open-discussion
open-discussion > RE: Gradients are excluded
Nov 1, 2018 04:11 PM | karen
RE: Gradients are excluded
Dear Martin,
Thank you for your quick response!
1. It is the gradient-wise checking (see attached QC report).
Parameters:
TranslationThreshold: 1.31773
RotationThreshold: 0.5
2. The gradient directions look ok when loading the nrrd-file into the DTIPrep GUI. We've used DWIConvert from the command line and not created separate header files. When I convert in Slicer and save a separate header file, the gradient directions have a different precision. Might this have to do with which space the data is in? (LPS vs. RAS)? The contents of the .nhdr are found below (since I can't attach two files). Anyway, it looks ok in DTIPrep.
It should perhaps be mentioned that we're processing older data (~10 years).
Best,
Karen
NRRD0005
# Complete NRRD file format specification at:
# http://teem.sourceforge.net/nrrd/format....
type: short
dimension: 4
space: right-anterior-superior
sizes: 38 256 256 64
space directions: none (-0.97659999132156361,0,0) (0,-0.97659999132156361,0) (0,0,2)
kinds: list domain domain domain
endian: little
encoding: gzip
space origin: (124.70899963378905,134.45399540662763,-79.152496337890625)
measurement frame: (-1,0,0) (0,-1,0) (0,0,1)
data file: test.raw.gz
DWMRI_b-value:=1000.000000
DWMRI_gradient_0000:=0.000000 0.000000 0.000000
DWMRI_gradient_0001:=0.000000 0.000000 0.000000
DWMRI_gradient_0002:=0.000000 0.000000 0.000000
DWMRI_gradient_0003:=0.000000 0.000000 0.000000
DWMRI_gradient_0004:=0.000000 0.000000 0.000000
DWMRI_gradient_0005:=0.000000 0.000000 0.000000
DWMRI_gradient_0006:=-1.000000 0.000000 0.000000
DWMRI_gradient_0007:=-0.494198 -0.869349 0.000000
DWMRI_gradient_0008:=0.120009 -0.641050 0.758059
DWMRI_gradient_0009:=-0.919038 0.331014 -0.214009
DWMRI_gradient_0010:=0.111970 0.630833 0.767797
DWMRI_gradient_0011:=0.914305 0.236079 0.329110
DWMRI_gradient_0012:=-0.680844 -0.302930 0.666847
DWMRI_gradient_0013:=-0.066978 -0.997670 -0.012996
DWMRI_gradient_0014:=-0.917623 -0.152937 0.366849
DWMRI_gradient_0015:=-0.443231 0.890464 0.103054
DWMRI_gradient_0016:=-0.215975 0.926892 -0.306964
DWMRI_gradient_0017:=-0.480032 0.671045 -0.565038
DWMRI_gradient_0018:=0.549943 0.477950 0.684928
DWMRI_gradient_0019:=0.700688 -0.692691 0.170924
DWMRI_gradient_0020:=0.429108 0.007002 -0.903226
DWMRI_gradient_0021:=0.698790 0.639808 0.319904
DWMRI_gradient_0022:=-0.725825 -0.090978 -0.681836
DWMRI_gradient_0023:=-0.389830 0.248892 -0.886614
DWMRI_gradient_0024:=0.172056 0.881289 -0.440144
DWMRI_gradient_0025:=0.609674 -0.640657 -0.466750
DWMRI_gradient_0026:=-0.598760 -0.688724 0.408836
DWMRI_gradient_0027:=0.727829 -0.221948 -0.648848
DWMRI_gradient_0028:=-0.882959 0.397981 0.248988
DWMRI_gradient_0029:=-0.320210 -0.548360 0.772507
DWMRI_gradient_0030:=0.044018 0.268107 -0.962383
DWMRI_gradient_0031:=-0.188896 0.876518 0.442757
DWMRI_gradient_0032:=-0.732165 0.333075 -0.594134
DWMRI_gradient_0033:=-0.308976 0.549957 0.775939
DWMRI_gradient_0034:=-0.285959 -0.857876 -0.426938
DWMRI_gradient_0035:=-0.859154 -0.504090 0.088016
DWMRI_gradient_0036:=0.106972 -0.214945 -0.970750
DWMRI_gradient_0037:=0.297951 0.177970 0.937844
modality:=DWMRI
space:=left-posterior-superior
Thank you for your quick response!
