[#8118] dcm2niix and DICOM from Siemens Prisma VE11b

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State: more information
Closed
Date:
2016-06-28 06:16
Priority: more information
3
Submitted By:
Jonathan Brooks (jonb)
Assigned To: more information
Nobody (None)
Hardware: 
Macintosh
Product: 
None
Operating System: 
MacOS X
Component: 
None
Version: 
None
Severity: 
major
Resolution: 
None
Summary: more information
dcm2niix and DICOM from Siemens Prisma VE11b

Detailed description

Hi,

I'm not sure if I'm experiencing expected problems with the new version of dcm2niix (previously I've only used dcm2nii):

I have several sets of data acquired on a Siemens Prisma with a variety of different acquisitions: whole head EPI, ZoomIT EPI (restricted/non-square FoV), and ZoomiT EP2D_diff (same deal just diffusion data). When I run the conversion I point dcm2niix to the DICOM download folder (foo), which has 3 subfolders:
I.e.
foo/001
foo/002
foo/003

Command I ran was:
dcm2niix -f %p_%s -z y -o "/Users/jon/converted" foo

Lots of warnings and errors, including the mysterious "Oh Dear!!!!" and the output never ends up in the folder "converted" it always gets written to the source folder.

One thing that seemed to cause problems was the existence of a .dcm2nii config file in my home folder, renaming this seemed to solve the problem with the program creating 4 outputs per series.

FYI there were approximately 3 separate localizers, and 2 fieldmaps during the course of scan. OsiriX was able to make sense of it all.

Please let me know if you need more information.

