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Updated CLI Manual (markdown) authored by Iosif Spartalis's avatar Iosif Spartalis
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...@@ -136,41 +136,3 @@ The above files are created even if no valid/invalid sequences/dicoms files have ...@@ -136,41 +136,3 @@ The above files are created even if no valid/invalid sequences/dicoms files have
Please refer to the repo wiki section [Reports - Descriptions and Details](https://github.com/aueb-wim/DataQualityControlTool/wiki/Reports---Descriptions-and-Details) for a detailed explanation of the content of this report. Please refer to the repo wiki section [Reports - Descriptions and Details](https://github.com/aueb-wim/DataQualityControlTool/wiki/Reports---Descriptions-and-Details) for a detailed explanation of the content of this report.
### validsequences.csv
If there are valid sequences then the tool will create this csv file. This file contains all the valid MRI sequences that found in given DICOM folder with the following headers discribing each sequence:
`PatientID`, `StudyID`, `SeriesNumber`, `SeriesDescription`, `SeriesDate`
The value of the sequence tags `SeriesDescription` and `SeriesDate` are dirived from the headers in the dicom files - more specifically, the value of a sequence tag is the most frequent value of this particular tag found in the sequence's dicom files.
### invalidsequences.csv
If there are invalid sequences the tool will create this csv file with the following headers:
`PatientID`, `StudyID`, `SeriesNumber`, `Slices`, `Invalid_dicoms`, `SeriesDescription`, `Error1`, `Error2`, `Error3`, `Error4`, `Error5`, `Error6`
- `Slices` is the number of dicom files that the current sequence is consist of (sum of valid and invalid dicoms).
- `Invilid_dicoms` is the number of invalid dicom files the current sequence.
- `Error1` - `Error6` is an error description that explains the reason why the sequence is characterized as 'invalid'
### invaliddicoms.csv
If a dicom file does not have at least one of the mandatory tags as described in the MIP specification found [here](https://hbpmedical.github.io/deployment/data/), then it will be characterized as 'invald'.
If there are invalid dicoms in the DICOM dataset, the tool will create this csv file with the following headers:
`Folder`, `File`, `PatientID`, `StudyID`, `SeriesNumber`, `InstanceNumber`, `MissingTags`
- `MissingTags` is a list of the missing mandatory DICOM tags.
### notprocessed.csv
If in the given root folder are some files that the QC tool can not process (not dicom files, corrupted dicom files etc), the tool will create this csv file with the following headers describing the location of those files:
`Folder`, `File`
### mri_visits.csv
This file contains MRI visit information for each patient. This file is necessary for the HBP MIP DataFactory's [Step3_B](https://github.com/HBPMedical/ehr-datafactory-template#importing-the-volumetric-brain-features-into-the-i2b2-capture-database) and it has the following headers:
`PATIENT_ID`, `VISIT_ID`, `VISIT_DATE`
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