[Insight-developers] Re: Nrrd format changes

Tue Jan 17 01:34:03 EST 2006

hello,

sorry- realized I never actually answered your specific question-  
here's my guess about what an updated header would look like.

There are actually two guesses here:
1) what the b-value is (1000 s/mm^2 is common),
2) what the measurement frame is (actually its very rarely the  
identity transform).

Unfortunately I don't have a suggested way of transforming old to new  
headers.  It would be nice to have some kind of "NRRD DWI Wizard"  
that could step one through the creation of the header, but its not  
something I'm about to develop.

Do let me know if there are any other questions, or comments on the  
info page:
http://www.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format

Gordon

NRRD0005
content: dwi
type: short
dimension: 4
space: right-anterior-superior
sizes: 256 256 50 31
thicknesses:  NaN  NaN 4  NaN
space directions: (0.9375,0,0) (0,0.9375,0) (0,0,2.5) none
centerings: cell cell cell none
kinds: space space space list
endian: little
encoding: raw
space units: "mm" "mm" "mm"
space origin: (0, 0, 0)
measurement frame: (1,0,0) (0,1,0) (0,0,1)
data file: xt_dwi.img
modality:=DWMRI
DWMRI_b-value:=1000
DWMRI_gradient_0001:=-1.000000 	 0.000000 	 0.000000
DWMRI_gradient_0002:=-0.166000 	 0.986000 	 0.000000
DWMRI_gradient_0003:=0.110000 	 0.664000 	 0.740000
DWMRI_gradient_0004:=-0.901000 	 -0.419000 	 -0.110000
DWMRI_gradient_0005:=0.169000 	 -0.601000 	 0.781000
DWMRI_gradient_0006:=0.815000 	 -0.386000 	 0.433000
DWMRI_gradient_0007:=-0.656000 	 0.366000 	 0.660000
DWMRI_gradient_0008:=-0.582000 	 0.800000 	 0.143000
DWMRI_gradient_0009:=-0.900000 	 0.259000 	 0.350000
DWMRI_gradient_0010:=-0.693000 	 -0.698000 	 0.178000
DWMRI_gradient_0011:=-0.357000 	 -0.924000 	 -0.140000
DWMRI_gradient_0012:=-0.543000 	 -0.488000 	 -0.683000
DWMRI_gradient_0013:=0.525000 	 -0.396000 	 0.753000
DWMRI_gradient_0014:=0.639000 	 0.689000 	 0.341000
DWMRI_gradient_0015:=0.330000 	 -0.013000 	 -0.944000
DWMRI_gradient_0016:=0.524000 	 -0.783000 	 0.335000
DWMRI_gradient_0017:=-0.609000 	 -0.065000 	 -0.791000
DWMRI_gradient_0018:=-0.220000 	 -0.233000 	 -0.947000
DWMRI_gradient_0019:=0.004000 	 -0.910000 	 -0.415000
DWMRI_gradient_0020:=0.511000 	 0.627000 	 -0.589000
DWMRI_gradient_0021:=-0.414000 	 0.737000 	 0.535000
DWMRI_gradient_0022:=0.679000 	 0.139000 	 -0.721000
DWMRI_gradient_0023:=-0.884000 	 -0.296000 	 0.362000
DWMRI_gradient_0024:=-0.262000 	 0.432000 	 0.863000
DWMRI_gradient_0025:=-0.088000 	 0.185000 	 -0.979000
DWMRI_gradient_0026:=-0.294000 	 -0.907000 	 0.302000
DWMRI_gradient_0027:=-0.887000 	 -0.089000 	 -0.453000
DWMRI_gradient_0028:=-0.257000 	 -0.443000 	 0.859000
DWMRI_gradient_0029:=-0.086000 	 0.867000 	 -0.491000
DWMRI_gradient_0030:=-0.863000 	 0.504000 	 -0.0250000

On Jan 10, 2006, at 11:21 AM, Karthik Krishnan wrote:

> Hi Gordon,
>
> I have some old DWI headers for Nrrd. There were some nrrd format
> changes, probably for more efficient iteration in terms of reading  
> each
> gradient image etc.. Do you have a quick and dirty program that does
> this re-ordering ? I presume you've had the need to do this  
> yourself. If
> you don't that's ok, its an easy thing thing to do.
>
> Could you please tell me what the new header is supposed to look  
> like ?
> Here is the old header.
>
> ----------------------
> NRRD0004
> content: dwi
> type: short
> dimension: 4
> space: right-anterior-superior
> sizes: 256 256 50 31
> thicknesses:  NaN  NaN 4  NaN
> space directions: (0.9375,0,0) (0,0.9375,0) (0,0,2.5) none
> centerings: cell cell cell none
> kinds: space space space list
> endian: little
> encoding: raw
> space units: "mm" "mm" "mm"
> space origin: (0, 0, 0)
> data file: xt_dwi.img
> modality:=DW
> DW_gradient_001:=-1.000000 	 0.000000 	 0.000000
> DW_gradient_002:=-0.166000 	 0.986000 	 0.000000
> DW_gradient_003:=0.110000 	 0.664000 	 0.740000
> DW_gradient_004:=-0.901000 	 -0.419000 	 -0.110000
> DW_gradient_005:=0.169000 	 -0.601000 	 0.781000
> DW_gradient_006:=0.815000 	 -0.386000 	 0.433000
> DW_gradient_007:=-0.656000 	 0.366000 	 0.660000
> DW_gradient_008:=-0.582000 	 0.800000 	 0.143000
> DW_gradient_009:=-0.900000 	 0.259000 	 0.350000
> DW_gradient_010:=-0.693000 	 -0.698000 	 0.178000
> DW_gradient_011:=-0.357000 	 -0.924000 	 -0.140000
> DW_gradient_012:=-0.543000 	 -0.488000 	 -0.683000
> DW_gradient_013:=0.525000 	 -0.396000 	 0.753000
> DW_gradient_014:=0.639000 	 0.689000 	 0.341000
> DW_gradient_015:=0.330000 	 -0.013000 	 -0.944000
> DW_gradient_016:=0.524000 	 -0.783000 	 0.335000
> DW_gradient_017:=-0.609000 	 -0.065000 	 -0.791000
> DW_gradient_018:=-0.220000 	 -0.233000 	 -0.947000
> DW_gradient_019:=0.004000 	 -0.910000 	 -0.415000
> DW_gradient_020:=0.511000 	 0.627000 	 -0.589000
> DW_gradient_021:=-0.414000 	 0.737000 	 0.535000
> DW_gradient_022:=0.679000 	 0.139000 	 -0.721000
> DW_gradient_023:=-0.884000 	 -0.296000 	 0.362000
> DW_gradient_024:=-0.262000 	 0.432000 	 0.863000
> DW_gradient_025:=-0.088000 	 0.185000 	 -0.979000
> DW_gradient_026:=-0.294000 	 -0.907000 	 0.302000
> DW_gradient_027:=-0.887000 	 -0.089000 	 -0.453000
> DW_gradient_028:=-0.257000 	 -0.443000 	 0.859000
> DW_gradient_029:=-0.086000 	 0.867000 	 -0.491000
> DW_gradient_030:=-0.863000 	 0.504000 	 -0.025000
> -----------------------------------
>
> I presume the image dwi.img should be re-ordered so that
> sizes: 31 256 256 50
> instead of
> sizes: 256 256 50 31
>
> so that the gradients vary the fastest.
>
> Is that the only change ?
>
> Thanks
> karthik
>
>
>
>