Best wishes,

Jon

Chris Rorden's dcm2niiX version 5May2016o (64-bit)
Version 5May2016o (64-bit)
Found 2005 DICOM image(s)
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050000/17409995
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050000/17417753
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050000/17417796
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050000/17417839
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050000/17417882
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050000/17417925
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050000/17417968
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050000/17418011
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050000/17418054
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050000/17418097
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050000/17418140
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050000/17418183
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050000/17418226
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050000/17418269
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050000/17418312
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050000/17418355
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050000/17418398
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050000/17418441
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050000/17418527
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050000/17418570
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050000/17418613
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050000/17418656
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050000/17418699
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050000/17418742
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050000/17418785
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050000/17418828
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050000/17418871
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050000/17418914
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050000/17418957
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050000/17419000
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050000/17419043
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050000/17419086
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050000/17419129
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050000/17419172
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050000/17419215
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17354347
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17354390
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17354433
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17354476
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17371013
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17371056
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17371099
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17371142
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17371185
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17371228
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17371271
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17371314
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17371357
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17371400
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17371443
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17371486
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17371529
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17371572
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17371615
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17371658
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17371701
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17371787
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17371830
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17371873
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17371916
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17371959
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17372002
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17372045
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17372088
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17372131
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17372174
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17372217
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17372260
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17372303
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17372346
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17372470
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17372513
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17372556
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17372599
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17372642
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17372685
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17372728
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17372771
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17372814
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17372857
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17372900
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17372943
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17372986
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17373029
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17373072
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17373115
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17373158
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17373201
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17373244
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17373287
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17373330
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17373373
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17373416
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17373459
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17373502
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17373545
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17373588
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17373631
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17373671
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17381389
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17381432
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17381475
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17381518
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17381561
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17381604
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17381647
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17381690
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17382555
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17382598
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17382641
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17382684
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17382727
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17382770
