I am running into an error using the following command. derivatives/ is the output from fMRIPrep, which was run with --output-spaces MNI152NLin6Asym:res-2. Did I set up correctly?
singularity run fmripost_aroma.sif
derivatives/ aroma_out/ participant
--participant-label sub-01
--denoising-method nonaggr
-w scratch/
PUT VERSION HERE
Singularity
PASTE VALIDATOR OUTPUT HERE
2024-12-09 19:24:20,493 [ WARNING] Telemetry disabled because sentry_sdk is not installed.
241209-19:24:44,629 nipype.workflow IMPORTANT:
Building fMRIPost-AROMA's workflow:
* BIDS dataset path: derivatives.
* Participant list: ['01'].
* Run identifier: 20241209-192418_58a61b4d-f766-4d7b-bb7f-282d96a3fdbf.
* Output spaces: None.
2024-12-09 19:24:44,629 [IMPORTANT] Building fMRIPost-AROMA's workflow:
* BIDS dataset path: derivatives.
* Participant list: ['01'].
* Run identifier: 20241209-192418_58a61b4d-f766-4d7b-bb7f-282d96a3fdbf.
* Output spaces: None.
241209-19:24:45,192 nipype.workflow INFO:
Derivatives-only workflow mode enabled
2024-12-09 19:24:45,192 [ INFO] Derivatives-only workflow mode enabled
241209-19:24:45,522 nipype.workflow INFO:
Collected subject data:
!!python/object/apply:collections.defaultdict
args:
- !!python/name:builtins.list ''
dictitems:
anat2mni152nlin6asym: null
anat_dseg: derivatives/sub-01/anat/sub-01_run-01_dseg.nii.gz
anat_mni152nlin6asym: derivatives/sub-01/anat/sub-01_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_T1w.nii.gz
bold: &id001
- derivatives/sub-01/func/sub-01_task-rest_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
- derivatives/sub-01/func/sub-01_task-ta1_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
- derivatives/sub-01/func/sub-01_task-ta2_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
bold_confounds:
-derivatives/sub-01/func/sub-01_task-rest_run-01_desc-confounds_timeseries.tsv
- derivatives/sub-01/func/sub-01_task-ta1_run-01_desc-confounds_timeseries.tsv
- derivatives/sub-01/func/sub-01_task-ta2_run-01_desc-confounds_timeseries.tsv
bold_hmc:
- derivatives/sub-01/func/sub-01_task-rest_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
- derivatives/sub-01/func/sub-01_task-ta1_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
- derivatives/sub-01/func/sub-01_task-ta2_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
bold_mask_mni152nlin6asym:
- derivatives/sub-01/func/sub-01_task-rest_run-01_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
- derivatives/sub-01/func/sub-01_task-ta1_run-01_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
- derivatives/sub-01/func/sub-01_task-ta2_run-01_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
bold_mask_native:
- derivatives/sub-01/func/sub-01_task-rest_run-01_desc-brain_mask.nii.gz
- derivatives/sub-01/func/sub-01_task-ta1_run-01_desc-brain_mask.nii.gz
- derivatives/sub-01/func/sub-01_task-ta2_run-01_desc-brain_mask.nii.gz
bold_mni152nlin6asym: *id001
boldref2anat:
- derivatives/sub-01/func/sub-01_task-rest_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
- /derivatives/sub-01/func/sub-01_task-ta1_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
- derivatives/sub-01/func/sub-01_task-ta2_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
boldref2fmap: null
2024-12-09 19:24:45,522 [ INFO] Collected subject data:
!!python/object/apply:collections.defaultdict
args:
- !!python/name:builtins.list ''
dictitems:
anat2mni152nlin6asym: null
anat_dseg: derivatives/sub-01/anat/sub-01_run-01_dseg.nii.gz
