Save Slices to DICOM -->Invalid DICOM Format Error

[William McCuddy]

Need help with error when trying to save slices to dicom after successfully marking tracks on slices. I followed all the steps listed in the manual for  "Export tractography to T1W/T2W images for DBS, focused ultrasound, or surgical navigation." This included: 1) Open subject fib.gz, 2) load tracts, 3) insert T1 slices, 4) mark tracts on slices. 

When I try to save to slices to dicom, a popup window says "Please assign the original DICOM files." I then go to the same T1 3D axial dicom folder and select all the dicoms that were selected in step 3 above. The program tries to write new dicoms to disk, but throws error "Invalid DICOM Format."

Relevant DICOM header information below. Please help! 

Thank you!

FileSize: 436666

                                         Format: 'DICOM'

                                  FormatVersion: 3

                                          Width: 1024

                                         Height: 1024

                                       BitDepth: 12

                                      ColorType: 'grayscale'

                 FileMetaInformationGroupLength: 198

                     FileMetaInformationVersion: [2×1 uint8]

                           SpecificCharacterSet: 'ISO_IR 100'

                                      ImageType: 'ORIGINAL\PRIMARY\PROJECTION IMAGE\M\FFE'

                                       Modality: 'MR'

                                   Manufacturer: 'Philips Healthcare'

                               StudyDescription: 'MRI BRAIN STEALTH PLANNING W/WO'

                          ProcedureCodeSequence: [1×1 struct]

                              SeriesDescription: 'T1 POST 3D RECON AX'

                               BodyPartExamined: 'BRAIN'

                               ScanningSequence: 'GR'

                                SequenceVariant: 'MP'

                              MRAcquisitionType: '3D'

                                 SliceThickness: 0.9000

                                 RepetitionTime: 7.3165

                                       EchoTime: 3.3560

                               NumberOfAverages: 1

                               ImagingFrequency: 63.8726

                                  ImagedNucleus: '1H'

                                    EchoNumbers: 1

                          MagneticFieldStrength: 1.5000

                           SpacingBetweenSlices: 0.9000

                     NumberOfPhaseEncodingSteps: 232

                                EchoTrainLength: 216

                                PercentSampling: 100

                        PercentPhaseFieldOfView: 93.0000

                                 PixelBandwidth: 217

                       SecondaryCaptureDeviceID: ''

                         ReconstructionDiameter: 256

                                ReceiveCoilName: 'MULTI COIL'

                               TransmitCoilName: 'BODY'

                              AcquisitionMatrix: [4×1 uint16]

                                      FlipAngle: 8

                                            SAR: 0.0093

                                           dBdt: 58.1562

                                          B1rms: 0.6549

                   DiffusionGradientOrientation: [3×1 double]

                                  SliceLocation: 77.8525

                                  ImageComments: ''

                                SamplesPerPixel: 1

                                           Rows: 1024

                                        Columns: 1024

                                   PixelSpacing: [2×1 double]

                                  BitsAllocated: 16

                                     BitsStored: 12

                                        HighBit: 11

                                   WindowCenter: 224.8300

                                    WindowWidth: 441.3900

[Frank Yeh]

The current routine only supports 2D DICOM.

If you can send a sample of your 3D DICOM using the upload link, then I will do my best to see if I can extend the support to your data.

Best regards,

Frank

--
You received this message because you are subscribed to the Google Groups "DSI Studio" group.
To unsubscribe from this group and stop receiving emails from it, send an email to dsi-studio+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/7d93f573-fa1d-4b59-a371-1bae200a62a9n%40googlegroups.com.

[William McCuddy]

I appreciate the offer to help. Would like to clean and deface dicoms before uploading. Any idea for a quick and easy way to do this on pc (i don't have freesurfer at work) The only other way i know how to deface is spm, but only nifti files, not dicom. I should be able to use freesurfer's mri_deface on my mac when I get home and can upload later tonight. 

To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/CAG_Qrt%2B5bD09Zn2Uvg5Y%2Bojwu4m1nOu1k%2BPz0yOjascwm2zSSQ%40mail.gmail.com.

[Frank Yeh]

DSI Studio can do it by manually drawing a face-covering region and use [Regions][Mark region on slice]->assign 0.

But now we have a chicken-egg problem...

Frank

To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/CAC92sr1VX1ONvNtfd1v729DKSX4n_euntCFbeK2rEbPaBazp5A%40mail.gmail.com.

[William McCuddy]

Used 3dSlicer to deface dicom files. After exporting dicoms from 3dslicer, i decided to mark the new defaced dicoms with a couple of wm tracts in dsi studio. After marking the tracts, i was able to save slices to dicom without issue. So it looks like the process of importing and exporting dicoms to/from 3dslicer fixed the issue somehow. I guess the dicoms coming off the scanner have some label that is throwing things off? Have you seen this before? Anything in the header info in my first post that could be causing this issue? At least I have a work around for the time being.

To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/CAG_QrtJhCe4dzxxFYsJGYwxzpLNbqVLfNyMZKoG3zEwuShQdgw%40mail.gmail.com.

[Frank Yeh]

I have no idea. This is why checking the data is the only chance to
fix the issue.
Frank

> To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/CAC92sr2%3DGHq4DoHs2T%3DCxna4WVcbk%3Drsex3TSRJN6gr7euuhRg%40mail.gmail.com.