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17382813
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17382856
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17382899
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17382942
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17382985
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17383028
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17383071
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17383114
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17383157
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17383200
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17383243
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17383286
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17383329
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17383372
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17383415
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17383458
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17383501
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17383544
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17383587
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17383630
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17383673
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17383716
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17383759
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17383802
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17383845
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17383888
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17383931
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17383974
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17384017
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17384060
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17384100
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17397279
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17397322
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17397365
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17397408
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17397451
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17397494
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17397537
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17397580
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17397623
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17397666
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17397709
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17397752
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17397795
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17397838
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17397881
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17397924
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17397967
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17398010
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17398053
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17398096
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17398139
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17398182
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17398225
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17398268
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17398311
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17398354
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17398397
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17398440
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17398483
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17398526
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17398569
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17398612
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17398655
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17398698
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17398741
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17398784
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17398824
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17407140
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17407183
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17407226
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17407269
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17407312
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17407355
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17407398
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17407441
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17407484
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17407527
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17407570
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17407613
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17407656
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17407699
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17407742
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17407785
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17407828
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17407871
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17407914
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17407957
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17408000
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17408043
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17408086
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17408129
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17408172
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17408215
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17408258
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17408301
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17408344
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17408387
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17408430
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17408473
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17408516
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17408559
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17408602
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17408645
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17408685
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17410035
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050001/17418484
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050002/17354516
Serious error: spatial orientation ambiguous (tag 0020,0037 not found): 20160623/17050002/17371744
Unable to determine spatial orientation: old Siemens RGB header does not report slice orient (DICOM 0020,0037)!
WARNING: Unable to determine slice direction: please check whether slices are flipped
Warning: bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Convert 36 DICOM as 20160623/ep2d_diff_30dir_1av_ZoomIt_AP_23 (108x34x36x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/ep2d_diff_30dir_1av_ZoomIt_AP_23.nii"
Oh dear!!!!
Convert 36 DICOM as 20160623/ep2d_diff_30dir_1av_ZoomIt_AP_21 (108x34x36x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/ep2d_diff_30dir_1av_ZoomIt_AP_21.nii"