anat_mni152nlin6asym: /derivatives/sub-01/anat/sub-01_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_T1w.nii.gz
bold: &id001
- derivatives/sub-01/func/sub-01_task-rest_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
-derivatives/sub-01/func/sub-01_task-ta1_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
- derivatives/sub-01/func/sub-01_task-ta2_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
bold_confounds:
- derivatives/sub-01/func/sub-01_task-rest_run-01_desc-confounds_timeseries.tsv
-derivatives/sub-01/func/sub-01_task-ta1_run-01_desc-confounds_timeseries.tsv
- derivatives/sub-01/func/sub-01_task-ta2_run-01_desc-confounds_timeseries.tsv
bold_hmc:
- derivatives/sub-01/func/sub-01_task-rest_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
- derivatives/sub-01/func/sub-01_task-ta1_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
- derivatives/sub-01/func/sub-01_task-ta2_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
bold_mask_mni152nlin6asym:
- derivatives/sub-01/func/sub-01_task-rest_run-01_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
- derivatives/sub-01/func/sub-01_task-ta1_run-01_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
-derivatives/sub-01/func/sub-01_task-ta2_run-01_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
bold_mask_native:
- derivatives/sub-01/func/sub-01_task-rest_run-01_desc-brain_mask.nii.gz
-derivatives/sub-01/func/sub-01_task-ta1_run-01_desc-brain_mask.nii.gz
- derivatives/sub-01/func/sub-01_task-ta2_run-01_desc-brain_mask.nii.gz
bold_mni152nlin6asym: *id001
boldref2anat:
- derivatives/sub-01/func/sub-01_task-rest_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
- /derivatives/sub-01/func/sub-01_task-ta1_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
- derivatives/sub-01/func/sub-01_task-ta2_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
boldref2fmap: null
Process Process-2:
Traceback (most recent call last):
File "/opt/conda/envs/fmripost_aroma/lib/python3.11/multiprocessing/process.py", line 314, in _bootstrap
self.run()
File "/opt/conda/envs/fmripost_aroma/lib/python3.11/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/opt/conda/envs/fmripost_aroma/lib/python3.11/site-packages/fmripost_aroma/cli/workflow.py", line 115, in build_workflow
retval['workflow'] = init_fmripost_aroma_wf()
^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/fmripost_aroma/lib/python3.11/site-packages/fmripost_aroma/workflows/base.py", line 71, in init_fmripost_aroma_wf
single_subject_wf = init_single_subject_wf(subject_id)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/fmripost_aroma/lib/python3.11/site-packages/fmripost_aroma/workflows/base.py", line 280, in init_single_subject_wf
single_run_wf = init_single_run_wf(bold_file)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/fmripost_aroma/lib/python3.11/site-packages/fmripost_aroma/workflows/base.py", line 346, in init_single_run_wf
collect_derivatives(
File "/opt/conda/envs/fmripost_aroma/lib/python3.11/site-packages/fmripost_aroma/utils/bids.py", line 214, in collect_derivatives
raise ValueError(
ValueError: Transforms to the following requested spaces not found: MNI152NLin6Asym.
Steven
December 10, 2024, 3:07am
2
Hi @Yuhua_Yu ,
In the future, please organize your post with the software support post template, you can see I reorganized it for you this time. Can you post the tree output of your fmriprep subject’s output folder? And also report which version of fmripost-aroma you are using?
