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questions > RE: Multiple nii files from the same Dicom folder
Apr 14, 2017 01:04 PM | Yishi Wang
RE: Multiple nii files from the same Dicom folder
Dear Chris,
Thank you for your reply. So I just updated dcm2nii to dcm2niix a minute ago and try it again. Now I got the following messages:
Chris Rorden's dcm2niiX version v1.0.20170403 (OpenJPEG build) GCC4.8.4 (64-bit Linux)
Found 5398 DICOM image(s)
slices stacked despite varying acquisition numbers (if this is not desired please recompile)
Some images have identical time, series, acquisition and image values. DUPLICATES REMOVED.
Note: B0 not the first volume in the series (FSL eddy reference volume is 30)
Warning: DTI gradient directions only tested for axial (transverse) acquisitions. Please validate bvec files.
Convert 2511 DICOM as LIU ZHI HUI dti/LIU ZHI HUI dti_ep2d_diff_MDDW_30_p2_20140507001838_100_c2a (128x128x81x31)
Convert 81 DICOM as LIU ZHI HUI dti/LIU ZHI HUI dti_ep2d_diff_MDDW_30_p2_20140507001838_6_c2a (128x128x81x1)
slices stacked despite varying acquisition numbers (if this is not desired please recompile)
Warning: DTI gradient directions only tested for axial (transverse) acquisitions. Please validate bvec files.
Convert 31 DICOM as LIU ZHI HUI dti/LIU ZHI HUI dti_ep2d_diff_MDDW_30_p2_20140507001838_3_c2a (128x128x81x31)
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Unable to determine spatial orientation: 0020,0037 missing (probably not a problem: derived image)
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Convert 81 DICOM as LIU ZHI HUI dti/LIU ZHI HUI dti_ep2d_diff_MDDW_30_p2_20140507001838_8a (128x128x81x1)
Convert 81 DICOM as LIU ZHI HUI dti/LIU ZHI HUI dti_ep2d_diff_MDDW_30_p2_20140507001838_5_c2a (128x128x81x1)
Convert 81 DICOM as LIU ZHI HUI dti/LIU ZHI HUI dti_ep2d_diff_MDDW_30_p2_20140507001838_4_c2a (128x128x81x1)
Convert 176 DICOM as LIU ZHI HUI dti/LIU ZHI HUI dti_t1_mprage_20140507001838_2_c2a (256x256x176x1)
Convert 81 DICOM as LIU ZHI HUI dti/LIU ZHI HUI dti_ep2d_diff_MDDW_30_p2_20140507001838_7_c2a (128x128x81x1)
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [1 0 0 0 0 -1]
Convert 1 DICOM as LIU ZHI HUI dti/LIU ZHI HUI dti_localizer_20140507001838_1c (512x512x1x1)
Warning: Check that 2D images are not mirrored.
slices not stacked: orientation varies (localizer?) [1 0 0 0 0 -1] != [0 1 0 0 0 -1]
Warning: Weird CSA 'ProtocolSliceNumber' (2): SPATIAL, SLICE-ORDER AND DTI TRANSFORMS UNTESTED
Convert 1 DICOM as LIU ZHI HUI dti/LIU ZHI HUI dti_localizer_20140507001838_1d (512x512x1x1)
Warning: Check that 2D images are not mirrored.
Convert 1 DICOM as LIU ZHI HUI dti/LIU ZHI HUI dti_localizer_20140507001838_1e (512x512x1x1)
Warning: Check that 2D images are not mirrored.
Conversion required 0.779247 seconds (0.777262 for core code).
I still don't quite understand which files should I choose for the next step.
Thanks
Yishi
Thank you for your reply. So I just updated dcm2nii to dcm2niix a minute ago and try it again. Now I got the following messages:
Chris Rorden's dcm2niiX version v1.0.20170403 (OpenJPEG build) GCC4.8.4 (64-bit Linux)
Found 5398 DICOM image(s)
slices stacked despite varying acquisition numbers (if this is not desired please recompile)
Some images have identical time, series, acquisition and image values. DUPLICATES REMOVED.
Note: B0 not the first volume in the series (FSL eddy reference volume is 30)
Warning: DTI gradient directions only tested for axial (transverse) acquisitions. Please validate bvec files.
Convert 2511 DICOM as LIU ZHI HUI dti/LIU ZHI HUI dti_ep2d_diff_MDDW_30_p2_20140507001838_100_c2a (128x128x81x31)
Convert 81 DICOM as LIU ZHI HUI dti/LIU ZHI HUI dti_ep2d_diff_MDDW_30_p2_20140507001838_6_c2a (128x128x81x1)
slices stacked despite varying acquisition numbers (if this is not desired please recompile)
Warning: DTI gradient directions only tested for axial (transverse) acquisitions. Please validate bvec files.
Convert 31 DICOM as LIU ZHI HUI dti/LIU ZHI HUI dti_ep2d_diff_MDDW_30_p2_20140507001838_3_c2a (128x128x81x31)
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Unable to determine spatial orientation: 0020,0037 missing (probably not a problem: derived image)
Warning: Bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Convert 81 DICOM as LIU ZHI HUI dti/LIU ZHI HUI dti_ep2d_diff_MDDW_30_p2_20140507001838_8a (128x128x81x1)
Convert 81 DICOM as LIU ZHI HUI dti/LIU ZHI HUI dti_ep2d_diff_MDDW_30_p2_20140507001838_5_c2a (128x128x81x1)
Convert 81 DICOM as LIU ZHI HUI dti/LIU ZHI HUI dti_ep2d_diff_MDDW_30_p2_20140507001838_4_c2a (128x128x81x1)
Convert 176 DICOM as LIU ZHI HUI dti/LIU ZHI HUI dti_t1_mprage_20140507001838_2_c2a (256x256x176x1)
Convert 81 DICOM as LIU ZHI HUI dti/LIU ZHI HUI dti_ep2d_diff_MDDW_30_p2_20140507001838_7_c2a (128x128x81x1)
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [1 0 0 0 0 -1]
Convert 1 DICOM as LIU ZHI HUI dti/LIU ZHI HUI dti_localizer_20140507001838_1c (512x512x1x1)
Warning: Check that 2D images are not mirrored.
slices not stacked: orientation varies (localizer?) [1 0 0 0 0 -1] != [0 1 0 0 0 -1]
Warning: Weird CSA 'ProtocolSliceNumber' (2): SPATIAL, SLICE-ORDER AND DTI TRANSFORMS UNTESTED
Convert 1 DICOM as LIU ZHI HUI dti/LIU ZHI HUI dti_localizer_20140507001838_1d (512x512x1x1)
Warning: Check that 2D images are not mirrored.
Convert 1 DICOM as LIU ZHI HUI dti/LIU ZHI HUI dti_localizer_20140507001838_1e (512x512x1x1)
Warning: Check that 2D images are not mirrored.
Conversion required 0.779247 seconds (0.777262 for core code).
I still don't quite understand which files should I choose for the next step.
Thanks
Yishi
Threaded View
Title | Author | Date |
---|---|---|
Yishi Wang | Apr 14, 2017 | |
Chris Rorden | Apr 14, 2017 | |
Yishi Wang | Apr 14, 2017 | |
Chris Rorden | Apr 14, 2017 | |
Yishi Wang | Apr 15, 2017 | |
Chris Rorden | Apr 14, 2017 | |
Yishi Wang | Apr 14, 2017 | |