Oh dear!!!!
Convert 36 DICOM as 20160623/ep2d_diff_30dir_1av_ZoomIt_AP_22 (108x34x36x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/ep2d_diff_30dir_1av_ZoomIt_AP_22.nii"
Oh dear!!!!
Convert 100 DICOM as 20160623/ep2d_REST_ZOOMit_1.3x1.3x4.0_18 (96x36x36x100)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/ep2d_REST_ZOOMit_1.3x1.3x4.0_18.nii"
Oh dear!!!!
WARNING: DTI gradient directions only tested for axial (transverse) acquisitions. Please validate bvec files.
Convert 31 DICOM as 20160623/ep2d_diff_30dir_1av_ZoomIt_AP_19 (108x34x36x31)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/ep2d_diff_30dir_1av_ZoomIt_AP_19.nii"
Oh dear!!!!
Convert 36 DICOM as 20160623/ep2d_diff_30dir_1av_ZoomIt_AP_20 (108x34x36x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/ep2d_diff_30dir_1av_ZoomIt_AP_20.nii"
Oh dear!!!!
slices not stacked: orientation varies (localizer?) [0 1 0 0 0 -1] != [1 0 0 0 1 0]
slices not stacked: orientation varies (localizer?) [0 1 0 0 0 -1] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [0 1 0 0 0 -1] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [0 1 0 0 0 -1] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [0 1 0 0 0 -1] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [0 1 0 0 0 -1] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [0 1 0 0 0 -1] != [1 0 0 0 1 0]
slices not stacked: orientation varies (localizer?) [0 1 0 0 0 -1] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [0 1 0 0 0 -1] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [0 1 0 0 0 -1] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [0 1 0 0 0 -1] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [0 1 0 0 0 -1] != [1 0 0 0 0 -1]
Convert 3 DICOM as 20160623/localizer_15 (512x512x3x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/localizer_15.nii"
Oh dear!!!!
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [0 1 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [0 1 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [0 1 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [0 1 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [0 1 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [0 1 0 0 0 -1]
Convert 1 DICOM as 20160623/localizer_16 (512x512x1x1)
WARNING: check that 2D images are not mirrored.
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/localizer_16.nii"
Oh dear!!!!
slices not stacked: orientation varies (localizer?) [1 0 0 0 0 -1] != [0 1 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 0 -1] != [0 1 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 0 -1] != [0 1 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 0 -1] != [0 1 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 0 -1] != [0 1 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 0 -1] != [0 1 0 0 0 -1]
Convert 5 DICOM as 20160623/localizer_16a (512x512x5x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/localizer_16a.nii"
Oh dear!!!!
Convert 3 DICOM as 20160623/localizer_16b (512x512x3x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/localizer_16b.nii"
Oh dear!!!!
Convert 12 DICOM as 20160623/cerv_t1_tse_sag_17 (256x256x12x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/cerv_t1_tse_sag_17.nii"
Oh dear!!!!
slices not stacked: orientation varies (localizer?) [1 0 0 -0 1 0] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 -0 1 0] != [1 0 0 0 0 -1]
Convert 1 DICOM as 20160623/1.3.12.2.1107.5.2.43.66075.201_5001 (512x512x1x1)
WARNING: check that 2D images are not mirrored.
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/1.3.12.2.1107.5.2.43.66075.201_5001.nii"
Oh dear!!!!
Convert 1 DICOM as 20160623/1.3.12.2.1107.5.2.43.66075.201_5001a (512x512x1x1)
WARNING: check that 2D images are not mirrored.
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/1.3.12.2.1107.5.2.43.66075.201_5001a.nii"
Oh dear!!!!
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
Convert 36 DICOM as 20160623/gre_field_mapping_3mm_13 (64x64x36x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/gre_field_mapping_3mm_13.nii"
Oh dear!!!!
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
Convert 36 DICOM as 20160623/gre_field_mapping_3mm_13_e2 (64x64x36x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/gre_field_mapping_3mm_13_e2.nii"
Oh dear!!!!
Convert 36 DICOM as 20160623/gre_field_mapping_3mm_14_e2_ph (64x64x36x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/gre_field_mapping_3mm_14_e2_ph.nii"
Oh dear!!!!
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [1 0 0 0 0 -1]
Convert 1 DICOM as 20160623/localizer_15a (512x512x1x1)
WARNING: check that 2D images are not mirrored.
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/localizer_15a.nii"
Oh dear!!!!
Convert 5 DICOM as 20160623/localizer_15b (512x512x5x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/localizer_15b.nii"
Oh dear!!!!
Convert 100 DICOM as 20160623/ep2d_bold_p2_FoV160_12 (112x112x41x100)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/ep2d_bold_p2_FoV160_12.nii"
Oh dear!!!!
Convert 128 DICOM as 20160623/AAHead_Scout_32ch-head-coil_8 (160x160x128x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/AAHead_Scout_32ch-head-coil_8.nii"
slices not stacked: orientation varies (localizer?) [-0.0018392 0.980703 0.195497 0.00444285 0.195504 -0.980693] != [0.568673 0.794868 0.211648 9.34477e-05 0.25724 -0.966348]
slices not stacked: orientation varies (localizer?) [-0.0018392 0.980703 0.195497 0.00444285 0.195504 -0.980693] != [-0.00126261 0.997552 0.0699118 0.00463976 0.069917 -0.997542]
slices not stacked: orientation varies (localizer?) [-0.0018392 0.980703 0.195497 0.00444285 0.195504 -0.980693] != [-0.551399 0.806181 0.214551 9.34477e-05 0.25724 -0.966348]
slices not stacked: orientation varies (localizer?) [-0.0018392 0.980703 0.195497 0.00444285 0.195504 -0.980693] != [0.568673 0.794868 0.211648 9.34477e-05 0.25724 -0.966348]
slices not stacked: orientation varies (localizer?) [-0.0018392 0.980703 0.195497 0.00444285 0.195504 -0.980693] != [-0.00126261 0.997552 0.0699118 0.00463976 0.069917 -0.997542]
slices not stacked: orientation varies (localizer?) [-0.0018392 0.980703 0.195497 0.00444285 0.195504 -0.980693] != [-0.551399 0.806181 0.214551 9.34477e-05 0.25724 -0.966348]
Convert 2 DICOM as 20160623/AAHead_Scout_32ch-head-coil_9 (162x162x2x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/AAHead_Scout_32ch-head-coil_9.nii"
slices not stacked: orientation varies (localizer?) [0.568673 0.794868 0.211648 9.34477e-05 0.25724 -0.966348] != [-0.00126261 0.997552 0.0699118 0.00463976 0.069917 -0.997542]
slices not stacked: orientation varies (localizer?) [0.568673 0.794868 0.211648 9.34477e-05 0.25724 -0.966348] != [-0.551399 0.806181 0.214551 9.34477e-05 0.25724 -0.966348]
slices not stacked: orientation varies (localizer?) [0.568673 0.794868 0.211648 9.34477e-05 0.25724 -0.966348] != [-0.0018392 0.980703 0.195497 0.00444285 0.195504 -0.980693]
slices not stacked: orientation varies (localizer?) [0.568673 0.794868 0.211648 9.34477e-05 0.25724 -0.966348] != [-0.00126261 0.997552 0.0699118 0.00463976 0.069917 -0.997542]
slices not stacked: orientation varies (localizer?) [0.568673 0.794868 0.211648 9.34477e-05 0.25724 -0.966348] != [-0.551399 0.806181 0.214551 9.34477e-05 0.25724 -0.966348]