Thanks,
Sorry about that!!
├── dataset_description.json
├── desc-aparcaseg_dseg.tsv
├── desc-aseg_dseg.tsv
├── sub-01
│ ├── anat
│ │ ├── sub-01_run-01_desc-brain_mask.json
│ │ ├── sub-01_run-01_desc-brain_mask.nii.gz
│ │ ├── sub-01_run-01_desc-preproc_T1w.json
│ │ ├── sub-01_run-01_desc-preproc_T1w.nii.gz
│ │ ├── sub-01_run-01_desc-ribbon_mask.json
│ │ ├── sub-01_run-01_desc-ribbon_mask.nii.gz
│ │ ├── sub-01_run-01_dseg.nii.gz
│ │ ├── sub-01_run-01_from-fsnative_to-T1w_mode-image_xfm.txt
│ │ ├── sub-01_run-01_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
│ │ ├── sub-01_run-01_from-MNI152NLin6Asym_to-T1w_mode-image_xfm.h5
│ │ ├── sub-01_run-01_from-T1w_to-fsnative_mode-image_xfm.txt
│ │ ├── sub-01_run-01_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
│ │ ├── sub-01_run-01_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5
│ │ ├── sub-01_run-01_hemi-L_midthickness.surf.gii
│ │ ├── sub-01_run-01_hemi-L_pial.surf.gii
│ │ ├── sub-01_run-01_hemi-L_space-fsaverage_desc-reg_sphere.surf.gii
│ │ ├── sub-01_run-01_hemi-L_space-fsLR_desc-msmsulc_sphere.surf.gii
│ │ ├── sub-01_run-01_hemi-L_space-fsLR_desc-reg_sphere.surf.gii
│ │ ├── sub-01_run-01_hemi-L_sphere.surf.gii
│ │ ├── sub-01_run-01_hemi-L_sulc.shape.gii
│ │ ├── sub-01_run-01_hemi-L_thickness.shape.gii
│ │ ├── sub-01_run-01_hemi-L_white.surf.gii
│ │ ├── sub-01_run-01_hemi-R_midthickness.surf.gii
│ │ ├── sub-01_run-01_hemi-R_pial.surf.gii
│ │ ├── sub-01_run-01_hemi-R_space-fsaverage_desc-reg_sphere.surf.gii
│ │ ├── sub-01_run-01_hemi-R_space-fsLR_desc-msmsulc_sphere.surf.gii
│ │ ├── sub-01_run-01_hemi-R_space-fsLR_desc-reg_sphere.surf.gii
│ │ ├── sub-01_run-01_hemi-R_sphere.surf.gii
│ │ ├── sub-01_run-01_hemi-R_sulc.shape.gii
│ │ ├── sub-01_run-01_hemi-R_thickness.shape.gii
│ │ ├── sub-01_run-01_hemi-R_white.surf.gii
│ │ ├── sub-01_run-01_label-CSF_probseg.nii.gz
│ │ ├── sub-01_run-01_label-GM_probseg.nii.gz
│ │ ├── sub-01_run-01_label-WM_probseg.nii.gz
│ │ ├── sub-01_run-01_space-MNI152NLin6Asym_res-2_desc-brain_mask.json
│ │ ├── sub-01_run-01_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
│ │ ├── sub-01_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_T1w.json
│ │ ├── sub-01_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_T1w.nii.gz
│ │ ├── sub-01_run-01_space-MNI152NLin6Asym_res-2_dseg.json
│ │ ├── sub-01_run-01_space-MNI152NLin6Asym_res-2_dseg.nii.gz
│ │ ├── sub-01_run-01_space-MNI152NLin6Asym_res-2_label-CSF_probseg.nii.gz
│ │ ├── sub-01_run-01_space-MNI152NLin6Asym_res-2_label-GM_probseg.nii.gz
│ │ └── sub-01_run-01_space-MNI152NLin6Asym_res-2_label-WM_probseg.nii.gz
│ ├── figures
│ │ ├── sub-01_desc-about_T1w.html
│ │ ├── sub-01_desc-summary_T1w.html
│ │ ├── sub-01_run-01_desc-conform_T1w.html
│ │ ├── sub-01_run-01_desc-reconall_T1w.svg
│ │ ├── sub-01_run-01_dseg.svg
│ │ ├── sub-01_run-01_fmapid-auto00000_desc-phasediff_fieldmap.svg
│ │ ├── sub-01_run-01_space-MNI152NLin6Asym_T1w.svg
│ │ ├── sub-01_task-rest_run-01_desc-carpetplot_bold.svg
│ │ ├── sub-01_task-rest_run-01_desc-compcorvar_bold.svg
│ │ ├── sub-01_task-rest_run-01_desc-confoundcorr_bold.svg
│ │ ├── sub-01_task-rest_run-01_desc-coreg_bold.svg
│ │ ├── sub-01_task-rest_run-01_desc-fmapCoreg_bold.svg
│ │ ├── sub-01_task-rest_run-01_desc-rois_bold.svg
│ │ ├── sub-01_task-rest_run-01_desc-sdc_bold.svg
│ │ ├── sub-01_task-rest_run-01_desc-summary_bold.html
