Hello All,

Apologies if i am asking some weird nonlogical question.

I have a qsm data in .dcm format after running medi-tool box pipeline on it. I am looking forward to converting it into a nifty format using to3d/dimon. However when i do so i get many errors apparently because of improper header information after running medi pipeline on .dcm images.

Following are the messages spitted out after running dimon,

-- scanning for first volume
++ DICOM WARNING: Slice_Spacing=1.000000 smaller than Slice_Thickness=2.000000

++ Setting environment variable AFNI_SLICE_SPACING_IS_GAP ++
++ to YES will make the center-to-center slice distance ++
++ be set to Slice_Spacing+Slice_Thickness= 3.000. ++
++ This is against the DICOM standard [attribute (0018,0088) ++
++ is defined as the center-to-center spacing between slices, ++
++ NOT as the edge-to-edge gap between slices], but it seems ++
++ to be necessary for some GE scanners. ++
++ ++
++ This correction has been made on this data: dz= 3.000. ++
++ ++
++ Setting AFNI_SLICE_SPACING_IS_GAP to NO means that the ++
++ DICOM Slice_Spacing variable will be used for dz, replacing ++
++ the Slice_Thickness variable. This usage may be required ++
++ for some pulse sequences on Phillips scanners. ++

++ DICOM WARNING: Slice_Spacing=1.000000 smaller than Slice_Thickness=2.000000
++ DICOM WARNING: no more Slice_Spacing messages will be printed
*+ WARNING: Bad DICOM header - assuming oblique scaling direction!

-- first volume found (1 slices)
-- scanning for additional volumes...
-- run 99: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33
** volume match failure (bad zoff -87.480904 != -88.480904)
(estimated index 1.000000, want index 0)
(for more details, replace -no_wait with -quit)


final run statistics:
volume info :
slices : 1
z_first : -88.48
z_last : -88.48
z_delta : 1
oblique : no
mos_nslices : 0

run # 99 : volumes = 33, first file (#0) = /Users/spkadam/Desktop/DICOM/SORTED/99/1.dcm

Inorder to tackle this, i am planning to use header info of non processed(i.e dcm file before running qsm/medi pipeline) dicom images. However with the errors as above i am not sure how to go ahead with this.
Can anyone suggest if its possible for to3d command to use header info from one dicom file to convert another set of dicom images to nii?

Any thoughts?

KashiV