slices not stacked: orientation varies (localizer?) [0.568673 0.794868 0.211648 9.34477e-05 0.25724 -0.966348] != [-0.0018392 0.980703 0.195497 0.00444285 0.195504 -0.980693]
Convert 1 DICOM as 20160623/AAHead_Scout_32ch-head-coil_9a (162x162x1x1)
WARNING: check that 2D images are not mirrored.
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/AAHead_Scout_32ch-head-coil_9a.nii"
slices not stacked: orientation varies (localizer?) [-0.00126261 0.997552 0.0699118 0.00463976 0.069917 -0.997542] != [-0.551399 0.806181 0.214551 9.34477e-05 0.25724 -0.966348]
slices not stacked: orientation varies (localizer?) [-0.00126261 0.997552 0.0699118 0.00463976 0.069917 -0.997542] != [-0.0018392 0.980703 0.195497 0.00444285 0.195504 -0.980693]
slices not stacked: orientation varies (localizer?) [-0.00126261 0.997552 0.0699118 0.00463976 0.069917 -0.997542] != [-0.551399 0.806181 0.214551 9.34477e-05 0.25724 -0.966348]
slices not stacked: orientation varies (localizer?) [-0.00126261 0.997552 0.0699118 0.00463976 0.069917 -0.997542] != [-0.0018392 0.980703 0.195497 0.00444285 0.195504 -0.980693]
Convert 1 DICOM as 20160623/AAHead_Scout_32ch-head-coil_9b (162x162x1x1)
WARNING: check that 2D images are not mirrored.
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/AAHead_Scout_32ch-head-coil_9b.nii"
slices not stacked: orientation varies (localizer?) [-0.551399 0.806181 0.214551 9.34477e-05 0.25724 -0.966348] != [-0.0018392 0.980703 0.195497 0.00444285 0.195504 -0.980693]
slices not stacked: orientation varies (localizer?) [-0.551399 0.806181 0.214551 9.34477e-05 0.25724 -0.966348] != [-0.0018392 0.980703 0.195497 0.00444285 0.195504 -0.980693]
Convert 1 DICOM as 20160623/AAHead_Scout_32ch-head-coil_9c (162x162x1x1)
WARNING: check that 2D images are not mirrored.
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/AAHead_Scout_32ch-head-coil_9c.nii"
slices not stacked: orientation varies (localizer?) [0.99876 0.0105047 0.0486544 0.0477972 0.0704361 -0.99637] != [0.999988 0.000935129 0.00471668 0.00463976 0.069917 -0.997542]
slices not stacked: orientation varies (localizer?) [0.99876 0.0105047 0.0486544 0.0477972 0.0704361 -0.99637] != [0.999995 0.00139715 0.0029523 0.00286575 0.0583541 -0.998292]
slices not stacked: orientation varies (localizer?) [0.99876 0.0105047 0.0486544 0.0477972 0.0704361 -0.99637] != [0.999988 0.000935129 0.00471668 0.00463976 0.069917 -0.997542]
slices not stacked: orientation varies (localizer?) [0.99876 0.0105047 0.0486544 0.0477972 0.0704361 -0.99637] != [0.999995 0.00139715 0.0029523 0.00286575 0.0583541 -0.998292]
Convert 1 DICOM as 20160623/AAHead_Scout_32ch-head-coil_10 (162x162x1x1)
WARNING: check that 2D images are not mirrored.
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/AAHead_Scout_32ch-head-coil_10.nii"
slices not stacked: orientation varies (localizer?) [0.999988 0.000935129 0.00471668 0.00463976 0.069917 -0.997542] != [0.999995 0.00139715 0.0029523 0.00286575 0.0583541 -0.998292]
slices not stacked: orientation varies (localizer?) [0.999988 0.000935129 0.00471668 0.00463976 0.069917 -0.997542] != [0.999995 0.00139715 0.0029523 0.00286575 0.0583541 -0.998292]
Convert 1 DICOM as 20160623/AAHead_Scout_32ch-head-coil_10a (162x162x1x1)
WARNING: check that 2D images are not mirrored.
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/AAHead_Scout_32ch-head-coil_10a.nii"
Convert 1 DICOM as 20160623/AAHead_Scout_32ch-head-coil_10b (162x162x1x1)
WARNING: check that 2D images are not mirrored.
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/AAHead_Scout_32ch-head-coil_10b.nii"
slices not stacked: orientation varies (localizer?) [0.999988 0.000935129 0.00471668 -0.000306927 0.99132 -0.131467] != [0.999998 0.00202172 0.000634879 -0.002117 0.966345 0.257239]
slices not stacked: orientation varies (localizer?) [0.999988 0.000935129 0.00471668 -0.000306927 0.99132 -0.131467] != [0.99876 0.0105047 0.0486544 -0.0138936 0.997461 0.0698467]
slices not stacked: orientation varies (localizer?) [0.999988 0.000935129 0.00471668 -0.000306927 0.99132 -0.131467] != [0.999998 0.00202172 0.000634879 -0.002117 0.966345 0.257239]
slices not stacked: orientation varies (localizer?) [0.999988 0.000935129 0.00471668 -0.000306927 0.99132 -0.131467] != [0.99876 0.0105047 0.0486544 -0.0138936 0.997461 0.0698467]
Convert 1 DICOM as 20160623/AAHead_Scout_32ch-head-coil_11 (162x162x1x1)
WARNING: check that 2D images are not mirrored.
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/AAHead_Scout_32ch-head-coil_11.nii"
slices not stacked: orientation varies (localizer?) [0.999998 0.00202172 0.000634879 -0.002117 0.966345 0.257239] != [0.99876 0.0105047 0.0486544 -0.0138936 0.997461 0.0698467]
slices not stacked: orientation varies (localizer?) [0.999998 0.00202172 0.000634879 -0.002117 0.966345 0.257239] != [0.99876 0.0105047 0.0486544 -0.0138936 0.997461 0.0698467]
Convert 1 DICOM as 20160623/AAHead_Scout_32ch-head-coil_11a (162x162x1x1)
WARNING: check that 2D images are not mirrored.
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/AAHead_Scout_32ch-head-coil_11a.nii"
Convert 1 DICOM as 20160623/AAHead_Scout_32ch-head-coil_11b (162x162x1x1)
WARNING: check that 2D images are not mirrored.
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/AAHead_Scout_32ch-head-coil_11b.nii"
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
slices not stacked: echo varies (TE 7.38, 4.92; echo 2, 1)
Convert 36 DICOM as 20160623/gre_field_mapping_3mm_6_e2 (64x64x36x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/gre_field_mapping_3mm_6_e2.nii"
Oh dear!!!!
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
Convert 36 DICOM as 20160623/gre_field_mapping_3mm_6 (64x64x36x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/gre_field_mapping_3mm_6.nii"
Oh dear!!!!
Convert 36 DICOM as 20160623/gre_field_mapping_3mm_7_e2_ph (64x64x36x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/gre_field_mapping_3mm_7_e2_ph.nii"
Oh dear!!!!
Convert 100 DICOM as 20160623/ep2d_bold_p2_FoV160_5 (112x112x41x100)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/ep2d_bold_p2_FoV160_5.nii"
Oh dear!!!!
Convert 128 DICOM as 20160623/AAHead_Scout_32ch-head-coil_1 (160x160x128x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/AAHead_Scout_32ch-head-coil_1.nii"
slices not stacked: orientation varies (localizer?) [-0.0148874 0.989882 0.141107 0.0217255 0.141409 -0.989713] != [0.567597 0.802073 0.185774 0.0129807 0.216897 -0.976108]
slices not stacked: orientation varies (localizer?) [-0.0148874 0.989882 0.141107 0.0217255 0.141409 -0.989713] != [-0.0125415 0.99923 0.0371663 0.023159 0.0374496 -0.99903]
slices not stacked: orientation varies (localizer?) [-0.0148874 0.989882 0.141107 0.0217255 0.141409 -0.989713] != [-0.557663 0.811843 0.17298 0.0129807 0.216897 -0.976108]
slices not stacked: orientation varies (localizer?) [-0.0148874 0.989882 0.141107 0.0217255 0.141409 -0.989713] != [0.567597 0.802073 0.185774 0.0129807 0.216897 -0.976108]
slices not stacked: orientation varies (localizer?) [-0.0148874 0.989882 0.141107 0.0217255 0.141409 -0.989713] != [-0.0125415 0.99923 0.0371663 0.023159 0.0374496 -0.99903]
slices not stacked: orientation varies (localizer?) [-0.0148874 0.989882 0.141107 0.0217255 0.141409 -0.989713] != [-0.557663 0.811843 0.17298 0.0129807 0.216897 -0.976108]
Convert 2 DICOM as 20160623/AAHead_Scout_32ch-head-coil_2 (162x162x2x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/AAHead_Scout_32ch-head-coil_2.nii"