│ │ ├── sub-01_task-rest_run-01_desc-validation_bold.html
│ │ ├── sub-01_task-ta1_run-01_desc-carpetplot_bold.svg
│ │ ├── sub-01_task-ta1_run-01_desc-compcorvar_bold.svg
│ │ ├── sub-01_task-ta1_run-01_desc-confoundcorr_bold.svg
│ │ ├── sub-01_task-ta1_run-01_desc-coreg_bold.svg
│ │ ├── sub-01_task-ta1_run-01_desc-fmapCoreg_bold.svg
│ │ ├── sub-01_task-ta1_run-01_desc-rois_bold.svg
│ │ ├── sub-01_task-ta1_run-01_desc-sdc_bold.svg
│ │ ├── sub-01_task-ta1_run-01_desc-summary_bold.html
│ │ ├── sub-01_task-ta1_run-01_desc-validation_bold.html
│ │ ├── sub-01_task-ta2_run-01_desc-carpetplot_bold.svg
│ │ ├── sub-01_task-ta2_run-01_desc-compcorvar_bold.svg
│ │ ├── sub-01_task-ta2_run-01_desc-confoundcorr_bold.svg
│ │ ├── sub-01_task-ta2_run-01_desc-coreg_bold.svg
│ │ ├── sub-01_task-ta2_run-01_desc-fmapCoreg_bold.svg
│ │ ├── sub-01_task-ta2_run-01_desc-rois_bold.svg
│ │ ├── sub-01_task-ta2_run-01_desc-sdc_bold.svg
│ │ ├── sub-01_task-ta2_run-01_desc-summary_bold.html
│ │ └── sub-01_task-ta2_run-01_desc-validation_bold.html
│ ├── fmap
│ │ ├── sub-01_run-01_fmapid-auto00000_desc-coeff_fieldmap.nii.gz
│ │ ├── sub-01_run-01_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz
│ │ ├── sub-01_run-01_fmapid-auto00000_desc-preproc_fieldmap.json
│ │ └── sub-01_run-01_fmapid-auto00000_desc-preproc_fieldmap.nii.gz
│ ├── func
│ │ ├── sub-01_task-rest_run-01_desc-brain_mask.json
│ │ ├── sub-01_task-rest_run-01_desc-brain_mask.nii.gz
│ │ ├── sub-01_task-rest_run-01_desc-confounds_timeseries.json
│ │ ├── sub-01_task-rest_run-01_desc-confounds_timeseries.tsv
│ │ ├── sub-01_task-rest_run-01_desc-coreg_boldref.json
│ │ ├── sub-01_task-rest_run-01_desc-coreg_boldref.nii.gz
│ │ ├── sub-01_task-rest_run-01_desc-hmc_boldref.json
│ │ ├── sub-01_task-rest_run-01_desc-hmc_boldref.nii.gz
│ │ ├── sub-01_task-rest_run-01_from-boldref_to-auto00000_mode-image_xfm.json
│ │ ├── sub-01_task-rest_run-01_from-boldref_to-auto00000_mode-image_xfm.txt
│ │ ├── sub-01_task-rest_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
│ │ ├── sub-01_task-rest_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
│ │ ├── sub-01_task-rest_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
│ │ ├── sub-01_task-rest_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
│ │ ├── sub-01_task-rest_run-01_space-MNI152NLin6Asym_res-2_boldref.json
│ │ ├── sub-01_task-rest_run-01_space-MNI152NLin6Asym_res-2_boldref.nii.gz
│ │ ├── sub-01_task-rest_run-01_space-MNI152NLin6Asym_res-2_desc-brain_mask.json
│ │ ├── sub-01_task-rest_run-01_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
│ │ ├── sub-01_task-rest_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_bold.json
│ │ ├── sub-01_task-rest_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
│ │ ├── sub-01_task-ta1_run-01_desc-brain_mask.json
│ │ ├── sub-01_task-ta1_run-01_desc-brain_mask.nii.gz
│ │ ├── sub-01_task-ta1_run-01_desc-confounds_timeseries.json
│ │ ├── sub-01_run-01_hemi-L_sphere.surf.gii
│ │ ├── sub-01_task-ta1_run-01_desc-confounds_timeseries.tsv
│ │ ├── sub-01_task-ta1_run-01_desc-coreg_boldref.json
│ │ ├── sub-01_task-ta1_run-01_desc-coreg_boldref.nii.gz
│ │ ├── sub-01_task-ta1_run-01_desc-hmc_boldref.json
│ │ ├── sub-01_task-ta1_run-01_desc-hmc_boldref.nii.gz
│ │ ├── sub-01_task-ta1_run-01_from-boldref_to-auto00000_mode-image_xfm.json
│ │ ├── sub-01_task-ta1_run-01_from-boldref_to-auto00000_mode-image_xfm.txt
│ │ ├── sub-01_task-ta1_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
