Hi, Peer,
It’s almost one year since your workshop at Marburg, shame that I am still struggle about the basics. The good thing is that I didn’t give up ;-).
Your are right, I didn’t check the ‘append’ and ‘=’ carefully. Now all the data were converted!
But validator still report one error on DTI data and 2 warnings.
The error says that
The number of volumes in this scan does not match the number of volumes in the corresponding .bvec and .bval files
I guess it is related to this issue here, but it has been solved in 2017:
Below is the error log I downloaded:
File Path: The number of volumes in this scan does not match the number of volumes in the corresponding .bvec and .bval files.
Type: Error
File: sub-001_ses-01_run-2_dwi.nii.gz
Location: Nifti/sub-001/ses-01/dwi/sub-001_ses-01_run-2_dwi.nii.gz
Reason: The number of volumes in this scan does not match the number of volumes in the corresponding .bvec and .bval files.======================================================
File Path: Not all subjects/sessions/runs have the same scanning parameters.
Type: Warning
File: sub-001_ses-01_run-2_dwi.nii.gz
Location: Nifti/sub-001/ses-01/dwi/sub-001_ses-01_run-2_dwi.nii.gz
Reason: The most common set of dimensions is: 128,128,72,65 (voxels), This file has the dimensions: 128,128,72 (voxels). The most common resolution is: 2.00mm x 2.00mm x 2.00mm x 9.10s, This file has the resolution: 2.00mm x 2.00mm x 2.00mm.======================================================
File Path: Tabular file contains custom columns not described in a data dictionary
Type: Warning
File: participants.tsv
Location: Nifti/participants.tsv
Reason: Tabular file contains custom columns not described in a data dictionary
Evidence: Columns: age, sex, group not defined, please define in: /participants.jsonType: Warning
File: sub-001_ses-01_task-exp_events.tsv
Location: Nifti/sub-001/ses-01/func/sub-001_ses-01_task-exp_events.tsv
Reason: Tabular file contains custom columns not described in a data dictionary
Evidence: Columns: TODO – fill in rows and add more tab-separated columns if desired not defined, please define in: /task-exp_events.json, /events.json,/sub-001/sub-001_task-exp_events.json,/sub-001/sub-001_events.json,/sub-001/ses-01/sub-001_ses-01_task-exp_events.json,/sub-001/ses-01/sub-001_ses-01_events.json,/sub-001/ses-01/func/sub-001_ses-01_task-exp_events.json,/sub-001/ses-01/func/sub-001_ses-01_events.jsonType: Warning
File: sub-001_ses-01_task-fam_events.tsv
Location: Nifti/sub-001/ses-01/func/sub-001_ses-01_task-fam_events.tsv
Reason: Tabular file contains custom columns not described in a data dictionary
Evidence: Columns: TODO – fill in rows and add more tab-separated columns if desired not defined, please define in: /task-fam_events.json, /events.json,/sub-001/sub-001_task-fam_events.json,/sub-001/sub-001_events.json,/sub-001/ses-01/sub-001_ses-01_task-fam_events.json,/sub-001/ses-01/sub-001_ses-01_events.json,/sub-001/ses-01/func/sub-001_ses-01_task-fam_events.json,/sub-001/ses-01/func/sub-001_ses-01_events.jsonType: Warning
File: sub-001_ses-01_task-rest_run-1_events.tsv
Location: Nifti/sub-001/ses-01/func/sub-001_ses-01_task-rest_run-1_events.tsv
Reason: Tabular file contains custom columns not described in a data dictionary
Evidence: Columns: TODO – fill in rows and add more tab-separated columns if desired not defined, please define in: /sub-001/ses-01/func/sub-001_ses-01_events.json, /sub-001/ses-01/func/sub-001_ses-01_task-rest_events.json,/sub-001/ses-01/sub-001_ses-01_events.json,/sub-001/ses-01/sub-001_ses-01_task-rest_events.json,/sub-001/sub-001_events.json,/sub-001/sub-001_task-rest_events.json,/events.json,/task-rest_events.json,/sub-001/ses-01/func/sub-001_ses-01_task-rest_run-1_events.jsonType: Warning
File: sub-001_ses-01_task-rest_run-2_events.tsv
Location: Nifti/sub-001/ses-01/func/sub-001_ses-01_task-rest_run-2_events.tsv
Reason: Tabular file contains custom columns not described in a data dictionary
Evidence: Columns: TODO – fill in rows and add more tab-separated columns if desired not defined, please define in: /sub-001/ses-01/func/sub-001_ses-01_events.json, /sub-001/ses-01/func/sub-001_ses-01_task-rest_events.json,/sub-001/ses-01/sub-001_ses-01_events.json,/sub-001/ses-01/sub-001_ses-01_task-rest_events.json,/sub-001/sub-001_events.json,/sub-001/sub-001_task-rest_events.json,/events.json,/task-rest_events.json,/sub-001/ses-01/func/sub-001_ses-01_task-rest_run-2_events.jsonType: Warning
File: sub-001_ses-01_scans.tsv
Location: Nifti/sub-001/ses-01/sub-001_ses-01_scans.tsv
Reason: Tabular file contains custom columns not described in a data dictionary
Evidence: Columns: operator, randstr not defined, please define in: /scans.json, /sub-001/sub-001_scans.json,/sub-001/ses-01/sub-001_ses-01_scans.json======================================================
update:
I found that the dicominfo seems not quit right, but not sure.
so here is part information from the dicominfo.tsv:
| dcm_dir_name | unspecified2 | unspecified3 | dim1 | dim2 | dim3 | dim4 | TR | TE |
|---|---|---|---|---|---|---|---|---|
| localizer_Series0001 | - | - | 512 | 512 | 3 | 1 | 0.0086 | 4 |
| resting1_mb4_TR_1000_Series0002 | - | - | 72 | 84 | 60 | 480 | 1 | 29 |
| fmri_Tag1_mb4_TR_1000_fam_Series0003 | - | - | 72 | 84 | 60 | 217 | 1 | 29 |
| fmri_Tag1_mb4_TR_1000_Series0004 | - | - | 72 | 84 | 60 | 496 | 1 | 29 |
| resting2_mb4_TR_1000_Series0005 | - | - | 72 | 84 | 60 | 480 | 1 | 29 |
| t1_mpr_ns_sag_p2_iso08_Series0006 | - | - | 320 | 320 | 224 | 1 | 1.9 | 2.54 |
| t2_tse_tra_448_p2_3mm_Series0007 | - | - | 448 | 448 | 45 | 1 | 6.1 | 79 |
| gre_field_mapping_Series0008 | - | - | 64 | 64 | 100 | 1 | 1.03 | 7.35 |
| gre_field_mapping_Series0009 | - | - | 64 | 64 | 50 | 1 | 1.03 | 7.35 |
| ep2d_diff_mddw_64_p2_b=1000_Series0010 | - | - | 128 | 128 | 4680 | 1 | 9.1 | 85 |
| ep2d_diff_mddw_64_p2_b=1000_TRACEW_Series0011 | - | - | 128 | 128 | 72 | 1 | 9.1 | 85 |
Here is how my folder looks like, the dim4 of T1w, T2, gre_field, and DTI are all 1, but the number of dicom are not 1.