slices not stacked: orientation varies (localizer?) [0.567597 0.802073 0.185774 0.0129807 0.216897 -0.976108] != [-0.0125415 0.99923 0.0371663 0.023159 0.0374496 -0.99903]
slices not stacked: orientation varies (localizer?) [0.567597 0.802073 0.185774 0.0129807 0.216897 -0.976108] != [-0.557663 0.811843 0.17298 0.0129807 0.216897 -0.976108]
slices not stacked: orientation varies (localizer?) [0.567597 0.802073 0.185774 0.0129807 0.216897 -0.976108] != [-0.0148874 0.989882 0.141107 0.0217255 0.141409 -0.989713]
slices not stacked: orientation varies (localizer?) [0.567597 0.802073 0.185774 0.0129807 0.216897 -0.976108] != [-0.0125415 0.99923 0.0371663 0.023159 0.0374496 -0.99903]
slices not stacked: orientation varies (localizer?) [0.567597 0.802073 0.185774 0.0129807 0.216897 -0.976108] != [-0.557663 0.811843 0.17298 0.0129807 0.216897 -0.976108]
slices not stacked: orientation varies (localizer?) [0.567597 0.802073 0.185774 0.0129807 0.216897 -0.976108] != [-0.0148874 0.989882 0.141107 0.0217255 0.141409 -0.989713]
Convert 1 DICOM as 20160623/AAHead_Scout_32ch-head-coil_2a (162x162x1x1)
WARNING: check that 2D images are not mirrored.
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/AAHead_Scout_32ch-head-coil_2a.nii"
slices not stacked: orientation varies (localizer?) [-0.0125415 0.99923 0.0371663 0.023159 0.0374496 -0.99903] != [-0.557663 0.811843 0.17298 0.0129807 0.216897 -0.976108]
slices not stacked: orientation varies (localizer?) [-0.0125415 0.99923 0.0371663 0.023159 0.0374496 -0.99903] != [-0.0148874 0.989882 0.141107 0.0217255 0.141409 -0.989713]
slices not stacked: orientation varies (localizer?) [-0.0125415 0.99923 0.0371663 0.023159 0.0374496 -0.99903] != [-0.557663 0.811843 0.17298 0.0129807 0.216897 -0.976108]
slices not stacked: orientation varies (localizer?) [-0.0125415 0.99923 0.0371663 0.023159 0.0374496 -0.99903] != [-0.0148874 0.989882 0.141107 0.0217255 0.141409 -0.989713]
Convert 1 DICOM as 20160623/AAHead_Scout_32ch-head-coil_2b (162x162x1x1)
WARNING: check that 2D images are not mirrored.
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/AAHead_Scout_32ch-head-coil_2b.nii"
slices not stacked: orientation varies (localizer?) [-0.557663 0.811843 0.17298 0.0129807 0.216897 -0.976108] != [-0.0148874 0.989882 0.141107 0.0217255 0.141409 -0.989713]
slices not stacked: orientation varies (localizer?) [-0.557663 0.811843 0.17298 0.0129807 0.216897 -0.976108] != [-0.0148874 0.989882 0.141107 0.0217255 0.141409 -0.989713]
Convert 1 DICOM as 20160623/AAHead_Scout_32ch-head-coil_2c (162x162x1x1)
WARNING: check that 2D images are not mirrored.
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/AAHead_Scout_32ch-head-coil_2c.nii"
slices not stacked: orientation varies (localizer?) [0.997796 0.0220598 0.062575 0.0617001 0.0383292 -0.997359] != [0.999653 0.0116686 0.0236109 0.023159 0.0374496 -0.99903]
slices not stacked: orientation varies (localizer?) [0.997796 0.0220598 0.062575 0.0617001 0.0383292 -0.997359] != [0.999635 0.00506459 0.0265466 0.0264765 0.0134521 -0.999559]
slices not stacked: orientation varies (localizer?) [0.997796 0.0220598 0.062575 0.0617001 0.0383292 -0.997359] != [0.999653 0.0116686 0.0236109 0.023159 0.0374496 -0.99903]
slices not stacked: orientation varies (localizer?) [0.997796 0.0220598 0.062575 0.0617001 0.0383292 -0.997359] != [0.999635 0.00506459 0.0265466 0.0264765 0.0134521 -0.999559]
Convert 1 DICOM as 20160623/AAHead_Scout_32ch-head-coil_3 (162x162x1x1)
WARNING: check that 2D images are not mirrored.
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/AAHead_Scout_32ch-head-coil_3.nii"
slices not stacked: orientation varies (localizer?) [0.999653 0.0116686 0.0236109 0.023159 0.0374496 -0.99903] != [0.999635 0.00506459 0.0265466 0.0264765 0.0134521 -0.999559]
slices not stacked: orientation varies (localizer?) [0.999653 0.0116686 0.0236109 0.023159 0.0374496 -0.99903] != [0.999635 0.00506459 0.0265466 0.0264765 0.0134521 -0.999559]
Convert 1 DICOM as 20160623/AAHead_Scout_32ch-head-coil_3a (162x162x1x1)
WARNING: check that 2D images are not mirrored.
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/AAHead_Scout_32ch-head-coil_3a.nii"
Convert 1 DICOM as 20160623/AAHead_Scout_32ch-head-coil_3b (162x162x1x1)
WARNING: check that 2D images are not mirrored.
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/AAHead_Scout_32ch-head-coil_3b.nii"
slices not stacked: orientation varies (localizer?) [0.999653 0.0116686 0.0236109 -0.00732342 0.984295 -0.176379] != [0.999779 0.0133043 0.0162518 -0.0165114 0.976104 0.216676]
slices not stacked: orientation varies (localizer?) [0.999653 0.0116686 0.0236109 -0.00732342 0.984295 -0.176379] != [0.997796 0.0220598 0.062575 -0.0244 0.999022 0.0368837]
slices not stacked: orientation varies (localizer?) [0.999653 0.0116686 0.0236109 -0.00732342 0.984295 -0.176379] != [0.999779 0.0133043 0.0162518 -0.0165114 0.976104 0.216676]
slices not stacked: orientation varies (localizer?) [0.999653 0.0116686 0.0236109 -0.00732342 0.984295 -0.176379] != [0.997796 0.0220598 0.062575 -0.0244 0.999022 0.0368837]
Convert 1 DICOM as 20160623/AAHead_Scout_32ch-head-coil_4 (162x162x1x1)
WARNING: check that 2D images are not mirrored.
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/AAHead_Scout_32ch-head-coil_4.nii"
slices not stacked: orientation varies (localizer?) [0.999779 0.0133043 0.0162518 -0.0165114 0.976104 0.216676] != [0.997796 0.0220598 0.062575 -0.0244 0.999022 0.0368837]
slices not stacked: orientation varies (localizer?) [0.999779 0.0133043 0.0162518 -0.0165114 0.976104 0.216676] != [0.997796 0.0220598 0.062575 -0.0244 0.999022 0.0368837]
Convert 1 DICOM as 20160623/AAHead_Scout_32ch-head-coil_4a (162x162x1x1)
WARNING: check that 2D images are not mirrored.
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/AAHead_Scout_32ch-head-coil_4a.nii"
Convert 1 DICOM as 20160623/AAHead_Scout_32ch-head-coil_4b (162x162x1x1)
WARNING: check that 2D images are not mirrored.
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/AAHead_Scout_32ch-head-coil_4b.nii"
Unable to determine spatial orientation: old Siemens RGB header does not report slice orient (DICOM 0020,0037)!
WARNING: Unable to determine slice direction: please check whether slices are flipped
Warning: bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Convert 36 DICOM as 20160623/ep2d_diff_30dir_1av_ZoomIt_APT_56 (108x34x36x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/ep2d_diff_30dir_1av_ZoomIt_APT_56.nii"
Oh dear!!!!
Convert 36 DICOM as 20160623/ep2d_diff_30dir_1av_ZoomIt_APT_54 (108x34x36x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/ep2d_diff_30dir_1av_ZoomIt_APT_54.nii"
Oh dear!!!!
Convert 36 DICOM as 20160623/ep2d_diff_30dir_1av_ZoomIt_APT_55 (108x34x36x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/ep2d_diff_30dir_1av_ZoomIt_APT_55.nii"
Oh dear!!!!
Unable to determine spatial orientation: old Siemens RGB header does not report slice orient (DICOM 0020,0037)!
WARNING: Unable to determine slice direction: please check whether slices are flipped
Warning: bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Convert 36 DICOM as 20160623/ep2d_diff_30dir_1av_ZoomIt_PA_50 (108x34x36x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/ep2d_diff_30dir_1av_ZoomIt_PA_50.nii"
Oh dear!!!!