│ │ ├── sub-01_task-ta1_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
│ │ ├── sub-01_task-ta1_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
│ │ ├── sub-01_task-ta1_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
│ │ ├── sub-01_task-ta1_run-01_space-MNI152NLin6Asym_res-2_boldref.json
│ │ ├── sub-01_task-ta1_run-01_space-MNI152NLin6Asym_res-2_boldref.nii.gz
│ │ ├── sub-01_task-ta1_run-01_space-MNI152NLin6Asym_res-2_desc-brain_mask.json
│ │ ├── sub-01_task-ta1_run-01_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
│ │ ├── sub-01_task-ta1_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_bold.json
│ │ ├── sub-01_task-ta1_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
│ │ ├── sub-01_task-ta2_run-01_desc-brain_mask.json
│ │ ├── sub-01_task-ta2_run-01_desc-brain_mask.nii.gz
│ │ ├── sub-01_task-ta2_run-01_desc-confounds_timeseries.json
│ │ ├── sub-01_task-ta2_run-01_desc-confounds_timeseries.tsv
│ │ ├── sub-01_task-ta2_run-01_desc-coreg_boldref.json
│ │ ├── sub-01_task-ta2_run-01_desc-coreg_boldref.nii.gz
│ │ ├── sub-01_task-ta2_run-01_desc-hmc_boldref.json
│ │ ├── sub-01_task-ta2_run-01_desc-hmc_boldref.nii.gz
│ │ ├── sub-01_task-ta2_run-01_from-boldref_to-auto00000_mode-image_xfm.json
│ │ ├── sub-01_task-ta2_run-01_from-boldref_to-auto00000_mode-image_xfm.txt
│ │ ├── sub-01_task-ta2_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
│ │ ├── sub-01_task-ta2_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
│ │ ├── sub-01_task-ta2_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
│ │ ├── sub-01_task-ta2_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
│ │ ├── sub-01_task-ta2_run-01_space-MNI152NLin6Asym_res-2_boldref.json
│ │ ├── sub-01_task-ta2_run-01_space-MNI152NLin6Asym_res-2_boldref.nii.gz
│ │ ├── sub-01_task-ta2_run-01_space-MNI152NLin6Asym_res-2_desc-brain_mask.json
│ │ ├── sub-01_task-ta2_run-01_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
│ │ ├── sub-01_task-ta2_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_bold.json
│ │ └── sub-01_task-ta2_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
│ └── log
│ └── 20241209-092021_ae717b6e-552d-4db9-b3c7-a4bd54db5570
│ └── fmriprep.toml
└── sub-01.html
7 directories, 146 files
Steven
December 10, 2024, 3:56am
4
Ah I think I see what’s going on. @tsalo can you confirm this is the case?
I see in fmripost-aroma/src/fmripost_aroma/data/io_spec.json at 990d17527b7b05f0daca9a7b0a508cf642373cbd · nipreps/fmripost-aroma · GitHub
"anat2mni152nlin6asym": {
"datatype": "anat",
"run": null,
"from": ["anat", "T1w", "T2w"],
"to": "MNI152NLin6Asym",
"space": null,
"res": null,
"den": null,
"mode": "image",
"desc": null,
"suffix": "xfm",
"extension": ".h5"
}
Perhaps the "run": null, means they are expecting no run label, whereas you have run-01. As a test, can you try removing that from the transform file and rerunning?
Best,
Oh my. This makes it pass the initial error, and exit without error. But it does not compute AROMA. Here is the log:
241209-21:45:50,592 nipype.workflow IMPORTANT:
Building fMRIPost-AROMA's workflow:
* BIDS dataset path: derivatives.
* Participant list: ['01'].
* Run identifier: 20241209-214533_83263065-f162-43d4-979f-058251106465.
* Output spaces: None.
2024-12-09 21:45:50,592 [IMPORTANT] Building fMRIPost-AROMA's workflow:
* BIDS dataset path: derivatives.
* Participant list: ['01'].
* Run identifier: 20241209-214533_83263065-f162-43d4-979f-058251106465.
* Output spaces: None.