1. It is the gradient-wise checking (see attached QC report).
Parameters:
TranslationThreshold: 1.31773
RotationThreshold: 0.5
2. The gradient directions look ok when loading the nrrd-file into the DTIPrep GUI. We've used DWIConvert from the command line and not created separate header files. When I convert in Slicer and save a separate header file, the gradient directions have a different precision. Might this have to do with which space the data is in? (LPS vs. RAS)? The contents of the .nhdr are found below (since I can't attach two files). Anyway, it looks ok in DTIPrep.
It should perhaps be mentioned that we're processing older data (~10 years).
Best,
Karen
NRRD0005
# Complete NRRD file format specification at:
# http://teem.sourceforge.net/nrrd/format....
type: short
dimension: 4
space: right-anterior-superior
sizes: 38 256 256 64
space directions: none (-0.97659999132156361,0,0) (0,-0.97659999132156361,0) (0,0,2)
kinds: list domain domain domain
endian: little
encoding: gzip
space origin: (124.70899963378905,134.45399540662763,-79.152496337890625)
measurement frame: (-1,0,0) (0,-1,0) (0,0,1)
data file: test.raw.gz
DWMRI_b-value:=1000.000000
DWMRI_gradient_0000:=0.000000 0.000000 0.000000
DWMRI_gradient_0001:=0.000000 0.000000 0.000000
DWMRI_gradient_0002:=0.000000 0.000000 0.000000
DWMRI_gradient_0003:=0.000000 0.000000 0.000000
DWMRI_gradient_0004:=0.000000 0.000000 0.000000
DWMRI_gradient_0005:=0.000000 0.000000 0.000000
DWMRI_gradient_0006:=-1.000000 0.000000 0.000000
DWMRI_gradient_0007:=-0.494198 -0.869349 0.000000
DWMRI_gradient_0008:=0.120009 -0.641050 0.758059
DWMRI_gradient_0009:=-0.919038 0.331014 -0.214009
DWMRI_gradient_0010:=0.111970 0.630833 0.767797
DWMRI_gradient_0011:=0.914305 0.236079 0.329110
DWMRI_gradient_0012:=-0.680844 -0.302930 0.666847
DWMRI_gradient_0013:=-0.066978 -0.997670 -0.012996
DWMRI_gradient_0014:=-0.917623 -0.152937 0.366849
DWMRI_gradient_0015:=-0.443231 0.890464 0.103054
DWMRI_gradient_0016:=-0.215975 0.926892 -0.306964
DWMRI_gradient_0017:=-0.480032 0.671045 -0.565038
DWMRI_gradient_0018:=0.549943 0.477950 0.684928
DWMRI_gradient_0019:=0.700688 -0.692691 0.170924
DWMRI_gradient_0020:=0.429108 0.007002 -0.903226
DWMRI_gradient_0021:=0.698790 0.639808 0.319904
DWMRI_gradient_0022:=-0.725825 -0.090978 -0.681836
DWMRI_gradient_0023:=-0.389830 0.248892 -0.886614
DWMRI_gradient_0024:=0.172056 0.881289 -0.440144
DWMRI_gradient_0025:=0.609674 -0.640657 -0.466750
DWMRI_gradient_0026:=-0.598760 -0.688724 0.408836
DWMRI_gradient_0027:=0.727829 -0.221948 -0.648848
DWMRI_gradient_0028:=-0.882959 0.397981 0.248988
DWMRI_gradient_0029:=-0.320210 -0.548360 0.772507
DWMRI_gradient_0030:=0.044018 0.268107 -0.962383
DWMRI_gradient_0031:=-0.188896 0.876518 0.442757
DWMRI_gradient_0032:=-0.732165 0.333075 -0.594134
DWMRI_gradient_0033:=-0.308976 0.549957 0.775939
DWMRI_gradient_0034:=-0.285959 -0.857876 -0.426938
DWMRI_gradient_0035:=-0.859154 -0.504090 0.088016
DWMRI_gradient_0036:=0.106972 -0.214945 -0.970750
DWMRI_gradient_0037:=0.297951 0.177970 0.937844
modality:=DWMRI
space:=left-posterior-superior
Threaded View
Title | Author | Date |
---|---|---|
karen | Oct 31, 2018 | |
Martin Styner | Oct 31, 2018 | |
karen | Nov 1, 2018 | |
Martin Styner | Nov 2, 2018 | |
karen | Nov 6, 2018 | |