WARNING: DTI gradient directions only tested for axial (transverse) acquisitions. Please validate bvec files.
Convert 31 DICOM as 20160623/ep2d_diff_30dir_1av_ZoomIt_APT_52 (108x34x36x31)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/ep2d_diff_30dir_1av_ZoomIt_APT_52.nii"
Oh dear!!!!
Convert 36 DICOM as 20160623/ep2d_diff_30dir_1av_ZoomIt_APT_53 (108x34x36x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/ep2d_diff_30dir_1av_ZoomIt_APT_53.nii"
Oh dear!!!!
Convert 36 DICOM as 20160623/ep2d_diff_30dir_1av_ZoomIt_PA_47 (108x34x36x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/ep2d_diff_30dir_1av_ZoomIt_PA_47.nii"
Oh dear!!!!
Convert 36 DICOM as 20160623/ep2d_diff_30dir_1av_ZoomIt_PA_48 (108x34x36x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/ep2d_diff_30dir_1av_ZoomIt_PA_48.nii"
Oh dear!!!!
Convert 36 DICOM as 20160623/ep2d_diff_30dir_1av_ZoomIt_PA_49 (108x34x36x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/ep2d_diff_30dir_1av_ZoomIt_PA_49.nii"
Oh dear!!!!
Convert 36 DICOM as 20160623/ep2d_diff_60dir_1av_ZoomIt_AP_43 (108x34x36x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/ep2d_diff_60dir_1av_ZoomIt_AP_43.nii"
Oh dear!!!!
Unable to determine spatial orientation: old Siemens RGB header does not report slice orient (DICOM 0020,0037)!
WARNING: Unable to determine slice direction: please check whether slices are flipped
Warning: bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Convert 36 DICOM as 20160623/ep2d_diff_60dir_1av_ZoomIt_AP_44 (108x34x36x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/ep2d_diff_60dir_1av_ZoomIt_AP_44.nii"
Oh dear!!!!
WARNING: DTI gradient directions only tested for axial (transverse) acquisitions. Please validate bvec files.
Convert 31 DICOM as 20160623/ep2d_diff_30dir_1av_ZoomIt_PA_46 (108x34x36x31)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/ep2d_diff_30dir_1av_ZoomIt_PA_46.nii"
Oh dear!!!!
WARNING: DTI gradient directions only tested for axial (transverse) acquisitions. Please validate bvec files.
Convert 31 DICOM as 20160623/ep2d_diff_60dir_1av_ZoomIt_AP_40 (108x34x36x31)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/ep2d_diff_60dir_1av_ZoomIt_AP_40.nii"
Oh dear!!!!
Convert 36 DICOM as 20160623/ep2d_diff_60dir_1av_ZoomIt_AP_41 (108x34x36x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/ep2d_diff_60dir_1av_ZoomIt_AP_41.nii"
Oh dear!!!!
Convert 36 DICOM as 20160623/ep2d_diff_60dir_1av_ZoomIt_AP_42 (108x34x36x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/ep2d_diff_60dir_1av_ZoomIt_AP_42.nii"
Oh dear!!!!
Convert 100 DICOM as 20160623/ep2d_REST_ZOOMit_1.3x1.3x4.0_39 (96x36x36x100)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/ep2d_REST_ZOOMit_1.3x1.3x4.0_39.nii"
Oh dear!!!!
Convert 36 DICOM as 20160623/ep2d_diff_30dir_1av_ZoomIt_APT_34 (108x34x36x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/ep2d_diff_30dir_1av_ZoomIt_APT_34.nii"
Oh dear!!!!
Unable to determine spatial orientation: old Siemens RGB header does not report slice orient (DICOM 0020,0037)!
WARNING: Unable to determine slice direction: please check whether slices are flipped
Warning: bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Convert 36 DICOM as 20160623/ep2d_diff_30dir_1av_ZoomIt_APT_35 (108x34x36x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/ep2d_diff_30dir_1av_ZoomIt_APT_35.nii"
Oh dear!!!!
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [0 1 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [0 1 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [0 1 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [0 1 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [0 1 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 1 0] != [0 1 0 0 0 -1]
Convert 1 DICOM as 20160623/localizer_37 (512x512x1x1)
WARNING: check that 2D images are not mirrored.
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/localizer_37.nii"
Oh dear!!!!
slices not stacked: orientation varies (localizer?) [1 0 0 0 0 -1] != [0 1 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 0 -1] != [0 1 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 0 -1] != [0 1 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 0 -1] != [0 1 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 0 -1] != [0 1 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 0 0 -1] != [0 1 0 0 0 -1]
Convert 5 DICOM as 20160623/localizer_37a (512x512x5x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/localizer_37a.nii"
Oh dear!!!!
Convert 3 DICOM as 20160623/localizer_37b (512x512x3x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/localizer_37b.nii"
Oh dear!!!!
Convert 12 DICOM as 20160623/cerv_t1_tse_sag_38 (256x256x12x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/cerv_t1_tse_sag_38.nii"
Oh dear!!!!
slices not stacked: orientation varies (localizer?) [1 0 0 -0 1 0] != [1 0 0 0 0 -1]
slices not stacked: orientation varies (localizer?) [1 0 0 -0 1 0] != [1 0 0 0 0 -1]
Convert 1 DICOM as 20160623/1.3.12.2.1107.5.2.43.66075.201_5002 (512x512x1x1)
WARNING: check that 2D images are not mirrored.
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/1.3.12.2.1107.5.2.43.66075.201_5002.nii"
Oh dear!!!!
Convert 1 DICOM as 20160623/1.3.12.2.1107.5.2.43.66075.201_5002a (512x512x1x1)
WARNING: check that 2D images are not mirrored.
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/1.3.12.2.1107.5.2.43.66075.201_5002a.nii"
Oh dear!!!!
WARNING: DTI gradient directions only tested for axial (transverse) acquisitions. Please validate bvec files.
Convert 31 DICOM as 20160623/ep2d_diff_30dir_1av_ZoomIt_APT_31 (108x34x36x31)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/ep2d_diff_30dir_1av_ZoomIt_APT_31.nii"
Oh dear!!!!
Convert 36 DICOM as 20160623/ep2d_diff_30dir_1av_ZoomIt_APT_32 (108x34x36x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/ep2d_diff_30dir_1av_ZoomIt_APT_32.nii"
Oh dear!!!!
Convert 36 DICOM as 20160623/ep2d_diff_30dir_1av_ZoomIt_APT_33 (108x34x36x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/ep2d_diff_30dir_1av_ZoomIt_APT_33.nii"
Oh dear!!!!
Convert 36 DICOM as 20160623/ep2d_diff_30dir_1av_ZoomIt_PA_27 (108x34x36x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/ep2d_diff_30dir_1av_ZoomIt_PA_27.nii"
Oh dear!!!!
Convert 36 DICOM as 20160623/ep2d_diff_30dir_1av_ZoomIt_PA_28 (108x34x36x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/ep2d_diff_30dir_1av_ZoomIt_PA_28.nii"
Oh dear!!!!
Unable to determine spatial orientation: old Siemens RGB header does not report slice orient (DICOM 0020,0037)!
WARNING: Unable to determine slice direction: please check whether slices are flipped
Warning: bogus spatial matrix (perhaps non-spatial image): inspect spatial orientation
Convert 36 DICOM as 20160623/ep2d_diff_30dir_1av_ZoomIt_PA_29 (108x34x36x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/ep2d_diff_30dir_1av_ZoomIt_PA_29.nii"
Oh dear!!!!
WARNING: DTI gradient directions only tested for axial (transverse) acquisitions. Please validate bvec files.
Convert 31 DICOM as 20160623/ep2d_diff_30dir_1av_ZoomIt_PA_25 (108x34x36x31)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/ep2d_diff_30dir_1av_ZoomIt_PA_25.nii"
Oh dear!!!!
Convert 36 DICOM as 20160623/ep2d_diff_30dir_1av_ZoomIt_PA_26 (108x34x36x1)
compress: "/usr/local/bin/pigz_mricron" -n -f "20160623/ep2d_diff_30dir_1av_ZoomIt_PA_26.nii"
Oh dear!!!!
Conversion required 1.374470 seconds.