241209-21:45:51,418 nipype.workflow INFO:
Derivatives-only workflow mode enabled
2024-12-09 21:45:51,418 [ INFO] Derivatives-only workflow mode enabled
241209-21:45:51,704 nipype.workflow INFO:
Collected subject data:
!!python/object/apply:collections.defaultdict
args:
- !!python/name:builtins.list ''
dictitems:
anat2mni152nlin6asym: derivatives/sub-01/anat/sub-01_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5
anat_dseg: derivatives/sub-01/anat/sub-01_dseg.nii.gz
anat_mni152nlin6asym: derivatives/sub-01/anat/sub-01_space-MNI152NLin6Asym_res-2_desc-preproc_T1w.nii.gz
bold: &id001
- derivatives/sub-01/func/sub-01_task-rest_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
- derivatives/sub-01/func/sub-01_task-ta1_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
- derivatives/sub-01/func/sub-01_task-ta2_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
bold_confounds:
- derivatives/sub-01/func/sub-01_task-rest_run-01_desc-confounds_timeseries.tsv
- derivatives/sub-01/func/sub-01_task-ta1_run-01_desc-confounds_timeseries.tsv
- derivatives/sub-01/func/sub-01_task-ta2_run-01_desc-confounds_timeseries.tsv
bold_hmc:
- derivatives/sub-01/func/sub-01_task-rest_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
- derivatives/sub-01/func/sub-01_task-ta1_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
- derivatives/sub-01/func/sub-01_task-ta2_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
bold_mask_mni152nlin6asym:
- derivatives/sub-01/func/sub-01_task-rest_run-01_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
- derivatives/sub-01/func/sub-01_task-ta1_run-01_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
- derivatives/sub-01/func/sub-01_task-ta2_run-01_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
bold_mask_native:
- derivatives/sub-01/func/sub-01_task-rest_run-01_desc-brain_mask.nii.gz
- derivatives/sub-01/func/sub-01_task-ta1_run-01_desc-brain_mask.nii.gz
- derivatives/sub-01/func/sub-01_task-ta2_run-01_desc-brain_mask.nii.gz
bold_mni152nlin6asym: *id001
boldref2anat:
- derivatives/sub-01/func/sub-01_task-rest_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
- derivatives/sub-01/func/sub-01_task-ta1_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
- derivatives/sub-01/func/sub-01_task-ta2_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
boldref2fmap: null
2024-12-09 21:45:51,704 [ INFO] Collected subject data:
!!python/object/apply:collections.defaultdict
args:
- !!python/name:builtins.list ''
dictitems:
anat2mni152nlin6asym: derivatives/sub-01/anat/sub-01_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5
anat_dseg: derivatives/sub-01/anat/sub-01_dseg.nii.gz
anat_mni152nlin6asym: derivatives/sub-01/anat/sub-01_space-MNI152NLin6Asym_res-2_desc-preproc_T1w.nii.gz
bold: &id001
- derivatives/sub-01/func/sub-01_task-rest_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
- derivatives/sub-01/func/sub-01_task-ta1_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
- derivatives/sub-01/func/sub-01_task-ta2_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
bold_confounds:
- derivatives/sub-01/func/sub-01_task-rest_run-01_desc-confounds_timeseries.tsv
- derivatives/sub-01/func/sub-01_task-ta1_run-01_desc-confounds_timeseries.tsv
- derivatives/sub-01/func/sub-01_task-ta2_run-01_desc-confounds_timeseries.tsv
bold_hmc:
- derivatives/sub-01/func/sub-01_task-rest_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
- derivatives/sub-01/func/sub-01_task-ta1_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
- derivatives/sub-01/func/sub-01_task-ta2_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
bold_mask_mni152nlin6asym:
- derivatives/sub-01/func/sub-01_task-rest_run-01_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
- derivatives/sub-01/func/sub-01_task-ta1_run-01_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
- derivatives/sub-01/func/sub-01_task-ta2_run-01_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
bold_mask_native:
- derivatives/sub-01/func/sub-01_task-rest_run-01_desc-brain_mask.nii.gz
- derivatives/sub-01/func/sub-01_task-ta1_run-01_desc-brain_mask.nii.gz
- derivatives/sub-01/func/sub-01_task-ta2_run-01_desc-brain_mask.nii.gz
bold_mni152nlin6asym: *id001
boldref2anat:
- derivatives/sub-01/func/sub-01_task-rest_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
- derivatives/sub-01/func/sub-01_task-ta1_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
- derivatives/sub-01/func/sub-01_task-ta2_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
boldref2fmap: null
241209-21:45:52,470 nipype.workflow INFO:
Collected run data for sub-01_task-rest_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz:
!!python/object/apply:collections.defaultdict
args:
- !!python/name:builtins.list ''
dictitems:
anat2mni152nlin6asym: derivatives/sub-01/anat/sub-01_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5
anat2outputspaces_xfm:
- derivatives/sub-01/anat/sub-01_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5
anat_dseg: derivatives/sub-01/anat/sub-01_dseg.nii.gz
anat_mni152nlin6asym: derivatives/sub-01/anat/sub-01_space-MNI152NLin6Asym_res-2_desc-preproc_T1w.nii.gz
bold_confounds: derivatives/sub-01/func/sub-01_task-rest_run-01_desc-confounds_timeseries.tsv
bold_hmc: null
bold_mask_mni152nlin6asym: derivatives/sub-01/func/sub-01_task-rest_run-01_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
bold_mask_native: null
bold_mask_outputspaces:
- derivatives/sub-01/func/sub-01_task-rest_run-01_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
bold_mni152nlin6asym: derivatives/sub-01/func/sub-01_task-rest_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
bold_outputspaces:
- derivatives/sub-01/func/sub-01_task-rest_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
boldref2anat: null
boldref2fmap: null
2024-12-09 21:45:52,470 [ INFO] Collected run data for sub-01_task-rest_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz:
!!python/object/apply:collections.defaultdict
args:
- !!python/name:builtins.list ''
dictitems:
anat2mni152nlin6asym: derivatives/sub-01/anat/sub-01_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5
anat2outputspaces_xfm:
- derivatives/sub-01/anat/sub-01_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5
anat_dseg: derivatives/sub-01/anat/sub-01_dseg.nii.gz
anat_mni152nlin6asym: derivatives/sub-01/anat/sub-01_space-MNI152NLin6Asym_res-2_desc-preproc_T1w.nii.gz
bold_confounds: derivatives/sub-01/func/sub-01_task-rest_run-01_desc-confounds_timeseries.tsv
bold_hmc: null
bold_mask_mni152nlin6asym: derivatives/sub-01/func/sub-01_task-rest_run-01_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
bold_mask_native: null
bold_mask_outputspaces:
- derivatives/sub-01/func/sub-01_task-rest_run-01_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
bold_mni152nlin6asym: derivatives/sub-01/func/sub-01_task-rest_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
bold_outputspaces:
- derivatives/sub-01/func/sub-01_task-rest_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
boldref2anat: null
boldref2fmap: null
Downloading https://templateflow.s3.amazonaws.com/tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-02_desc-brain_T1w.nii.gz
0%| | 0.00/429k [00:00<?, ?B/s]
22%|██▏ | 95.2k/429k [00:00<00:00, 952kB/s]
85%|████████▌ | 366k/429k [00:00<00:00, 1.89MB/s]
100%|██████████| 429k/429k [00:00<00:00, 2.05MB/s]
241209-21:45:54,390 nipype.workflow INFO:
Collected run data for sub-01_task-ta1_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz:
!!python/object/apply:collections.defaultdict
args:
- !!python/name:builtins.list ''
dictitems:
anat2mni152nlin6asym: derivatives/sub-01/anat/sub-01_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5
anat2outputspaces_xfm:
- derivatives/sub-01/anat/sub-01_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5
anat_dseg: derivatives/sub-01/anat/sub-01_dseg.nii.gz
anat_mni152nlin6asym: derivatives/sub-01/anat/sub-01_space-MNI152NLin6Asym_res-2_desc-preproc_T1w.nii.gz
bold_confounds: derivatives/sub-01/func/sub-01_task-ta1_run-01_desc-confounds_timeseries.tsv
bold_hmc: null
bold_mask_mni152nlin6asym: derivatives/sub-01/func/sub-01_task-ta1_run-01_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
bold_mask_native: null
bold_mask_outputspaces:
- derivatives/sub-01/func/sub-01_task-ta1_run-01_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
bold_mni152nlin6asym: derivatives/sub-01/func/sub-01_task-ta1_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
bold_outputspaces:
- derivatives/sub-01/func/sub-01_task-ta1_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
boldref2anat: null
boldref2fmap: null
2024-12-09 21:45:54,390 [ INFO] Collected run data for sub-01_task-ta1_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz:
!!python/object/apply:collections.defaultdict
args:
- !!python/name:builtins.list ''
dictitems:
anat2mni152nlin6asym: derivatives/sub-01/anat/sub-01_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5
anat2outputspaces_xfm:
- derivatives/sub-01/anat/sub-01_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5
anat_dseg: derivatives/sub-01/anat/sub-01_dseg.nii.gz
anat_mni152nlin6asym: derivatives/sub-01/anat/sub-01_space-MNI152NLin6Asym_res-2_desc-preproc_T1w.nii.gz
bold_confounds: derivatives/sub-01/func/sub-01_task-ta1_run-01_desc-confounds_timeseries.tsv
bold_hmc: null
bold_mask_mni152nlin6asym: derivatives/sub-01/func/sub-01_task-ta1_run-01_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
bold_mask_native: null
bold_mask_outputspaces:
- derivatives/sub-01/func/sub-01_task-ta1_run-01_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
bold_mni152nlin6asym: derivatives/sub-01/func/sub-01_task-ta1_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
bold_outputspaces:
- derivatives/sub-01/func/sub-01_task-ta1_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
boldref2anat: null
boldref2fmap: null
241209-21:45:54,933 nipype.workflow INFO:
Collected run data for sub-01_task-ta2_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz:
!!python/object/apply:collections.defaultdict
args:
- !!python/name:builtins.list ''
dictitems:
anat2mni152nlin6asym: derivatives/sub-01/anat/sub-01_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5
anat2outputspaces_xfm:
- derivatives/sub-01/anat/sub-01_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5
anat_dseg: derivatives/sub-01/anat/sub-01_dseg.nii.gz
anat_mni152nlin6asym: derivatives/sub-01/anat/sub-01_space-MNI152NLin6Asym_res-2_desc-preproc_T1w.nii.gz
bold_confounds: derivatives/sub-01/func/sub-01_task-ta2_run-01_desc-confounds_timeseries.tsv
bold_hmc: null
bold_mask_mni152nlin6asym: derivatives/sub-01/func/sub-01_task-ta2_run-01_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
bold_mask_native: null
bold_mask_outputspaces:
- derivatives/sub-01/func/sub-01_task-ta2_run-01_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
bold_mni152nlin6asym: derivatives/sub-01/func/sub-01_task-ta2_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
bold_outputspaces:
- derivatives/sub-01/func/sub-01_task-ta2_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
boldref2anat: null
boldref2fmap: null
2024-12-09 21:45:54,933 [ INFO] Collected run data for sub-01_task-ta2_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz:
!!python/object/apply:collections.defaultdict
args:
- !!python/name:builtins.list ''
dictitems:
anat2mni152nlin6asym: derivatives/sub-01/anat/sub-01_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5
anat2outputspaces_xfm:
- derivatives/sub-01/anat/sub-01_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5
anat_dseg: derivatives/sub-01/anat/sub-01_dseg.nii.gz
anat_mni152nlin6asym: derivatives/sub-01/anat/sub-01_space-MNI152NLin6Asym_res-2_desc-preproc_T1w.nii.gz
bold_confounds: derivatives/sub-01/func/sub-01_task-ta2_run-01_desc-confounds_timeseries.tsv
bold_hmc: null
bold_mask_mni152nlin6asym: derivatives/sub-01/func/sub-01_task-ta2_run-01_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
bold_mask_native: null
bold_mask_outputspaces:
- derivatives/sub-01/func/sub-01_task-ta2_run-01_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
bold_mni152nlin6asym: derivatives/sub-01/func/sub-01_task-ta2_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
bold_outputspaces:
- derivatives/sub-01/func/sub-01_task-ta2_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
boldref2anat: null
boldref2fmap: null
241209-21:45:59,849 nipype.workflow INFO:
fMRIPost-AROMA workflow graph with 137 nodes built successfully.
2024-12-09 21:45:59,849 [ INFO] fMRIPost-AROMA workflow graph with 137 nodes built successfully.
To update on this. It actually went through on another try, and produced all the results. Not sure what I fiddled with, probably removed an --error-on-warnings flag?
Anyhow, thanks for the help!
1 Like