DTI
For example, for sample
20201125_163219_LH_327912_7__wt_male_1_1
the diffusion scan is #4, so go into this folder and open the "method" file
To ensure that you are looking at the right file. The 4th line from the top should read
##$Method=<Bruker:DtiStandard>
The diffusion direction vectors are in this section
##$PVM_DwGradVec=( 32, 3 )
0 0 0 0 0 0 0.160443466334042 0.0338821506150016 0.69286742786796
-0.186388451408642 0.126483180184267 0.675438175506764 -0.0811641595504953
-0.226242125903943 0.670210607414467 0.240639920336997 -0.266205973343464
0.614965191792516 0.176243756117012 0.330040320695937 0.605777932715144
-0.133723133613356 0.416226288258137 0.561986814008498 -0.380661634852261
-0.123594127544688 0.588877398112726 -0.323837495149411 -0.424680888886333
0.470882998174719 0.0200300936328484 -0.507846602177571 0.498644164335349
0.50257404801711 -0.150848249646976 0.481268646867924 0.46712688926276
0.163554801468216 0.511857084413543 0.0656238418590197 0.601473070293477
0.375338561449985 -0.394253082842529 0.426880232801722 0.411452490735264
-0.517780568731468 0.145449033270092 0.466586797911018 -0.592822625860051
-0.165704260505179 0.357853057746849 0.0414859220008916 -0.672503362610115
0.230159779661365 0.367121009435077 -0.470281368958531 0.388603881943817
0.672490594778731 -0.0382643357477777 0.230754456433399 0.609950760141532
0.298408194236622 0.214168154577538 0.371124520983468 0.47106300251961
0.383824981211417 -0.214237696264885 0.647392144929402 0.204795016547686
-0.514839872275181 0.47710717177048 0.119432119552461 -0.667320292240901
0.189342840320499 0.160587343843865 -0.55891263457098 -0.415334895649226
0.148556285605544 -0.286743684108905 -0.61134523485147 0.225810633204014
0.326328964838842 -0.623369664142736 0.108972689944435 0.598199094238384
-0.3476938870151 0.167994592783969 0.702251532720486 0.106897743642017
-0.048693283067768 0.409089296551388 0.57625115684454 0.0868097362187176
0.095813966675022 0.70255231724975 0.0647711659378418
And the effective b-values are here:
##$PVM_DwEffBval=( 32 )
28.5624697716184 28.5624697716184 5010.57311459592 5002.5110757139
5002.49166785672 5002.28656385482 5002.25245525807 5002.08987645233
5002.18971037251 5001.75164463696 5011.08141170736 5001.79020237221
5001.9037649345 5003.22095929645 5001.53100307288 5001.73569457383
5001.33200994228 5007.80208598717 5001.44617538088 5008.28324824497
5000.79856570403 5001.4284332451 5000.76376701352 5000.44684892012
5000.59964171037 5000.55497523146 5000.84178954318 5000.40801726602
5000.62714184561 5007.06920177447 5000.32573513542 5002.32194880641
Note that this is a train of 3 variables of x,y,z, so the GradVec above will need to be arranged as
0 0 0
0 0 0
0.160443466334042 0.0338821506150016 0.69286742786796
etc
Depending on the software you use you can use the DwEffBval above, or you may simplify this with a train of 0, 0, 5000, 5000 etc
If using mrtrix, the above will be gradient-bval set can be combined as:
0 0 0 0
0 0 0 0
0.160443466334042 0.0338821506150016 0.69286742786796 5000
etc
If using fsl format, then you will need to transpose the row x column in DwGradVec into to fsl bvecs format:
x1,x2,etc
y1,x2
z1,y2
and bvals = the info in PVM_DwEffBval
b1,b2,b3 etc
You should only need to do this once, as the acquisition method is kept the same for all samples.
There are two options of dicom files in the processed folder 4/pdata:
4/pdata/1 is the dicom as acquired by the scanner
4/pdata/2 has a factor of 1.5 zerofill prior to fourier transform to enhance the digital resolution.
In most cases, pdata/1 is the one to use.
Example File from Nov 20
“method” from scan 5 on 20201124_134341_LH_316956_1__hom_female_1_1