Response

Message

Date: 2016-06-28 06:40
Sender: Chris Rorden

Thanks for sending me the samples.

All these images appear to have converted fine and the warnings seem legitimate though perhaps overly verbose:

1.) Some of your warnings are generated by the FA maps created by Siemens. Unfortunately, Siemens does not retain spatial orientation for derived images. Without this information the spatial orientation is ambiguous so a warning is warranted. I personally would not generate FA maps on the scanner (you will create better derived images after you run TOPUP/EDDY), but alternatively you may not want to export these. Since this is a common problem for Siemens users, the upcoming release of my software will change the warning generated if it detects the DICOM file is derived rather than raw data. The error will change from
  Serious error: spatial orientation ambiguous (tag 0020,0037 not found)
to read
  Unable to determine spatial orientation: 0020,0037 missing (probably not a problem: derived image)
I personally wish Siemens software would retain spatial information when generating derived images, but this is not a requirement of the DICOM format.

2.) The NIfTI format requires that all slices in a volume lie in the same plane. This is not the case with localizer scans where coronal/axial/sagittal slices are stored in the same series. I think it is appropriate for my software to warn the user and store each slice in a different NIfTI volume. Since localizers are not used for subsequent analyses a simple way to avoid these warnings is simply not to export your localizers. This explains the warning
   slices not stacked: orientation varies (localizer?)


3.) My software will create 4D data for fMRI time series and diffusion directions. However, when it encounters multiple echo times it saves each as separate files (the second/third echo has 'e2'/'e3' appended to the name). This explains the warning from your field map:
  slices not stacked: echo varies (TE 4.92, 7.38; echo 1, 2)
the new software only generates this warning once per echo.

If you want to try the new, less verbose version of dcm2niix (28June2016) you can grab it from Github.

Attached Files:

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Changes:

Field Old Value Date By
status_idOpen2016-06-29 06:27crlab
MessageWe have not had our upgrade to VE yet, so hard to make a firm diagnosis, but I suspect you issue is that these are not DICOM Part 10 compliant files, and do not have the required meta data
  https://github.com/neurolabusc/dcm2niix/issues/15
In brief, if these files are really omitting 0020,0037 (Image Orientation Patient) than any converter should generate a lot of warnings. I am guessing you pulled the raw data files from the scanner rather than exporting them to a DICOM server. If this is correct, you might be able to resolve the problem by simply having the console export the data. 

If you do you send me a sample I would be happy to take a look, as we are on the schedule for a VE11 upgrade I would like to resolve this for my own selfish reasons. You are using the current stable release but you might also want to grab the latest version from Github, which does attempt to reduce the verbosity of the messages.
2016-06-29 06:17crlab
New Message2016-06-28 06:40crlab