Everything that follows (segmentation, landmarks, planning and the guide) depends on the scan you upload. This article explains how to prepare a CT scan and upload it when you create a case.
What you can upload
DICOM: the standard export from your scanner or PACS. Upload a ZIP file (ZIPs inside ZIPs are fine), a folder, or individual files (.dcm, .dicom or files without an extension).
STL: an existing 3D model, when your workflow starts from a mesh. Clinicians, Medical Assistants and Sales Reps can upload DICOM only.
From PACS: if your organization uses the CustoMED PACS Gateway, click Remote import, then choose the study under Select from Pacs. See PACS Gateway & Pending DICOM.
Note: CustoMED recognizes DICOM files by their standard file header. Other files in a ZIP or folder, such as viewer software, reports or system files, are skipped. Leaving them out keeps the upload smaller.
Preparing a good scan
Use a thin, consistent slice thickness and even spacing. CustoMED flags slices thicker than 1.5 mm and an average slice spacing of 1.5 mm or more. For the full scan protocol, see Supported File Formats & Scan Protocols.
Cover the full region of interest plus any reference anatomy the procedure needs (for example, the contralateral hip for HRA).
Export the complete series; don't crop or downsample. A CT series needs at least 30 slices.
Avoid mixing unrelated series, and never mix scans from different patients in one upload.
Uploading
Start a new case. See Create a New Case. The upload area is the first section.
Drag your files onto Drag & Drop or Choose file to upload, or click it to browse. You can add more files the same way.
Review the preview. Series are grouped as CT Imaging, MRI, X-ray and Others. Scroll through the slices with the mouse wheel or the slider, drag on the image to adjust window/level, and double-click to view it full screen.
Click the series to use for segmentation. The most suitable one is already selected when the preview opens. To leave a series out, hover over it and click the trash icon.
Click Upload All.
Your browser first anonymizes the files (Anonymization) and then uploads them (File Uploading...). Every valid series is uploaded with the case; the series you selected is used for segmentation. Large scans take time, so keep the tab open until the upload finishes.
Choose a CT series for segmentation unless your procedure's Technical Data Sheet says otherwise. Other series are shown and uploaded with the case.
Important: Once the case is created, only your Organization Back Office or the CustoMED back-office team can add or replace imaging, so check the series before you continue.
Reading the series checks
Each series shows its number of slices and slice thickness. An info icon on a series means CustoMED found something to check; hover over it to see the details. Click the arrow to see the scan date, pixel spacing, slice spacing and other scan data; values that need checking are shown in orange.
Message | What it means |
Pixel spacing recommended to be less than 1.5mm | The image resolution is coarse. The series can be used, but model quality may suffer. |
Average distance between slices is too big | Slices are 1.5 mm or more apart. The series can be used, but model quality may suffer. |
Series Slice Thickness is ... more than recommended 1.5mm maximum | Slices are thicker than recommended. |
Scan date is older than 6 months | Check that this is the scan you want to plan on. |
Metadata outside normal range | The series is derived (reconstructed) rather than original. Prefer an original series if you have one. |
Already uploaded to these cases | The same series was already uploaded to another case in your organization. Hover over Cases to see which. |
Series mismatch patient data | The upload contains series from more than one patient. Remove the series that don't belong. |
Series that can't be used are listed under Unsupported with the reason, for example a series with fewer than 30 slices. See Imaging Upload & Segmentation Troubleshooting.
What happens next
After you create the case, CustoMED starts processing and the case page shows the progress (Segmenting...). If processing fails, the upload section shows "Last uploaded file's error:" with the reason.