,1.4125,0.47,1.5075,0.565,1.6025,0.66,1.695,0.7525,1.79,0.8475,1.885,0.9425) from /sub-CAM003/ses-01brain/func/sub-CAM003_ses-01brain_task-rest_run-01_bold.json"
},
{
"code": "SIDECAR_FIELD_OVERRIDE",
"subCode": "TaskName",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/func/sub-CAM003_ses-01brain_task-rest_run-01_bold.json",
"issueMessage": "Sidecar key defined in /task-rest_bold.json overrides previous value (TODO: full task name for rest) from /sub-CAM003/ses-01brain/func/sub-CAM003_ses-01brain_task-rest_run-01_bold.json"
},
{
"code": "SIDECAR_KEY_RECOMMENDED",
"subCode": "StimulusPresentation",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/func/sub-CAM003_ses-01brain_task-rest_run-01_events.tsv",
"issueMessage": "Field description: Object containing key-value pairs related to the software used to present\nthe stimuli during the experiment.\n",
"rule": "rules.sidecars.events.StimulusPresentation"
},
{
"code": "TSV_ADDITIONAL_COLUMNS_UNDEFINED",
"subCode": "TODO -- fill in rows and add more tab-separated columns if desired",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/func/sub-CAM003_ses-01brain_task-rest_run-01_events.tsv",
"rule": "rules.tabular_data.events.Events"
},
{
"code": "SUSPICIOUSLY_SHORT_EVENT_DESIGN",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/func/sub-CAM003_ses-01brain_task-rest_run-01_bold.nii.gz",
"rule": "rules.checks.hints.SuspiciouslyShortBOLDDesign"
},
{
"code": "SIDECAR_KEY_RECOMMENDED",
"subCode": "Instructions",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/func/sub-CAM003_ses-01brain_task-rest_run-01_bold.nii.gz",
"issueMessage": "Field description: Text of the instructions given to participants before the recording.\n",
"rule": "rules.sidecars.func.MRIFuncTaskInformation"
},
{
"code": "SIDECAR_KEY_RECOMMENDED",
"subCode": "TaskDescription",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/func/sub-CAM003_ses-01brain_task-rest_run-01_bold.nii.gz",
"issueMessage": "Field description: Longer description of the task.\n",
"rule": "rules.sidecars.func.MRIFuncTaskInformation"
},
{
"code": "SIDECAR_KEY_RECOMMENDED",
"subCode": "CogPOID",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/func/sub-CAM003_ses-01brain_task-rest_run-01_bold.nii.gz",
"issueMessage": "Field description: [URI](SPEC_ROOT/common-principles.md#uniform-resource-indicator)\nof the corresponding [CogPO](http://www.cogpo.org/) term.\n",
"rule": "rules.sidecars.func.MRIFuncTaskInformation"
},
{
"code": "SIDECAR_KEY_RECOMMENDED",
"subCode": "MatrixCoilMode",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/func/sub-CAM003_ses-01brain_task-rest_run-01_bold.nii.gz",
"issueMessage": "Field description: (If used)\nA method for reducing the number of independent channels by combining in\nanalog the signals from multiple coil elements.\nThere are typically different default modes when using un-accelerated or\naccelerated (for example, `\"GRAPPA\"`, `\"SENSE\"`) imaging.\n",
"rule": "rules.sidecars.mri.MRIHardware"
},
{
"code": "SIDECAR_KEY_RECOMMENDED",
"subCode": "PulseSequenceType",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/func/sub-CAM003_ses-01brain_task-rest_run-01_bold.nii.gz",
"issueMessage": "Field description: A general description of the pulse sequence used for the scan.\n",
"rule": "rules.sidecars.mri.MRISequenceSpecifics"
},
{
"code": "SIDECAR_KEY_RECOMMENDED",
"subCode": "PartialFourierDirection",
"severity": "warning",
"location": "/sub-CAM003/ses-01brain/func/sub-CAM003_ses-01brain_task-rest_run-01_bold.nii.gz",
"issueMessage": "Field description: The direction where only partial Fourier information was collected.\nCorresponds to [DICOM Tag 0018, 9036](https://dicomlookup.com/dicomtags/(0018,9036)) `Partial Fourier Direction`.\n",
"rule": "rules.sidecars.mri.MRIPartialFourier"
}
],
"codeMessages": {}
},
"summary": {
"sessions": [
"01brain"
],
"subjects": [
"CAM003"
],
"subjectMetadata": [
{
"participantId": "CAM003",
"age": 65,
"sex": "M",
"group": "control"
}
],
"tasks": [
"TODO: full task name for rest",
"rest"
],
"modalities": [
"MRI"
],
"secondaryModalities": [
"MRI_Structural",
"MRI_Diffusion",
"MRI_Functional"
],
"totalFiles": 31,
"size": 226325986,
"dataProcessed": false,
"pet": {},
"dataTypes": [
"dwi",
"fmap",
"anat",
"func"
],
"schemaVersion": "1.2.0"
}
}
Relevant log outputs (up to 20 lines): Is this relevant? I’m honestly not sure.
$ cat fmripost_aroma.toml
[environment]
cpu_count = 16
exec_env = "singularity"
free_mem = 247.2
overcommit_policy = "heuristic"
overcommit_limit = "50%"
nipype_version = "1.10.0"
templateflow_version = "25.1.1"
version = "0.1.dev1+g96a89a22b"
[execution]
bids_dir = "/fmriprep"
bids_database_dir = "/work/20260218-183830_b21830d7-ce05-4245-a427-c800cd056c04/bids_db"
bids_description_hash = "e9cca89d91069cc0695fb40f0ab8c94ab5e1c37d4919c5825d18eace20facc2a"
boilerplate_only = false
sloppy = false
debug = []
layout = "BIDS Layout: .../fmriprep | Subjects: 1 | Sessions: 1 | Runs: 1"
log_dir = "/out/logs"
log_level = 25
low_mem = false
md_only_boilerplate = false
notrack = true
track_carbon = false
country_code = "CAN"
output_dir = "/out"
aggr_ses_reports = 4
reports_only = false
run_uuid = "20260218-183830_b21830d7-ce05-4245-a427-c800cd056c04"
participant_label = [ "CAM003",]
templateflow_home = "/home/u7/dkp/.cache/templateflow"
work_dir = "/work"
write_graph = false
[workflow]
err_on_warn = false
melodic_dim = 0
denoise_method = [ "nonaggr",]
ignore = [ "fieldmaps",]
slice_time_ref = 0.5
spaces = "MNI152NLin6Asym"
[nipype]
crashfile_format = "txt"
get_linked_libs = false
nprocs = 16
omp_nthreads = 8
plugin = "MultiProc"
remove_unnecessary_outputs = true
resource_monitor = false
stop_on_first_crash = true
[seeds]
master = 58374
ants = 42709
numpy = 50838
melodic_seed = 1771465120
[execution.derivatives]
[execution.dataset_links]
input = "PosixPath('/fmriprep')"
templateflow = "PosixPath('/home/u7/dkp/.cache/templateflow')"
[nipype.plugin_args]
maxtasksperchild = 1
raise_insufficient = false